David Edwards

Building a successful international research community through data sharing

Publisher: F1000 Research Ltd

Date: 05-06-2020

DOI: 10.12688/F1000RESEARCH.23525.1

Abstract: The International Wheat Information System (WheatIS) Expert Working Group (EWG) was initiated in 2012 under the Wheat Initiative with a broad range of contributing organizations. The mission of the WheatIS EWG was to create an informational infrastructure, establish data standards, and build a single portal that allows search, retrieval, and display of globally distributed wheat data sets that are indexed in standard data formats at servers around the world. The web portal at WheatIS.org was released publicly in 2015, and by 2020, it expanded to 8 geographically-distributed nodes and around 20 organizations under its umbrella. In this paper, we present our experience, the challenges we faced, and the answer we brought for establishing an international research community to build an informational infrastructure. Our hope is that our experience with building wheatis.org will guide current and future research communities to facilitate institutional and international challenges to create global tools and resources to help their respective scientific communities.

Genetic and Genomic Resources for Soybean Breeding Research

Publisher: MDPI AG

Date: 27-04-2022

DOI: 10.3390/PLANTS11091181

Abstract: Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced genetic and genomic approaches for breeding. Genome technologies continue to advance rapidly, with an increasing number of high-quality genome assemblies becoming available. With accumulating data from marker arrays and whole-genome resequencing, studying variations between in iduals and populations is becoming increasingly accessible. Furthermore, the recent development of soybean pangenomes has highlighted the significant structural variation between in iduals, together with knowledge of what has been selected for or lost during domestication and breeding, information that can be applied for the breeding of improved cultivars. Because of this, resources such as genome assemblies, SNP datasets, pangenomes and associated databases are becoming increasingly important for research underlying soybean crop improvement.

Second-generation sequencing for gene discovery in the Brassicaceae

Publisher: Wiley

Date: 06-07-2012

DOI: 10.1111/J.1467-7652.2012.00719.X

Abstract: The Brassicaceae contains the most erse collection of agriculturally important crop species of all plant families. Yet, this is one of the few families that do not form functional symbiotic associations with mycorrhizal fungi in the soil for improved nutrient acquisition. The genes involved in this symbiosis were more recently recruited by legumes for symbiotic association with nitrogen-fixing rhizobia bacteria. This study applied second-generation sequencing (SGS) and analysis tools to discover that two such genes, NSP1 (Nodulation Signalling Pathway 1) and NSP2, remain conserved in erse members of the Brassicaceae despite the absence of these symbioses. We demonstrate the utility of SGS data for the discovery of putative gene homologs and their analysis in complex polyploid crop genomes with little prior sequence information. Furthermore, we show how this data can be applied to enhance downstream reverse genetics analyses. We hypothesize that Brassica NSP genes may function in the root in other plant-microbe interaction pathways that were recruited for mycorrhizal and rhizobial symbioses during evolution.

Climate change and the need for agricultural adaptation

Publisher: Elsevier BV

Date: 08-2020

DOI: 10.1016/J.PBI.2019.12.006

Plant pangenomics

Publisher: Elsevier BV

Date: 04-2020

DOI: 10.1016/J.PBI.2019.12.005

Abstract: With the assembly of increasing numbers of plant genomes, it is becoming accepted that a single reference assembly does not reflect the gene ersity of a species. The production of pangenomes, which reflect the structural variation and polymorphisms in genomes, enables in depth comparisons of variation within species or higher taxonomic groups. In this review, we discuss the current and emerging approaches for pangenome assembly, analysis and visualisation. In addition, we consider the potential of pangenomes for applied crop improvement, evolutionary and bio ersity studies. To fully exploit the value of pangenomes it is important to integrate broad information such as phenotypic, environmental, and expression data to gain insights into the role of variable regions within genomes.

RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism

Publisher: Elsevier BV

Date: 11-2017

DOI: 10.1016/J.BIORTECH.2017.06.003

Abstract: To map out key lipid-related pathways that lead to rapid triacylglyceride accumulation in oleaginous microalgae, RNA-Seq was performed with Tetraselmis sp. M8 at 24h after exhaustion of exogenous nitrogen to reveal molecular changes during early stationary phase. Further gene expression profiling by quantitative real-time PCR at 16-72h revealed a distinct shift in expression of the fatty acid/triacylglyceride biosynthesis and β-oxidation pathways, when cells transitioned from log-phase into early-stationary and stationary phase. Metabolic reconstruction modeling combined with real-time PCR and RNA-Seq gene expression data indicates that the increased lipid accumulation is a result of a decrease in lipid catabolism during the early-stationary phase combined with increased metabolic fluxes in lipid biosynthesis during the stationary phase. During these two stages, Tetraselmis shifts from reduced lipid consumption to active lipid production. This process appears to be independent from DGAT expression, a key gene for lipid accumulation in microalgae.

Databases for wheat genomics and crop improvement

Publisher: Springer New York

Date: 2017

DOI: 10.1007/978-1-4939-7337-8_18

Abstract: The genomics revolution brought on by advances in high-throughput sequencing has led to the production of vast amounts of data. Databases play an essential role in storing and managing this information to make it available to researchers and crop breeders. This chapter provides an outline of how to use databases and tools for wheat genome research.

Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale

Publisher: MDPI AG

Date: 21-09-2022

DOI: 10.3390/IJMS231911106

Abstract: Rye (Secale cereale) is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions for improved yield and disease resistance. Understanding the genomic ersity of rye will assist both the improvement of this crop and facilitate the introgression of more valuable traits into wheat. Here, we isolated and sequenced the short arm of rye chromosome 7 (7RS) from Triticale 380SD using flow cytometry and compared it to the public Lo7 rye whole genome reference assembly. We identify 2747 Lo7 genes present on the isolated chromosome arm and two clusters containing seven and sixty-five genes that are present on Triticale 380SD 7RS, but absent from Lo7 7RS. We identified 29 genes that are not assigned to chromosomal locations in the Lo7 assembly but are present on Triticale 380SD 7RS, suggesting a chromosome arm location for these genes. Our study supports the Lo7 reference assembly and provides a repertoire of genes on Triticale 7RS.

Sequence based DNA markers and genotyping for cereal genomics and breeding

Publisher: Springer Netherlands

Date: 2014

DOI: 10.1007/978-94-007-6401-9_3

Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola

Publisher: Frontiers Media SA

Date: 24-10-2016

DOI: 10.3389/FPLS.2016.01513

Bioinformatics and plant breeding.

Publisher: CABI

Date: 2020

DOI: 10.1079/9781789240214.0071

Bioinformatics

Publisher: Springer New York

Date: 2009

DOI: 10.1007/978-0-387-92738-1

Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species

Publisher: MDPI AG

Date: 08-11-2022

DOI: 10.3390/PLANTS11223010

Abstract: Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.

The pangenome of banana highlights differences between genera and genomes

Publisher: Wiley

Date: 05-07-2022

DOI: 10.1002/TPG2.20100

Abstract: Banana (Musaceae family) has a complex genetic history and includes a genus Musa with a variety of cultivated clones with edible fruits, Ensete species that are grown for their edible corm, and monospecific Musella whose generic status has been questioned. The most commonly exported banana cultivars belong to Cavendish, a subgroup of Musa triploid cultivars, which is under threat by fungal pathogens, though there are also related species M. balbisiana Colla (B genome), M. textilis Née (T genome), and M. schizocarpa N. W. Simmonds (S genome), along with hybrids of these genomes, which potentially host genes of agronomic interest. Here we present the first cross‐genus pangenome of banana, which contains representatives of the Musa and Ensete genera. Clusters based on gene presence–absence variation (PAV) clearly separate Musa and Ensete , while Musa is split further based on species. These results present the first pangenome study across genus boundaries and identifies genes that differentiate between Musaceae species, information that may support breeding programs in these crops.

Wheat Panache

Publisher: Wiley

Date: 29-05-2022

DOI: 10.1002/TPG2.20221

Abstract: Bread wheat ( Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence–absence variation (PAV) between cultivars, h ering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high‐quality reference genomes are becoming available, reflecting the genetic content of a erse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate because of the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess PAV between bread wheat genomes.

New technologies for ultrahigh-throughput genotyping in plant taxonomy

Publisher: Humana Press

Date: 19-12-2014

DOI: 10.1007/978-1-62703-767-9_8

Abstract: Molecular genetic markers represent one of the most powerful tools for the analysis of variation between plant genomes. Molecular marker technology has developed rapidly over the last decade, with the introduction of new DNA sequencing methods and the development of high-throughput genotyping methods. Single nucleotide polymorphisms (SNPs) now dominate applications in modern plant genetic analysis. The reducing cost of DNA sequencing and increasing availability of large sequence data sets permit the mining of this data for large numbers of SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, ersity analysis, association studies, and marker-assisted selection. Here we describe automated methods for the discovery of SNP molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Ex les include SNP discovery using autoSNPdb and wheatgenome.info as well as SNP genotyping using Illumina's GoldenGate™ and Infinium™ methods.

Integrating and interrogating diverse Brassica data within an EnsEMBL structured database

Publisher: International Society for Horticultural Science (ISHS)

Date: 04-2006

DOI: 10.17660/ACTAHORTIC.2006.706.7

Assembly of the non‐heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson

Publisher: Wiley

Date: 03-01-2021

DOI: 10.1111/PBI.13522

Marine heatwaves have minimal influence on the quality of adult Sydney rock oyster flesh

Publisher: Elsevier BV

Date: 11-2021

DOI: 10.1016/J.SCITOTENV.2021.148846

Current status of structural variation studies in plants

Publisher: Wiley

Date: 20-07-2021

DOI: 10.1111/PBI.13646

Abstract: Structural variations (SVs) including gene presence/absence variations and copy number variations are a common feature of genomes in plants and, together with single nucleotide polymorphisms and epigenetic differences, are responsible for the heritable phenotypic ersity observed within and between species. Understanding the contribution of SVs to plant phenotypic variation is important for plant breeders to assist in producing improved varieties. The low resolution of early genetic technologies and inefficient methods have previously limited our understanding of SVs in plants. However, with the rapid expansion in genomic technologies, it is possible to assess SVs with an ever‐greater resolution and accuracy. Here, we review the current status of SV studies in plants, examine the roles that SVs play in phenotypic traits, compare current technologies and assess future challenges for SV studies.

Analysis of the Brassica 'A' and 'C' genomes and comparison with the genome of Arabidopsis thaliana

Publisher: International Society for Horticultural Science (ISHS)

Date: 04-2006

DOI: 10.17660/ACTAHORTIC.2006.706.9

A High-Performance Spectral-Spatial Residual Network for Hyperspectral Image Classification with Small Training Data

Publisher: MDPI AG

Date: 24-09-2020

DOI: 10.3390/RS12193137

Abstract: In this paper, we propose a high performance Two-Stream spectral-spatial Residual Network (TSRN) for hyperspectral image classification. The first spectral residual network (sRN) stream is used to extract spectral characteristics, and the second spatial residual network (saRN) stream is concurrently used to extract spatial features. The sRN uses 1D convolutional layers to fit the spectral data structure, while the saRN uses 2D convolutional layers to match the hyperspectral spatial data structure. Furthermore, each convolutional layer is preceded by a Batch Normalization (BN) layer that works as a regularizer to speed up the training process and to improve the accuracy. We conducted experiments on three well-known hyperspectral datasets, and we compare our results with five contemporary methods across various sizes of training s les. The experimental results show that the proposed architecture can be trained with small size datasets and outperforms the state-of-the-art methods in terms of the Overall Accuracy, Average Accuracy, Kappa Value, and training time.

SNPServer: a real-time SNP discovery tool

Publisher: Oxford University Press (OUP)

Date: 07-2005

DOI: 10.1093/NAR/GKI462

Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in arabidopsis

Publisher: Oxford University Press (OUP)

Date: 07-1998

DOI: 10.1104/PP.117.3.1015

Abstract: The CCAAT motif is found in the promoters of many eukaryotic genes. In yeast a single complex of three proteins, termed HAP2, HAP3, and HAP5, binds to this sequence, and in mammals the three components of the equivalent complex (called variously NF-Y, CBF, or CP1) are also represented by single genes. Here we report the presence of multiple genes for each of the components of the CCAAT-binding complex, HAP2,3,5, from Arabidopsis. Three independent Arabidopsis HAP subunit 2 (AtHAP2) cDNAs were cloned by functional complementation of a yeast hap2 mutant, and two independent forms each of AtHAP3 and AtHAP5 cDNAs were detected in the expressed sequence tag database. Additional homologs (two of AtHAP3 and one of AtHAP5) have been identified from available Arabidopsis genomic sequences. Northern-blot analysis indicated ubiquitous expression for each AtHAP2 and AtHAP5 cDNA in a range of tissues, whereas expression of each AtHAP3 cDNA was under developmental and/or environmental regulation. The unexpected presence of multiple forms of each HAP homolog in Arabidopsis, compared with the single genes in yeast and vertebrates, suggests that the HAP2,3,5 complex may play erse roles in gene transcription in higher plants.

Current status of the multinational Arabidopsis community

Publisher: Wiley

Date: 07-2020

DOI: 10.1002/PLD3.248

Machine learning in agriculture

Publisher: Wiley

Date: 20-12-2021

DOI: 10.1111/PBI.13521

A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits

Publisher: Wiley

Date: 11-08-2022

DOI: 10.1111/TPJ.15885

Abstract: Narrow‐leafed lupin (NLL Lupinus angustifolius ) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten‐free, non‐genetically modified, alternative protein source to soybean ( Glycine max ) and as such has gained interest as a human food ingredient. Here, we present a chromosome‐length reference genome for the species and a pan‐genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan‐genomes of NLL and its close relative white lupin ( Lupinus albus ) are compared. Furthermore, we provide additional evidence supporting LaRAP2‐7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast‐track lupin crop improvement.

Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

Publisher: Frontiers Media SA

Date: 18-02-2021

DOI: 10.3389/FGENE.2021.600789

Abstract: Meeting the needs of a growing world population in the face of imminent climate change is a challenge breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic ersity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of ersity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with ersity, is set to lead the way in Brassica improvement however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

Advancing designer crops for climate resilience through an integrated genomics approach

Publisher: Elsevier BV

Date: 06-2022

DOI: 10.1016/J.PBI.2022.102220

Abstract: Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm ersity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.

Next generation sequencing and germplasm resources

Publisher: Springer Netherlands

Date: 07-11-2014

DOI: 10.1007/978-94-007-7572-5_15

Predicting polymorphic EST-SSRs in silico

Publisher: Wiley

Date: 11-02-2013

DOI: 10.1111/1755-0998.12078

Abstract: The public availability of large quantities of gene sequence data provides a valuable resource of the mining of Simple Sequence Repeat (SSR) molecular genetic markers for genetic analysis. These markers are inexpensive, require minimal labour to produce and can frequently be associated with functionally annotated genes. This study presents the characterization of barley EST-SSRs and the identification of putative polymorphic SSRs from EST data. Polymorphic SSRs are distinguished from monomorphic SSRs by the representation of varying motif lengths within an alignment of sequence reads. Two measures of confidence are calculated, redundancy of a polymorphism and co-segregation with accessions. The utility of this method is demonstrated through the discovery of 597 candidate polymorphic SSRs, from a total of 452 642 consensus expressed sequences. PCR lification primers were designed for the identified SSRs. Ten primer pairs were validated for polymorphism in barley and for transferability across species. Analysis of the polymorphisms in relation to SSR motif, length, position and annotation is discussed.

Genetic maps and the use of synteny

Publisher: Humana Press

Date: 2009

DOI: 10.1007/978-1-59745-427-8_3

Abstract: Genetic linkage maps represent the order of known molecular genetic markers along a given chromosome for a given species. This provides an insight into the organisation of a plant genome. In comparative genomics, synteny is the preserved order of genes on chromosomes of related species which results from descent from a common ancestor. Comparative mapping is a valuable technique to identify similarities and differences between species and enables the transfer of information from one map to another and assists in the reconstruction of ancestral genomes. This chapter demonstrates the application of online resources to identify candidate genes underlying a QTL, conduct genome comparisons, identify syntenic regions and view comparative genetic maps in grass and Brassica species.

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

Publisher: Wiley

Date: 24-06-2022

DOI: 10.1002/TPG2.20109

Abstract: The gene content of plants varies between in iduals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic ersity). Here we have assembled and analyzed a soybean ( Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic ersity, we found a significant reduction in the average number of protein‐coding genes per in idual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.

New technologies for ultra-high throughput genotyping in plants

Publisher: Humana Press

Date: 2009

DOI: 10.1007/978-1-59745-427-8_2

Abstract: Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods. Two forms of sequence-based marker, simple sequence repeats (SSRs), also known as microsatellites and single nucleotide polymorphisms (SNPs) now predominate applications in modern plant genetic analysis, along the anonymous marker systems such as lified fragment length polymorphisms (AFLPs) and ersity array technology (DArT). The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs and SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, ersity analysis, association studies and marker-assisted selection. Here, we describe automated methods for the discovery of molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Genotyping ex les include multiplexing of SSRs using Multiplex-Ready marker technology (MRT) DArT genotyping SNP genotyping using the Invader assay, the single base extension (SBE), oligonucleotide ligation assay (OLA) SNPlex system, and Illumina GoldenGate and Infinium methods.

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

Publisher: Springer Science and Business Media LLC

Date: 29-04-2019

DOI: 10.1038/S41588-019-0401-3

Abstract: We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines s led from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

Investigating drought tolerance in chickpea using genome-wide association mapping and genomic selection based on whole-genome resequencing data

Publisher: Frontiers Media SA

Date: 19-02-2018

DOI: 10.3389/FPLS.2018.00190

Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes

Publisher: Springer Science and Business Media LLC

Date: 10-10-2014

DOI: 10.1007/S11105-013-0669-X

The application of pangenomics and machine learning in genomic selection in plants.

Publisher: Wiley

Date: 20-07-2021

DOI: 10.1002/TPG2.20112

Abstract: Genomic selection approaches have increased the speed of plant breeding, leading to growing crop yields over the last decade. However, climate change is impacting current and future yields, resulting in the need to further accelerate breeding efforts to cope with these changing conditions. Here we present approaches to accelerate plant breeding and incorporate nonadditive effects in genomic selection by applying state-of-the-art machine learning approaches. These approaches are made more powerful by the inclusion of pangenomes, which represent the entire genome content of a species. Understanding the strengths and limitations of machine learning methods, compared with more traditional genomic selection efforts, is paramount to the successful application of these methods in crop breeding. We describe ex les of genomic selection and pangenome-based approaches in crop breeding, discuss machine learning-specific challenges, and highlight the potential for the application of machine learning in genomic selection. We believe that careful implementation of machine learning approaches will support crop improvement to help counter the adverse outcomes of climate change on crop production.

Whole-Genome DNA Methylation Analysis in Brassica rapa subsp. perviridis in Response to Albugo candida Infection

Publisher: Frontiers Media SA

Date: 23-06-2022

DOI: 10.3389/FPLS.2022.849358

Abstract: DNA methylation is an epigenetic mark associated with several mechanisms in plants including immunity mechanisms. However, little is known about the regulatory role of DNA methylation in the resistance response of Brassica species against fungal diseases. White rust, caused by the fungus Albugo candida , is one of the most widespread and destructive diseases of all the cultivated Brassica species, particularly Brassica rapa L. and Brassica juncea (L.) Czern and Coss. Here, we investigate whole-genome DNA methylation modifications of B. rapa subsp. perviridis in response to white rust. As a result, 233 and 275 differentially methylated regions (DMRs) in the susceptible cultivar “Misugi” and the resistant cultivar “Nanane” were identified, respectively. In both cultivars, more than half of the DMRs were associated with genes (DMR-genes). Gene expression analysis showed that 13 of these genes were also differentially expressed between control and infected s les. Gene ontology enrichment analysis of DMR genes revealed their involvement in various biological processes including defense mechanisms. DMRs were unevenly distributed around genes in susceptible and resistant cultivars. In “Misugi,” DMRs tended to be located within genes, while in “Nanane,” DMRs tended to be located up and downstream of the genes. However, CG DMRs were predominantly located within genes in both cultivars. Transposable elements also showed association with all three sequence contexts of DMRs but predominantly with CHG and CHH DMRs in both cultivars. Our findings indicate the occurrence of DNA methylation modifications in B. rapa in response to white rust infection and suggest a potential regulatory role of DNA methylation modification in defense mechanisms which could be exploited to improve disease resistance.

CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

Publisher: Oxford University Press (OUP)

Date: 2015

DOI: 10.1093/DATABASE/BAV078

Yield is negatively correlated with nucleotide-binding leucine-rich repeat gene content in soybean

Publisher: Cold Spring Harbor Laboratory

Date: 13-12-2021

DOI: 10.1101/2021.12.12.472330

Abstract: The availability of increasing quantities of crop pangenome data permits the detailed association of gene content with agronomic traits. Here, we investigate disease resistance gene content of erse soybean cultivars and report a significant negative correlation between the number of NLR resistance ( R ) genes and yield. We find no association between R- genes with seed weight, oil or protein content, and we find no correlation between yield and the number of RLK, RLP genes, or the total number of genes. These results suggest that recent yield improvement in soybean may be partially associated with the selective loss of NLR genes. Three quarters of soybean NLR genes do not show presence/absence variation, limiting the ability to select for their absence, and so the deletion or disabling of select NLR genes may support future yield improvement.

Population Diversity of Leptosphaeria maculans in Australia

Publisher: Canadian Center of Science and Education

Date: 03-05-2015

DOI: 10.5539/IJB.V7N3P18

MCE-ST: Classifying crop stress using hyperspectral data with a multiscale conformer encoder and spectral-based tokens

Publisher: Elsevier BV

Date: 04-2023

DOI: 10.1016/J.JAG.2023.103286

A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

Publisher: Springer Science and Business Media LLC

Date: 2013

DOI: 10.1186/1471-2164-14-277

Graph pangenomes find missing heritability

Publisher: Springer Science and Business Media LLC

Date: 23-06-2022

DOI: 10.1038/S41588-022-01099-8

RunBNG: A software package for BioNano genomic analysis on the command line

Publisher: Oxford University Press (OUP)

Date: 09-06-2017

DOI: 10.1093/BIOINFORMATICS/BTX366

Abstract: We developed runBNG, an open-source software package which wraps BioNano genomic analysis tools into a single script that can be run on the command line. runBNG can complete analyses, including quality control of single molecule maps, optical map de novo assembly, comparisons between different optical maps, super-scaffolding and structural variation detection. Compared to existing software BioNano IrysView and the KSU scripts, the major advantages of runBNG are that the whole pipeline runs on one single platform and it has a high customizability. runBNG is written in bash, with the requirement of BioNano IrysSolve packages, GCC, Perl and Python software. It is freely available at ppliedbioinformatics/runBNG. Supplementary data are available at Bioinformatics online.

Targeted identification of genomic regions using TAGdb

Publisher: Springer Science and Business Media LLC

Date: 20-08-2010

DOI: 10.1186/1746-4811-6-19

Abstract: The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR lification of the region in the target genome. The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

Publisher: MDPI AG

Date: 28-02-2022

DOI: 10.3390/IJMS23052671

Abstract: Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.

Bioinformatics and Plant Genomics for Staple Crops Improvement

Publisher: Wiley

Date: 02-10-2008

DOI: 10.1002/9780470376447.CH4

Identification of transposon‐tagged genes by the random sequencing of Mutator‐tagged DNA fragments from Zea mays

Publisher: Wiley

Date: 08-2000

DOI: 10.1046/J.1365-313X.2000.00830.X

Abstract: We have used a universal adaptor lification procedure to isolate random Mutator-tagged fragments from Mutator-active maize plants. Direct sequence characterization of 761 Mutator-tagged fragments indicated that a significant number were homologous to sequences within the public databases. The ability of Mutator-tagged fragments to detect homology was not related to the length of the sequence within the range 100-400 bp. However, fragments above this size did show an increased chance of detecting homology to either expressed sequence tags or genes. Characterization of the insertion sites of the Mutator elements suggested that while it does target transcribed regions, Mutator does not appear to have any site preference within the transcription unit. Hybridization of previously unidentified Mutator-tagged fragments to arrayed cDNA libraries confirmed that many of these also showed homology to transcribed regions of the genome. Examination of back-crossed progeny confirmed that all the insertions examined were germinal however, in all but one case, selfing five in idual Mutator-tagged lines failed to reveal an obvious phenotype. This study suggests that the random sequencing of Mutator-tagged fragments is capable of producing both a significant number of interesting transposon tagged genes and mutant plant lines, all of which could be extremely valuable in future gene discovery and functional genomics programmes.

A transcriptomics resource for wheat functional genomics

Publisher: Wiley

Date: 21-09-2004

DOI: 10.1111/J.1467-7652.2004.00096.X

Abstract: Grain development, germination and plant development under abiotic stresses are areas of biology that are of considerable interest to the cereal community. Within the Investigating Gene Function programme we have produced the resources required to investigate alterations in the transcriptome of hexaploid wheat during these developmental processes. We have single pass sequenced the cDNAs of between 700 and 1300 randomly picked clones from each of 35 cDNA libraries representing highly specific stages of grain and plant development. Annotated sequencing results have been stored in a publicly accessible, online database at www.cerealsdb.uk.net. Each of the tissue stages used has also been photographed in detail, resulting in a collection of high-quality micrograph images detailing wheat grain development. These images have been collated and annotated in order to produce a web site focused on wheat development (www.wheatbp.net/). We have also produced high-density microarrays of a publicly available wheat unigene set based on the 35 cDNA libraries and have completed a number of microarray experiments which validate their quality.

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

Publisher: Springer Science and Business Media LLC

Date: 10-03-2015

DOI: 10.1007/S00122-015-2488-Y

Abstract: We characterise the distribution of crossover and non-crossover recombination in Brassica napus and Cicer arietinum using a low-coverage genotyping by sequencing pipeline SkimGBS. The growth of next-generation DNA sequencing technologies has led to a rapid increase in sequence-based genotyping for applications including ersity assessment, genome structure validation and gene-trait association. We have established a skim-based genotyping by sequencing method for crop plants and applied this approach to genotype-segregating populations of Brassica napus and Cicer arietinum. Comparison of progeny genotypes with those of the parental in iduals allowed the identification of crossover and non-crossover (gene conversion) events. Our results identify the positions of recombination events with high resolution, permitting the mapping and frequency assessment of recombination in segregating populations.

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects

Publisher: Frontiers Media SA

Date: 11-08-2015

DOI: 10.3389/FPLS.2015.00563

Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus

Publisher: Frontiers Media SA

Date: 20-01-2017

DOI: 10.3389/FPLS.2016.02062

BioNanoAnalyst: A visualisation tool to assess genome assembly quality using BioNano data

Publisher: Springer Science and Business Media LLC

Date: 30-06-2017

DOI: 10.1186/S12859-017-1735-4

Sorghum pan-genome explores the functional utility to accelerate the genetic gain

Publisher: Cold Spring Harbor Laboratory

Date: 03-02-2021

DOI: 10.1101/2021.02.02.429137

Abstract: Sorghum ( Sorghum bicolor L.) is one of the most important food crops in the arid and rainfed production ecologies. It is a part of resilient farming and is projected as a smart crop to overcome the food and nutritional challenges in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome ersity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically erse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic ersity resources in sorghum which can be used in genome assisted crop improvement.

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

Publisher: Springer Science and Business Media LLC

Date: 12-2020

DOI: 10.1186/S12870-020-02756-Y

Abstract: Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus , flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus . An F 2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. Flowering time in the mapping population differed by up to 25 days between in iduals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC . These findings demonstrate the effectiveness of the ddRAD approach to s le the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F 2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.

Molecular characterization of disease resistance in Brassica juncea – The current status and the way forward

Publisher: Wiley

Date: 30-09-2021

DOI: 10.1111/PPA.13277

Single nucleotide polymorphism discovery in barley using autoSNPdb

Publisher: Wiley

Date: 13-04-2009

DOI: 10.1111/J.1467-7652.2009.00407.X

Abstract: Molecular markers are used to provide the link between genotype and phenotype, for the production of molecular genetic maps and to assess genetic ersity within and between related species. Single nucleotide polymorphisms (SNPs) are the most abundant molecular genetic marker. SNPs can be identified in silico, but care must be taken to ensure that the identified SNPs reflect true genetic variation and are not a result of errors associated with DNA sequencing. The SNP detection method autoSNP has been developed to identify SNPs from sequence data for any species. Confidence in the predicted SNPs is based on sequence redundancy, and haplotype co-segregation scores are calculated for a further independent measure of confidence. We have extended the autoSNP method to produce autoSNPdb, which integrates SNP and gene annotation information with a graphical viewer. We have applied this software to public barley expressed sequences, and the resulting database is available over the Internet. SNPs can be viewed and searched by sequence, functional annotation or predicted synteny with a reference genome, in this case rice. The correlation between SNPs and barley cultivar, expressed tissue type and development stage has been collated for ease of exploration. An average of one SNP per 240 bp was identified, with SNPs more prevalent in the 5' regions and simple sequence repeat (SSR) flanking sequences. Overall, autoSNPdb can provide a wealth of genetic polymorphism information for any species for which sequence data are available.

Revolution in genotyping platforms for crop improvement

Publisher: Springer International Publishing

Date: 2018

DOI: 10.1007/10_2017_47

Abstract: In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and ersity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and ersity analysis. The platforms driving the advances in genotyping are array technologies and genotyping by sequencing (GBS) methods, which include both low-coverage whole genome resequencing (skim sequencing) and reduced representation sequencing (RRS) approaches. Here, we outline and compare these genotyping platforms and provide a perspective on the promising future of crop genotyping. While SNP arrays provide high quality, simple handling, and unchallenging analysis, the lower cost of RRS and the greater data volume produced by skim sequencing suggest that use of GBS will become more prevalent in crop genomics as sequencing costs decrease and data analysis becomes more streamlined. Graphical Abstract.

Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution

Publisher: Oxford University Press (OUP)

Date: 18-04-2018

DOI: 10.1093/JXB/ERY147

Transcriptomic changes in coral holobionts provide insights into physiological challenges of future climate and ocean change

Publisher: Public Library of Science (PLoS)

Date: 28-10-2015

DOI: 10.1371/JOURNAL.PONE.0139223

Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data

Publisher: Oxford University Press (OUP)

Date: 05-2003

DOI: 10.1104/PP.102.019422

Abstract: We have developed a computer based method to identify candidate single nucleotide polymorphisms (SNPs) and small insertions/deletions from expressed sequence tag data. Using a redundancy-based approach, valid SNPs are distinguished from erroneous sequence by their representation multiple times in an alignment of sequence reads. A second measure of validity was also calculated based on the cosegregation of the SNP pattern between multiple SNP loci in an alignment. The utility of this method was demonstrated by applying it to 102,551 maize (Zea mays) expressed sequence tag sequences. A total of 14,832 candidate polymorphisms were identified with an SNP redundancy score of two or greater. Segregation of these SNPs with haplotype indicates that candidate SNPs with high redundancy and cosegregation confidence scores are likely to represent true SNPs. This was confirmed by validation of 264 candidate SNPs from 27 loci, with a range of redundancy and cosegregation scores, in four inbred maize lines. The SNP transition/transversion ratio and insertion/deletion size frequencies correspond to those observed by direct sequencing methods of SNP discovery and suggest that the majority of predicted SNPs and insertion/deletions identified using this approach represent true genetic variation in maize.

Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus

Publisher: Public Library of Science (PLoS)

Date: 09-07-2014

DOI: 10.1371/JOURNAL.PONE.0101673

Genome sequence data: Management, storage, and visualization

Publisher: Future Science Ltd

Date: 04-2009

DOI: 10.2144/000113134

Abstract: Over the last few years there has been a revolution in DNA sequencing technology that has brought down the cost of DNA sequencing and made the sequencing of an increasing number of genomes both feasible and cost effective. There has also been a dramatic shift in the type of sequence data being generated, with vast numbers of short reads or pairs of short reads replacing the traditional relatively long reads produced by Sanger sequencing. These changes in data quantity and format have led to a rethinking of sequence data management, storage, and visualization, and provide a challenge for bioinformatics. The vast amount of sequence data that will will be generated over the next few years will require a change in what data are stored and how users query the information.

Studying the genetic diversity of yam bean using a new draft genome assembly

Publisher: MDPI AG

Date: 11-05-2021

DOI: 10.3390/AGRONOMY11050953

Abstract: Yam bean (Pachyrhizus erosus Rich. Ex DC.) is an underutilized leguminous crop which has been used as a food source across central America and Asia. It is adapted to a range of environments and is closely related to major leguminous food crops, offering the potential to understand the genetic basis of environmental adaptation, and it may be used as a source of novel genes and alleles for the improvement of other legumes. Here, we assembled a draft genome of P. erosus of 460 Mbp in size containing 37,886 gene models. We used this assembly to compare three cultivars each of P. erosus and the closely related P. tuberosus and identified 10,187,899 candidate single nucleotide polymorphisms (SNPs). The SNP distribution reflects the geographic origin and morphology of the in iduals.

Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction

Publisher: Springer Science and Business Media LLC

Date: 08-04-2022

DOI: 10.1186/S12870-022-03559-Z

Abstract: Recent growth in crop genomic and trait data have opened opportunities for the application of novel approaches to accelerate crop improvement. Machine learning and deep learning are at the forefront of prediction-based data analysis. However, few approaches for genotype to phenotype prediction compare machine learning with deep learning and further interpret the models that support the predictions. This study uses genome wide molecular markers and traits across 1110 soybean in iduals to develop accurate prediction models. For 13/14 sets of predictions, XGBoost or random forest outperformed deep learning models in prediction performance. Top ranked SNPs by F-score were identified from XGBoost, and with further investigation found overlap with significantly associated loci identified from GWAS and previous literature. Feature importance rankings were used to reduce marker input by up to 90%, and subsequent models maintained or improved their prediction performance. These findings support interpretable machine learning as an approach for genomic based prediction of traits in soybean and other crops.

Modification of nitrogen remobilization, grain fill and leaf senescence in maize (Zea mays) by transposon insertional mutagenesis in a protease gene

Publisher: Wiley

Date: 08-11-2006

DOI: 10.1111/J.1469-8137.2006.01928.X

Abstract: A maize (Zea mays) senescence-associated legumain gene, See2beta, was characterized at the physiological and molecular levels to determine its role in senescence and resource allocation. A reverse-genetics screen of a maize Mutator (Mu) population identified a Mu insertion in See2beta. Maize plants homozygous for the insertion were produced. These See2 mutant and sibling wild-type plants were grown under high or low quantities of nitrogen (N). The early development of both genotypes was similar however, tassel tip and collar emergence occurred earlier in the mutant. Senescence of the mutant leaves followed a similar pattern to that of wild-type leaves, but at later s ling points mutant plants contained more chlorophyll than wild-type plants and showed a small extension in photosynthetic activity. Total plant weight was higher in the wild-type than in the mutant, and there was a genotype x N interaction. Mutant plants under low N maintained cob weight, in contrast to wild-type plants under the same treatment. It is concluded, on the basis of transposon mutagenesis, that See2beta has an important role in N-use and resource allocation under N-limited conditions, and a minor but significant function in the later stages of senescence.

Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat

Publisher: Wiley

Date: 22-08-2015

DOI: 10.1111/PBI.12240

Abstract: Despite being a major international crop, our understanding of the wheat genome is relatively poor due to its large size and complexity. To gain a greater understanding of wheat genome ersity, we have identified single nucleotide polymorphisms between 16 Australian bread wheat varieties. Whole-genome shotgun Illumina paired read sequence data were mapped to the draft assemblies of chromosomes 7A, 7B and 7D to identify more than 4 million intervarietal SNPs. SNP density varied between the three genomes, with much greater density observed on the A and B genomes than the D genome. This variation may be a result of substantial gene flow from the tetraploid Triticum turgidum, which possesses A and B genomes, during early co-cultivation of tetraploid and hexaploid wheat. In addition, we examined SNP density variation along the chromosome syntenic builds and identified genes in low-density regions which may have been selected during domestication and breeding. This study highlights the impact of evolution and breeding on the bread wheat genome and provides a substantial resource for trait association and crop improvement. All SNP data are publically available on a generic genome browser GBrowse at www.wheatgenome.info.

The conservation of gene models can support genome annotation

Publisher: Wiley

Date: 21-08-2023

DOI: 10.1002/TPG2.20377

Abstract: Many genome annotations include false‐positive gene models, leading to errors in phylogenetic and comparative studies. Here, we propose a method to support gene model prediction based on evolutionary conservation and use it to identify potentially erroneous annotations. Using this method, we developed a set of 15,345 representative gene models from 12 legume assemblies that can be used to support genome annotations for other legumes.

Author Correction: Plant pan-genomes are the new reference

Publisher: Springer Science and Business Media LLC

Date: 02-11-2020

DOI: 10.1038/S41477-020-00776-Y

Advances in Integrating Genomics and Bioinformatics in the Plant Breeding Pipeline

Publisher: MDPI AG

Date: 31-05-2018

DOI: 10.3390/AGRICULTURE8060075

Diversity of Phytosterols in Leaves of Wild Brassicaceae Species as Compared to Brassica napus Cultivars: Potential Traits for Insect Resistance and Abiotic Stress Tolerance

Publisher: MDPI AG

Date: 05-2023

DOI: 10.3390/PLANTS12091866

Abstract: Phytosterols are natural compounds found in all higher plants that have a wide variety of roles in plant growth regulation and stress tolerance. The phytosterol composition can also influence the development and reproductive rate of strict herbivorous insects and other important agronomic traits such as temperature and drought tolerance in plants. In this study, we analysed the phytosterol composition in 18 Brassica napus (Rapeseed/canola) cultivars and 20 accessions belonging to 10 related wild Brassicaceae species to explore erse and novel phytosterol profiles. Plants were grown in a controlled phytotron environment and their phytosterols were analysed using a saponification extraction method followed by GC-MS from the leaf s les. The B. napus cultivars showed slight ersity in eight phytosterols ( .02%) due to the genotypic effect, whereas the wild accessions showed significant variability in their phytosterol profiles. Of interest, a number of wild accessions were found with high levels of c esterol (HIN20, HIN23, HUN27, HIN30, SARS2, and UPM6563), stigmasterol (UPM6813, UPM6563, ALBA17, and ALBA2), and isofucosterol (SARS12, SAR6, and DMU2). These changes in in idual phytosterols, or ratios of phytosterols, can have a significant implication in plant tolerance to abiotic stress and plant insect resistance properties, which can be used in breeding for crop improvement.

Current biology special issue

Publisher: Elsevier BV

Date: 06-2020

DOI: 10.1016/J.CPB.2020.100155

Identification and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus

Publisher: Springer Science and Business Media LLC

Date: 05-11-2020

DOI: 10.1007/S00122-019-03469-Z

Abstract: Partially dominant resistance to Turnip yellows virus associated with one major QTL was identified in the natural allotetraploid oilseed rape cultivar Yudal. Turnip yellows virus (TuYV) is transmitted by the peach-potato aphid ( Myzus persicae ) and causes severe yield losses in commercial oilseed rape crops ( Brassica napus ). There is currently only one genetic resource for resistance to TuYV available in brassica, which was identified in the re-synthesised B. napus line ‘R54’. In our study, 27 mostly homozygous B. napus accessions, either doubled-haploid (DH) or inbred lines, representing a erse subset of the B. napus genepool, were screened for TuYV resistance/susceptibility. Partial resistance to TuYV was identified in the Korean spring oilseed rape, B. napus variety Yudal, whilst the dwarf French winter oilseed rape line Darmor- bzh was susceptible. QTL mapping using the established Darmor- bzh × Yudal DH mapping population (DYDH) revealed one major QTL explaining 36% and 18% of the phenotypic variation in two independent experiments. A DYDH line was crossed to Yudal, and reciprocal backcross (BC 1 ) populations from the F 1 with either the susceptible or resistant parent revealed the dominant inheritance of the TuYV resistance. The QTL on ChrA04 was verified in the segregating BC 1 population. A second minor QTL on ChrC05 was identified in one of the two DYDH experiments, and it was not observed in the BC 1 population. The TuYV resistance QTL in ‘R54’ is within the QTL interval on Chr A04 of Yudal however, the markers co-segregating with the ‘R54’ resistance are not conserved in Yudal, suggesting an independent origin of the TuYV resistances. This is the first report of the QTL mapping of TuYV resistance in natural B. napus .

Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network

Publisher: Oxford University Press (OUP)

Date: 06-01-2015

DOI: 10.1093/JXB/ERU510

Frontiers in dissecting and managing brassica diseases

Publisher: MDPI AG

Date: 25-11-2020

DOI: 10.3390/IJMS21238964

Abstract: The Brassica genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of Brassica genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for B. rapa, B. oleracea and B. napus. Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important Brassica genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible in iduals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA ersity characterised in the limited number of Brassica assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA ersity, greatly expanding breeding resources that can be utilised for crop improvement.

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Publisher: Springer Science and Business Media LLC

Date: 10-11-2021

DOI: 10.1038/S41586-021-04066-1

Abstract: Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources 1 . So far, few chickpea ( Cicer arietinum ) germplasm accessions have been characterized at the genome sequence level 2 . Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic ersity across cultivated chickpea and its wild progenitor accessions. A ergence tree using genes present in around 80% of in iduals in one species allowed us to estimate the ergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic ersity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic ersity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Progress in single-access information systems for wheat and rice crop improvement

Publisher: Oxford University Press (OUP)

Date: 05-04-2019

DOI: 10.1093/BIB/BBY016

Abstract: Improving productivity of the staple crops wheat and rice is essential to feed the growing global population, particularly in the context of a changing climate. However, current rates of yield gain are insufficient to support the predicted population growth. New approaches are required to accelerate the breeding process, and many of these are driven by the application of large-scale crop data. To leverage the substantial volumes and types of data that can be applied for precision breeding, the wheat and rice research communities are working towards the development of integrated systems to access and standardize the dispersed, heterogeneous available data. Here, we outline the initiatives of the International Wheat Information System (WheatIS) and the International Rice Informatics Consortium (IRIC) to establish Web-based single-access systems and data mining tools to make the available resources more accessible, drive discovery and accelerate the production of new crop varieties. We discuss the progress of WheatIS and IRIC towards unifying specialized wheat and rice databases and building custom software platforms to manage and interrogate these data. Single-access crop information systems will strengthen scientific collaboration, optimize the use of public research funds and help achieve the required yield gains in the two most important global food crops.

Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes

Publisher: Springer Science and Business Media LLC

Date: 25-03-2022

DOI: 10.1038/S41586-022-04660-X

WheatGenome.info: An integrated database and portal for wheat genome information

Publisher: Oxford University Press (OUP)

Date: 18-10-2012

DOI: 10.1093/PCP/PCR141

Abstract: Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between erse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

Publisher: Springer Science and Business Media LLC

Date: 30-06-2016

DOI: 10.1007/S00122-016-2746-7

Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools

Publisher: Elsevier BV

Date: 06-2023

DOI: 10.1016/J.TPLANTS.2023.01.006

A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus

Publisher: Springer Science and Business Media LLC

Date: 28-05-2015

DOI: 10.1186/S12864-015-1559-4

Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin

Publisher: Springer Science and Business Media LLC

Date: 20-01-2018

DOI: 10.1007/S00122-017-3045-7

A comparative map viewer integrating genetic maps for Brassica and Arabidopsis

Publisher: Springer Science and Business Media LLC

Date: 24-07-2007

DOI: 10.1186/1471-2229-7-40

Abstract: Molecular genetic maps provide a means to link heritable traits with underlying genome sequence variation. Several genetic maps have been constructed for Brassica species, yet to date, there has been no simple means to compare this information or to associate mapped traits with the genome sequence of the related model plant, Arabidopsis . We have developed a comparative genetic map database for the viewing, comparison and analysis of Brassica and Arabidopsis genetic, physical and trait map information. This web-based tool allows users to view and compare genetic and physical maps, search for traits and markers, and compare genetic linkage groups within and between the hidiploid and diploid Brassica genomes. The inclusion of Arabidopsis data enables comparison between Brassica maps that share no common markers. Analysis of conserved syntenic blocks between Arabidopsis and collated Brassica genetic maps validates the application of this system. This tool is freely available over the internet on bioinformatics.pbcbasc.latrobe.edu.au/cmap . This database enables users to interrogate the relationship between Brassica genetic maps and the sequenced genome of A. thaliana , permitting the comparison of genetic linkage groups and mapped traits and the rapid identification of candidate genes.

Effect of leptosphaeria maculans infection on promoter DNA methylation of defence genes in brassica napus

Publisher: MDPI AG

Date: 24-07-2020

DOI: 10.3390/AGRONOMY10081072

Abstract: Canola (Brassica napus) is an important crop species grown worldwide for its seeds, which are crushed for edible oil. Canola production is threatened by blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, which can lead up to 100% yield loss. A plant’s disease resistance response depends highly on the regulation of the expression of defence genes. DNA methylation, an epigenetic mark, is one of the most important regulatory mechanisms in a plant’s defence system. Here, the DNA methylation pattern of promoters of defence genes has been investigated between leaves from control and infected plants with L. maculans of resistant and susceptible cultivars of B. napus. In total, over 12,000 promoters were found to be differentially methylated between leaves from control and infected plants in the two cultivars, of which 225 promoters were related to defence genes and differentially methylated between the resistant and susceptible cultivars. The majority of defence gene promoters were hypo- or hyper-methylated in the first and second true leaves, but not in the third and fourth leaves. The outcomes will assist in developing an insight into genome-wide DNA methylation patterns in canola cultivars, and ultimately help breeders to optimise the breeding programmes for enhancing resistance against blackleg disease.

Gene loss in the fungal canola pathogen Leptosphaeria maculans

Publisher: Springer Science and Business Media LLC

Date: 25-11-2015

DOI: 10.1007/S10142-014-0412-1

Abstract: Recent comparisons of the increasing number of genome sequences have revealed that variation in gene content is considerably more prevalent than previously thought. This variation is likely to have a pronounced effect on phenotypic ersity and represents a crucial target for the assessment of genomic ersity. Leptosphaeria maculans, a causative agent of phoma stem canker, is the most devastating fungal pathogen of Brassica napus (oilseed rape/canola). A number of L. maculans genes are known to be present in some isolates but lost in the others. We analyse gene content variation within three L. maculans isolates using a hybrid mapping and genome assembly approach and identify genes which are present in one of the isolates but missing in the others. In total, 57 genes are shown to be missing in at least one isolate. The genes encode proteins involved in a range of processes including oxidative processes, DNA maintenance, cell signalling and sexual reproduction. The results demonstrate the effectiveness of the method and provide new insight into genomic ersity in L. maculans.

Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene

Publisher: Springer Science and Business Media LLC

Date: 11-04-2015

DOI: 10.1007/S00122-015-2512-2

Abstract: Making use of wheat chromosomal resources, we developed 11 gene-associated markers for the region of interest, which allowed reducing gene interval and spanning it by four BAC clones. Positional gene cloning and targeted marker development in bread wheat are h ered by high complexity and polyploidy of its nuclear genome. Aiming to clone a Russian wheat aphid resistance gene Dn2401 located on wheat chromosome arm 7DS, we have developed a strategy overcoming problems due to polyploidy and enabling efficient development of gene-associated markers from the region of interest. We employed information gathered by GenomeZipper, a synteny-based tool combining sequence data of rice, Brachypodium, sorghum and barley, and took advantage of a high-density linkage map of Aegilops tauschii. To ensure genome- and locus-specificity of markers, we made use of survey sequence assemblies of isolated wheat chromosomes 7A, 7B and 7D. Despite the low level of polymorphism of the wheat D subgenome, our approach allowed us to add in an efficient and cost-effective manner 11 new gene-associated markers in the Dn2401 region and narrow down the target interval to 0.83 cM. Screening 7DS-specific BAC library with the flanking markers revealed a contig of four BAC clones that span the Dn2401 region in wheat cultivar 'Chinese Spring'. With the availability of sequence assemblies and GenomeZippers for each of the wheat chromosome arms, the proposed strategy can be applied for focused marker development in any region of the wheat genome.

Moderating Factors in Tissue Tonometry and Bioimpedance Spectroscopy Measures in the Lower Extremity of Healthy Young People in Australia and Myanmar.

Publisher: Mary Ann Liebert Inc

Date: 06-2018

DOI: 10.1089/LRB.2017.0057

Abstract: Expected values for tissue tonometry and bioimpedance spectroscopy (BIS) in the lower extremity of young people have not been established. These measures are commonly used to assess tissue changes in adult, breast cancer-related lymphedema of the arm. In tropical regions, identification of tissue changes in the lower limbs related to lymphatic filariasis is required hence expected values and factors contributing to variation in tissue tonometry and BIS in two tropical populations were investigated. A convenience s le of healthy volunteers aged 8-21 in Myanmar and Australia was recruited. Tissue compressibility at the calf and anterior and posterior thigh was measured using three tonometry devices and free fluid in each leg was assessed using BIS. Data were collected about possible modifiers: leg dominance, age, gender, body mass index (BMI), hydration, and menstrual cycle. Paired t-test and linear regression compared the objective measures with possible modifiers within each population. Statistical significance was set at p < 0.05 with a 95% confidence interval. In Myanmar, increases in free fluid, tissue compressibility, and limb circumference were associated with being older, female, underweight, or in the second half of the menstrual cycle. In young Australians, increases in tissue compressibility and limb circumference were associated with being older or in the second half of the menstrual cycle. When assessing tissue compressibility and free fluid in young people using tonometry and gender, BIS, limb dominance and BMI should be considered in a local context and attempts should be made to minimize the potential influences of hydration and the female menstrual cycle.

Next-generation sequencing applications for wheat crop improvement

Publisher: Wiley

Date: 02-2012

DOI: 10.3732/AJB.1100309

Abstract: Bread wheat (Triticum aestivum Poaceae) is a crop plant of great importance. It provides nearly 20% of the world's daily food supply measured by calorie intake, similar to that provided by rice. The yield of wheat has doubled over the last 40 years due to a combination of advanced agronomic practice and improved germplasm through selective breeding. More recently, yield growth has been less dramatic, and a significant improvement in wheat production will be required if demand from the growing human population is to be met. Next-generation sequencing (NGS) technologies are revolutionizing biology and can be applied to address critical issues in plant biology. Technologies can produce draft sequences of genomes with a significant reduction to the cost and timeframe of traditional technologies. In addition, NGS technologies can be used to assess gene structure and expression, and importantly, to identify heritable genome variation underlying important agronomic traits. This review provides an overview of the wheat genome and NGS technologies, details some of the problems in applying NGS technology to wheat, and describes how NGS technologies are starting to impact wheat crop improvement.

Preface: Advances in DNA sequencing accelerating plant biotechnology

Publisher: Wiley

Date: 06-07-2012

DOI: 10.1111/J.1467-7652.2012.00724.X

An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth

Publisher: Springer US

Date: 2022

DOI: 10.1007/978-1-0716-2429-6_5

Abstract: Presence-absence variants (PAV) are genomic regions present in some in iduals of a species, but not others. PAVs have been shown to contribute to genomic ersity, especially in bacteria and plants. These structural variations have been linked to traits and can be used to track a species' evolutionary history. PAVs are usually called by aligning short read sequence data from one or more in iduals to a reference genome or pangenome assembly, and then comparing coverage. Regions where reads do not align define absence in that in idual, and the regions are classified as PAVs. The method below details how to align sequence reads to a reference and how to use the sequencing-coverage calculator Mosdepth to identify PAVs and construct a PAV table for use in downstream comparative genome analysis.

Discovering genetic polymorphisms in next-generation sequencing data: Review article

Publisher: Wiley

Date: 13-04-2009

DOI: 10.1111/J.1467-7652.2009.00406.X

Abstract: The ongoing revolution in DNA sequencing technology now enables the reading of thousands of millions of nucleotide bases in a single instrument run. However, this data quantity is often compromised by poor confidence in the read quality. The identification of genetic polymorphisms from this data is therefore problematic and, combined with the vast quantity of data, poses a major bioinformatics challenge. However, once these difficulties have been addressed, next-generation sequencing will offer a means to identify and characterize the wealth of genetic polymorphisms underlying the vast phenotypic variation in biological systems. We describe the recent advances in next-generation sequencing technology, together with preliminary approaches that can be applied for single nucleotide polymorphism discovery in plant species.

Rapid delivery systems for future food security

Publisher: Springer Science and Business Media LLC

Date: 28-09-2021

DOI: 10.1038/S41587-021-01079-Z

Searching for Homologous Genes Using Daisychain

Publisher: Springer US

Date: 2022

DOI: 10.1007/978-1-0716-2429-6_7

Abstract: Genome assemblies have become a standard tool of genomics research and are relatively inexpensive to produce due to falling sequencing costs. For many species, there are now several reference-grade genome assemblies. However, comparing different assemblies or the same or related in iduals is not an easy task, especially with different levels of quality of assembly and annotation. Tools are needed to visualise related genes with different IDs across genome assemblies. Here, we present a workflow to search and visualise related genes using Daisychain, a web-based tool aimed at researchers who wish to compare genes between assemblies.

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Publisher: American Association for the Advancement of Science (AAAS)

Date: 22-08-2014

DOI: 10.1126/SCIENCE.1253435

Abstract: Many domesticated plants arose through the meeting of multiple genomes through hybridization and genome doubling, known as polyploidy. Chalhoub et al. sequenced the polyploid genome of Brassica napus , which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed (canola), kale, and rutabaga. B. napus has undergone multiple events affecting differently sized genetic regions where a gene from one progenitor species has been converted to the copy from a second progenitor species. Some of these gene conversion events appear to have been selected by humans as part of the process of domestication and crop improvement. Science , this issue p. 950

Genetic and signalling pathways of dry fruit size: targets for genome editing‐based crop improvement

Publisher: Wiley

Date: 25-01-2020

DOI: 10.1111/PBI.13318

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

Publisher: Springer Science and Business Media LLC

Date: 2014

DOI: 10.1186/GB-2014-15-6-R77

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

Publisher: Elsevier BV

Date: 02-2020

DOI: 10.1016/J.TPLANTS.2019.10.012

CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat

Publisher: Wiley

Date: 28-01-2019

DOI: 10.1111/TPJ.14194

Abstract: Advances in sequencing technology have led to a rapid rise in the genomic data available for plants, driving new insights into the evolution, domestication and improvement of crops. Single nucleotide polymorphisms (SNPs) are a major component of crop genomic ersity, and are invaluable as genetic markers in research and breeding programs. High-throughput SNP arrays, or 'SNP chips', can generate reproducible sets of informative SNP markers and have been broadly adopted. Although there are many public repositories for sequencing data, which are routinely uploaded, there are no formal repositories for crop SNP array data. To make SNP array data more easily accessible, we have developed CropSNPdb (snpdb.appliedbioinformatics.com.au), a database for SNP array data produced by the Illumina Infinium™ hexaploid bread wheat (Triticum aestivum) 90K and Brassica 60K arrays. We currently host SNPs from datasets covering 526 Brassica lines and 309 bread wheat lines, and provide search, download and upload utilities for users. CropSNPdb provides a useful repository for these data, which can be applied for a range of genomics and molecular crop-breeding activities.

Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies

Publisher: MDPI AG

Date: 19-12-2021

DOI: 10.3390/AGRONOMY11122587

Abstract: Daisychain is an interactive graph visualisation and search tool for custom-built gene homology databases. The main goal of Daisychain is to allow researchers working with specific genes to identify homologs in other annotation releases. The gene-centric representation includes local gene neighborhood to distinguish orthologs and paralogs by local synteny. The software supports genome sequences in FASTA format and GFF3 formatted annotation files, and the process of building the homology database requires a minimum amount of user interaction. Daisychain includes an integrated web viewer that can be used for both data analysis and data publishing. The web interface extends KnetMaps.js and is based on JavaScript.

Use of multiple ‘omics techniques to accelerate the breeding of abiotic stress tolerant crops

Publisher: Elsevier BV

Date: 12-2022

DOI: 10.1016/J.CPB.2022.100262

Capturing Wheat Phenotypes at the Genome Level

Publisher: Frontiers Media SA

Date: 04-07-2022

DOI: 10.3389/FPLS.2022.851079

Abstract: Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat ( Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical ex le of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

Method for Genome-Wide Association Study

Publisher: Springer US

Date: 2020

DOI: 10.1007/978-1-0716-0235-5_7

Abstract: Genome-wide association studies (GWAS) are a valuable approach to identify single nucleotide polymorphisms (SNPs) associated with a phenotype of interest. There are now a variety of R-packages and command line tools available to perform GWAS. Here, we provide an ex le downloading and filtering SNP data, followed by GWAS analysis using the R-package rMVP.

Unfolding the secrets of coral–algal symbiosis

Publisher: Springer Science and Business Media LLC

Date: 24-10-2014

DOI: 10.1038/ISMEJ.2014.182

Bioinformatics tools and databases for analysis of next-generation sequence data

Publisher: Oxford University Press (OUP)

Date: 19-12-2012

DOI: 10.1093/BFGP/ELR037

Abstract: Genome sequencing has been revolutionized by next-generation technologies, which can rapidly produce vast quantities of data at relatively low cost. With data production now no longer being limited, there is a huge challenge to analyse the data flood and interpret biological meaning. Bioinformatics scientists have risen to the challenge and a large number of software tools and databases have been produced and these continue to evolve with this rapidly advancing field. Here, we outline some of the tools and databases commonly used for the analysis of next-generation sequence data with comment on their utility.

Legume pangenome construction using an iterative mapping and assembly approach

Publisher: Springer US

Date: 2020

DOI: 10.1007/978-1-0716-0235-5_3

Abstract: A pangenome is a collection of genomic sequences found in the entire species rather than a single in idual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.

Functional genomics to study stress responses in crop legumes: Progress and prospects

Publisher: CSIRO Publishing

Date: 2013

DOI: 10.1071/FP13191

Abstract: Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stress-responsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.

Application of pangenomics for wheat molecular breeding

Publisher: CABI

Date: 02-07-2021

DOI: 10.1079/9781789245431.0013

Advances in genomics for adapting crops to climate change

Publisher: Elsevier BV

Date: 10-2016

DOI: 10.1016/J.CPB.2016.09.001

Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing

Publisher: Springer Science and Business Media LLC

Date: 21-06-2013

DOI: 10.1007/S10142-013-0324-5

Abstract: Next generation sequencing technology allows rapid re-sequencing of in iduals, as well as the discovery of single nucleotide polymorphisms (SNPs), for genomic ersity and evolutionary analyses. By sequencing two isolates of the fungal plant pathogen Leptosphaeria maculans, the causal agent of blackleg disease in Brassica crops, we have generated a resource of over 76 million sequence reads aligned to the reference genome. We identified over 21,000 SNPs with an overall SNP frequency of one SNP every 2,065 bp. Sequence validation of a selection of these SNPs in additional isolates collected throughout Australia indicates a high degree of polymorphism in the Australian population. In preliminary phylogenetic analysis, isolates from Western Australia clustered together and those collected from Brassica juncea stubble were identical. These SNPs provide a novel marker resource to study the genetic ersity of this pathogen. We demonstrate that re-sequencing provides a method of validating previously characterised SNPs and analysing differences in important genes, such as the disease related avirulence genes of L. maculans. Understanding the genetic characteristics of this devastating pathogen is vital in developing long-term solutions to managing blackleg disease in Brassica crops.

Coverage-based consensus calling (CBCC) of short sequence reads and comparison of CBCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome

Publisher: Wiley

Date: 02-2012

DOI: 10.3732/AJB.1100419

Abstract: Next-generation sequencing (NGS) technologies are frequently used for resequencing and mining of single nucleotide polymorphisms (SNPs) by comparison to a reference genome. In crop species such as chickpea (Cicer arietinum) that lack a reference genome sequence, NGS-based SNP discovery is a challenge. Therefore, unlike probability-based statistical approaches for consensus calling and by comparison with a reference sequence, a coverage-based consensus calling (CbCC) approach was applied and two genotypes were compared for SNP identification. A CbCC approach is used in this study with four commonly used short read alignment tools (Maq, Bowtie, Novoalign, and SOAP2) and 15.7 and 22.1 million Illumina reads for chickpea genotypes ICC4958 and ICC1882, together with the chickpea trancriptome assembly (CaTA). A nonredundant set of 4543 SNPs was identified between two chickpea genotypes. Experimental validation of 224 randomly selected SNPs showed superiority of Maq among in idual tools, as 50.0% of SNPs predicted by Maq were true SNPs. For combinations of two tools, greatest accuracy (55.7%) was reported for Maq and Bowtie, with a combination of Bowtie, Maq, and Novoalign identifying 61.5% true SNPs. SNP prediction accuracy generally increased with increasing reads depth. This study provides a benchmark comparison of tools as well as read depths for four commonly used tools for NGS SNP discovery in a crop species without a reference genome sequence. In addition, a large number of SNPs have been identified in chickpea that would be useful for molecular breeding.

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

Publisher: Wiley

Date: 24-08-2021

DOI: 10.1111/PBI.13674

Abstract: Plant genomes demonstrate significant presence/absence variation (PAV) within a species however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.

Detection of Epistasis for Seed and Some Phytochemical Traits in Coriander under Different Irrigation Regimes

Publisher: MDPI AG

Date: 21-09-2021

DOI: 10.3390/AGRONOMY11091891

Abstract: Coriander (Coriander sativum L.) is an annual herb mainly cultivated for its seed characteristics. Drought stress is a major problem which affects coriander behaviour through biochemical responses. This study aimed to determine the nature and magnitude of epistasis in inheritance of seed yield (SY), percent of dehulled seed (PODS), percent of seed hulls (POSH), essential oil content (EOC), essential oil yield (EOY), dehulled seed fatty acid content (DSFAC), hull fatty acid content (HFAC), fatty acid content (FAC), and fatty acid yield (FAY), and to estimate additive and dominance variance for the traits not influenced by epistasic effects. Three testers, TN-59-158 (highly drought-susceptible), TN-58-230 (highly drought-tolerant, but low-yielding), and their F1 hybrid were each crossed for six genotypes. The experiment was performed under different levels of water deficit: control (C), moderate water deficit (MWD), and severe water deficit (SWD) conditions. Epistasis affected the expression of SY, EOC, EOY, FAC, and FAY in all water conditions, PODS in C, POSH in SWD, HFAC in MWD, and DSFAC in both C and MWD conditions. Total epistasic effects were partitioned, showing that both [i] and [j + l] type interactions were significant, with a prevalent influence of [i] type interactions on these traits except for POSH and FAC in the SWD condition, which exhibited a higher value of the [j + l] type. Both additive and non-additive gene actions were significant for those traits not significantly affected by epistasis in C, MWD, or SWD conditions. An additive type of gene action was preponderant for PODS in MWD and SWD, POSH in MWD, DSFAC in SWD, and HFAC in C and SWD conditions.

Genetic and molecular analysis of stem rot (Sclerotinia sclerotiorum) resistance in Brassica napus (canola type)

Publisher: Elsevier BV

Date: 09-2023

DOI: 10.1016/J.HELIYON.2023.E19237

Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana

Publisher: MDPI AG

Date: 26-05-2022

DOI: 10.3390/BIOLOGY11060821

Abstract: Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.

Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice

Publisher: Frontiers Media SA

Date: 02-09-2022

DOI: 10.3389/FPLS.2022.976669

Abstract: High seedling vigor can improve the ability to compete against weeds and flooding at the seedling stage and is essential for the direct seeding of rice. Early shoot length is an important performance index in seedling vigor evaluation. However, information on the identity of rice germplasm with high seedling vigor, and the genetic basis of seedling vigor are not well understood. In this study, we have conducted a genome-wide association study using 302 international erse rice accessions from the Rice Diversity Panel 2. Six quantitative trait loci (QTLs) were found to associate with shoot length (SL). The locus qSL2 was further analyzed for candidate gene characterization. We identified OsCPS1 , which encodes CDP synthase and functions in GA (Gibberellins) biosynthesis in rice, exhibits differential expression between long and short SL accessions. Using the Nipponbare genome sequence as the reference, we identified a 36 bp deletion in the 5’ UTR of OsCPS1 in long SL accessions, which is absent in short SL accessions. GA content analysis showed that the levels of bioactive GA 1 and GA 4 are considerably higher in long SL accessions than in short SL accessions. Genome-wide gene expression analysis indicated the expression of some photosynthesis genes is higher in long SL accessions than in short SL accessions. In contrast, genes involved in ABA (Abscisic Acid)-activated signal pathway showed lower expression in long SL accessions. Population analysis across wild rice, indica and japonica, suggested that OsCPS1 may be under selection in japonica during domestication. The results suggest that OsCPS1 is a candidate gene underlying qSL2 . These data provide a promising source for candidate genetic variation associated with seedling vigor, with practical applications in rice breeding.

Local haplotype visualization for trait association analysis with crosshap

Publisher: Cold Spring Harbor Laboratory

Date: 08-05-2023

DOI: 10.1101/2023.05.07.539781

Abstract: GWAS excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present ‘crosshap’, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture haplotype structures in a local genomic region of interest. Following this, ‘crosshap’ is equipped with visualization tools for choosing optimal clustering parameters (ε) before producing an intuitive figure that provides an overview of the complex relationships between linked variants, haplotype combinations, phenotypic traits and metadata. The ‘crosshap’ package is freely available under the MIT license and can be downloaded directly from CRAN with R .0.0. The development version is available on GitHub alongside issue support ( acobimarsh/crosshap ). Tutorial vignettes and documentation are available ( jacobimarsh.github.io/crosshap/ ).

Genome-wide identification and comparative analysis of resistance genes in Brassica juncea

Publisher: Springer Science and Business Media LLC

Date: 08-2020

DOI: 10.1007/S11032-020-01159-Z

Dissection of Genetic Effects, Heterosis, and Inbreeding Depression for Phytochemical Traits in Coriander

Publisher: MDPI AG

Date: 02-11-2022

DOI: 10.3390/PLANTS11212959

Abstract: Increasing seed yield, fatty acids, and essential oil content are the main objectives in breeding coriander. However, in order to achieve this, there is a need to understand the nature of gene action and quantify the heterosis and inbreeding depression. Towards this, six genetically erse parents, their 15 F1 one-way hybrids, and 15 F2 populations were evaluated under different water treatments. The genetic effects of general (GCA) and specific combining ability (SCA) and their interactions with water treatment were significant for five traits. Water deficit stress decreased all traits in both F1 and F2 generations except for the essential oil content, which was significantly increased due to water deficit stress. Under water deficit stress, a non-additive gene action was predominant in the F1 generation, while an additive gene action was predominant in the F2 generation for all the traits except seed yield under severe water deficit stress. There was a positive high heterosis for the traits examined in some hybrids. Furthermore, in the F2 generation, even after inbreeding depression, some promising populations displayed appropriate mean performance. The results show that the parents used for crossing had a rich, erse gene pool for the traits studied. Therefore, selection between the in iduals of relevant F2 populations could be used to develop high yielding hybrids or superior lines.

Rapid divergence of repetitive DNAs in Brassica relatives

Publisher: Elsevier BV

Date: 03-2011

DOI: 10.1016/J.YGENO.2010.12.002

Abstract: Centromeric, subtelomeric, and telomeric repetitive DNAs were characterized in Brassica species and the related Raphanus sativus and Arabidopsis thaliana. In general, rapid ergence of the repeats was found. The centromeric tandem satellite repeats were differentially distributed in the species studied, suggesting that centromeric repeats have erged during the evolution of the A/C and B genome lineages. Sequence analysis of centromeric repeats suggested rapid evolution. Pericentromere-associated retrotransposons were identified and showed ergence during the evolution of the lineages as centromeric repeats. A novel subtelomeric tandem repeat from B. nigra was found to be conserved across the diploid Brassica genomes however, this sequence was not identified in the related species. In contrast to previous studies, interstitial telomere-like repeats were identified in the pericentromeres of Brassica chromosomes, and these repeats may be associated with genomic stability. These results provide insight into genome evolution during polyploidization in Brassica and ergence within the Brassicaceae.

Delayed leaf greening involves a major shift in the expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)

Publisher: Springer Science and Business Media LLC

Date: 27-09-2023

DOI: 10.1007/S11104-023-06275-1

Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era

Publisher: MDPI AG

Date: 10-10-2020

DOI: 10.3390/PLANTS9101336

Abstract: Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host–pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.

Editorial overview

Publisher: Elsevier BV

Date: 10-0002

DOI: 10.1016/J.PBI.2018.08.004

A pangenome analysis pipeline provides insights into functional gene identification in rice

Publisher: Springer Science and Business Media LLC

Date: 26-01-2023

DOI: 10.1186/S13059-023-02861-9

Abstract: A pangenome aims to capture the complete genetic ersity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking. To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants’ position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 erse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic ersity. We characterize a new locus ( qPH8-1 ) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS). Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.

Genome editors take on crops

Publisher: American Association for the Advancement of Science (AAAS)

Date: 17-03-2017

DOI: 10.1126/SCIENCE.AAL4680

Abstract: Genome editing technologies may help to enhance global food security

A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes

Publisher: Springer Science and Business Media LLC

Date: 22-08-2014

DOI: 10.1007/S10142-014-0391-2

Abstract: Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic ersity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important hidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 s les screened. Although the assay was designed to B. napus, successful SNP lification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus in iduals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 s les.

Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology

Publisher: Wiley

Date: 09-2012

DOI: 10.3732/AJB.1200077

Abstract: The aim of this study was to assess the feasibility of developing chromosome-arm-specific microsatellite markers in wheat on a large scale based on chromosome survey sequences obtained with next-generation sequencing (NGS) technology. The Illumina Hi Seq2000 sequencing platform was used to sequence DNA of isolated wheat chromosome-arm 7DL. The data were assembled and microsatellite loci were identified computationally. In total, 16315 microsatellites were identified from 161061 assembled contigs. Thirty-three markers were randomly selected for validation across 20 erse wheat cultivars. Two nulli-tetrasomic stocks were also screened to validate the specificity of the newly developed markers. This is the first study on identification of chromosome-arm-specific microsatellite markers using NGS technology. These new chromosome-arm-specific markers will facilitate saturation of the 7DL genetic map, and their availability will support genetic mapping and positional cloning in wheat.

Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment

Publisher: Wiley

Date: 16-11-2022

DOI: 10.1002/TPG2.20166

Abstract: Achieving yield potential in chickpea ( Cicer arietinum L.) is limited by many constraints that include biotic and abiotic stresses. Combining next‐generation sequencing technology with advanced statistical modeling has the potential to increase genetic gain efficiently. Whole genome resequencing data was obtained from 315 advanced chickpea breeding lines from the Australian chickpea breeding program resulting in more than 298,000 single nucleotide polymorphisms (SNPs) discovered. Analysis of population structure revealed a distinct group of breeding lines with many alleles that are absent from recently released Australian cultivars. Genome‐wide association studies (GWAS) using these Australian breeding lines identified 20 SNPs significantly associated with grain yield in multiple field environments. A reduced level of nucleotide ersity and extended linkage disequilibrium suggested that some regions in these chickpea genomes may have been through selective breeding for yield or other traits. A large introgression segment that introduced from C. echinospermum for phytophthora root rot resistance was identified on chromosome 6, yet it also has unintended consequences of reducing yield due to linkage drag. We further investigated the effect of genotype by environment interaction on genomic prediction of yield. We found that the training set had better prediction accuracy when phenotyped under conditions relevant to the targeted environments. We also investigated the effect of SNP functional annotation on prediction accuracy using different subsets of SNPs based on their genomic locations: regulatory regions, exome, and alternative splice sites. Compared with the whole SNP dataset, a subset of SNPs did not significantly decrease prediction accuracy for grain yield despite consisting of a smaller number of SNPs.

Characterization of the flanking regions of Zea mays microsatellites reveals a large number of useful sequence polymorphisms

Publisher: Springer Science and Business Media LLC

Date: 09-2002

DOI: 10.1007/S00122-002-0897-1

Abstract: Sequence characterization of the flanking regions of 52 sequence-tagged microsatellite loci and two gene fragments from 11 Zea mays inbred lines identified a total of 324 sequence polymorphisms. The sequence polymorphisms consisted of both single-nucleotide polymorphisms and insertions/deletions in a ratio of approximately two to one. The level of sequence variation within the flanking regions of microsatellites linked to expressed sequence tags was lower than microsatellites that were unlinked to expressed sequence tags. However, both types of microsatellites generated a similar number of sequence-based alleles across the 11 genotypes surveyed. In two out of 20 microsatellites examined in detail, evidence was found for size-based allele homoplasy. Conversion of the observed sequence polymorphisms into allele-specific oligonucleotides followed by covalent binding to glass slides allowed the sequence polymorphisms to be used in a simple hybridization-based genotyping procedure. This procedure enabled us to discriminate between different inbred lines and allowed variations within a single inbred to be identified. The sequence information presented in this report could be used as a starting point for other programmes in the further development of a non-gel based, multi-locus, multi-allele screen for large-scale maize genotyping.

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata

Publisher: Public Library of Science (PLoS)

Date: 14-12-2012

DOI: 10.1371/JOURNAL.PONE.0051687

An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance

Publisher: Wiley

Date: 23-03-2017

DOI: 10.1111/PBI.12697

Genotype–Environment mismatch of kelp forests under climate change

Publisher: Wiley

Date: 16-06-2021

DOI: 10.1111/MEC.15993

Abstract: Climate change is increasingly impacting ecosystems globally. Understanding adaptive genetic ersity and whether it will keep pace with projected climatic change is necessary to assess species’ vulnerability and design efficient mitigation strategies such as assisted adaptation. Kelp forests are the foundations of temperate reefs globally but are declining in many regions due to climate stress. A lack of knowledge of kelp's adaptive genetic ersity hinders assessment of vulnerability under extant and future climates. Using 4245 single nucleotide polymorphisms (SNPs), we characterized patterns of neutral and putative adaptive genetic ersity for the dominant kelp in the southern hemisphere ( Ecklonia radiata ) from ~1000 km of coastline off Western Australia. Strong population structure and isolation‐by‐distance was underpinned by significant signatures of selection related to temperature and light. Gradient forest analysis of temperature‐linked SNPs under selection revealed a strong association with mean annual temperature range, suggesting adaptation to local thermal environments. Critically, modelling revealed that predicted climate‐mediated temperature changes will probably result in high genomic vulnerability via a mismatch between current and future predicted genotype–environment relationships such that kelp forests off Western Australia will need to significantly adapt to keep pace with projected climate change. Proactive management techniques such as assisted adaptation to boost resilience may be required to secure the future of these kelp forests and the immense ecological and economic values they support.

Genome structural evolution in Brassica crops

Publisher: Springer Science and Business Media LLC

Date: 27-05-2021

DOI: 10.1038/S41477-021-00928-8

Abstract: The cultivated Brassica species include numerous vegetable and oil crops of global importance. Three genomes (designated A, B and C) share mesohexapolyploid ancestry and occur both singly and in each pairwise combination to define the Brassica species. With organizational errors (such as misplaced genome segments) corrected, we showed that the fundamental structure of each of the genomes is the same, irrespective of the species in which it occurs. This enabled us to clarify genome evolutionary pathways, including updating the Ancestral Crucifer Karyotype (ACK) block organization and providing support for the Brassica mesohexaploidy having occurred via a two-step process. We then constructed genus-wide pan-genomes, drawing from genes present in any species in which the respective genome occurs, which enabled us to provide a global gene nomenclature system for the cultivated Brassica species and develop a methodology to cost-effectively elucidate the genomic impacts of alien introgressions. Our advances not only underpin knowledge-based approaches to the more efficient breeding of Brassica crops but also provide an exemplar for the study of other polyploids.

Genome-wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus

Publisher: CSIRO Publishing

Date: 2018

DOI: 10.1071/CP17214

Abstract: Plant disease-resistance genes play a critical role in providing resistance against pathogens. The largest family of resistance genes are the nucleotide-binding site (NBS) and leucine-rich repeat (LRR) genes. They are classified into two major subfamilies, toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and coiled-coil (CC)-NBS-LRR (CNL) proteins. We have identified and characterised 641 NBS-LRR genes in Brassica napus, 249 in B. rapa and 443 in B. oleracea. A ratio of 1 : 2 of CNL : TNL genes was found in the three species. Domain structure analysis revealed that 57% of the NBS-LRR genes are typical resistance genes and contain all three domains (TIR/CC, NBS, LRR), whereas the remaining genes are partially deleted or truncated. Of the NBS-LRR genes, 59% were found to be physically clustered, and in idual genes involved in clusters were more polymorphic than those not clustered. Of the NBS-LRR genes in B. napus, 50% were identified as duplicates, reflecting a high level of genomic duplication and rearrangement. Comparative analysis between B. napus and its progenitor species indicated that % of NBS-LRR genes are conserved in B. napus. This study provides a valuable resource for the identification and characterisation of candidate NBS-LRR genes.

Molecular marker databases

Publisher: Springer New York

Date: 03-10-2015

DOI: 10.1007/978-1-4939-1966-6_4

Abstract: The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range from species specific through to organism wide and often host a variety of additional related genetic, genomic, or phenotypic information. In this chapter, we will present some of the features of plant molecular genetic marker databases, highlight the various types of marker resources, and predict the potential future direction of crop marker databases.

Bioinformatics: Identification of Markers from Next-Generation Sequence Data

Publisher: Springer New York

Date: 03-10-2015

DOI: 10.1007/978-1-4939-1966-6_3

Abstract: With the advent of sequencing technology, next-generation sequencing (NGS) technology has dramatically revolutionized plant genomics. NGS technology combined with new software tools enables the discovery, validation, and assessment of genetic markers on a large scale. Among different markers systems, simple sequence repeats (SSRs) and Single nucleotide polymorphisms (SNPs) are the markers of choice for genetics and plant breeding. SSR markers have been a choice for large-scale characterization of germplasm collections, construction of genetic maps, and QTL identification. Similarly, SNPs are the most abundant genetic variations with higher frequencies throughout the genome of plant species. This chapter discusses various tools available for genome assembly and widely focuses on SSR and SNP marker discovery.

Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS

Publisher: Wiley

Date: 28-02-2011

DOI: 10.1111/J.1467-7652.2010.00587.X

Abstract: The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice (Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at www.wheatgenome.info. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop.

Bottlenecks for genome-edited crops on the road from lab to farm

Publisher: Springer Science and Business Media LLC

Date: 26-10-2018

DOI: 10.1186/S13059-018-1555-5

Characterising diversity in the Brassica genomes

Publisher: International Society for Horticultural Science (ISHS)

Date: 09-2013

DOI: 10.17660/ACTAHORTIC.2013.1005.1

A complex recombination pattern in the genome of allotetraploid Brassica napusas revealed by a high-density genetic map

Publisher: Public Library of Science (PLoS)

Date: 30-10-2014

DOI: 10.1371/JOURNAL.PONE.0109910

Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea

Publisher: MDPI AG

Date: 30-12-2020

DOI: 10.3390/BIOLOGY10010017

Abstract: Brassica juncea, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in B. juncea. In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of B. juncea, using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between B. juncea and its progenitor species, B. rapa and B. nigra, indicate that 83.62% RLKs and 41.98% RLPs are conserved in B. juncea, and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.

Status and advances in mining for blackleg (Leptosphaeria maculans) quantitative resistance (QR) in oilseed rape (Brassica napus)

Publisher: Springer Science and Business Media LLC

Date: 09-06-2021

DOI: 10.1007/S00122-021-03877-0

Abstract: Quantitative resistance (QR) loci discovered through genetic and genomic analyses are abundant in the Brassica napus genome, providing an opportunity for their utilization in enhancing blackleg resistance. Quantitative resistance (QR) has long been utilized to manage blackleg in Brassica napus (canola, oilseed rape), even before major resistance genes (R-genes) were extensively explored in breeding programmes. In contrast to R-gene-mediated qualitative resistance, QR reduces blackleg symptoms rather than completely eliminating the disease. As a polygenic trait, QR is controlled by numerous genes with modest effects, which exerts less pressure on the pathogen to evolve hence, its effectiveness is more durable compared to R-gene-mediated resistance. Furthermore, combining QR with major R-genes has been shown to enhance resistance against diseases in important crops, including oilseed rape. For these reasons, there has been a renewed interest among breeders in utilizing QR in crop improvement. However, the mechanisms governing QR are largely unknown, limiting its deployment. Advances in genomics are facilitating the dissection of the genetic and molecular underpinnings of QR, resulting in the discovery of several loci and genes that can be potentially deployed to enhance blackleg resistance. Here, we summarize the efforts undertaken to identify blackleg QR loci in oilseed rape using linkage and association analysis. We update the knowledge on the possible mechanisms governing QR and the advances in searching for the underlying genes. Lastly, we lay out strategies to accelerate the genetic improvement of blackleg QR in oilseed rape using improved phenotyping approaches and genomic prediction tools.

Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives

Publisher: MDPI AG

Date: 30-12-2020

DOI: 10.3390/IJMS22010313

Abstract: Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.

An efficient approach to BAC based assembly of complex genomes

Publisher: Springer Science and Business Media LLC

Date: 20-01-2016

DOI: 10.1186/S13007-016-0107-9

Genome sequencing approaches and successes

Publisher: Humana Press

Date: 2009

DOI: 10.1007/978-1-59745-427-8_18

Abstract: Sequence data is crucial to our understanding of crop growth and development, as differences in DNA sequence are responsible for almost all of the heritable differences between crop varieties and ecotypes. The sequence of a genome is often referred to as the genetic blueprint, and is the foundation for all additional information from the genome to the phenome. The value of DNA sequence is leading to rapid improvements in sequencing technology, increasing throughput, and reducing costs, and technological advances are accelerating with the introduction of novel approaches that are replacing the traditional Sanger-based methods. As genome sequencing becomes cheaper, it will be applied to a greater number of species with increasingly large and complex genomes. This will increase our understanding of how differences in the sequence relate to phenotypic observations, heritable traits, speciation, and evolution. Our understanding of plants will be greatly enhanced by this flow of sequence information, with direct benefit for crop improvement.

Application of crop wild relatives in modern breeding

Publisher: Frontiers Media SA

Date: 17-11-2022

DOI: 10.3389/FPLS.2022.1008904

Abstract: Global agricultural industries are under pressure to meet the future food demand however, the existing crop genetic ersity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic ersity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.

Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Publisher: Elsevier BV

Date: 07-2006

DOI: 10.1016/J.FGB.2006.01.013

Abstract: Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloë festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource. They permit the interrogation of 3806 Neotyphodium genes (Nchip microarray), and 4195 Neotyphodium and 920 Epichloë genes (EndoChip microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloë was performed.

Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

Publisher: Wiley

Date: 13-12-2021

DOI: 10.1002/TPG2.20177

Abstract: Since the first reported crop pangenome in 2014, advances in high‐throughput and cost‐effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape ( Brassica napus L.), soybean [ Glycine max (L.) Merr.], rice ( Oryza sativa L.), wheat ( Triticum aestivum L.), and barley ( Hordeum vulgare L.). Compared with single‐reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic ersity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.

Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis

Publisher: Frontiers Media SA

Date: 15-03-2023

DOI: 10.3389/FSUFS.2023.1124640

Abstract: The recent Russia–Ukraine conflict has raised significant concerns about global food security, leaving many countries with restricted access to imported staple food crops, particularly wheat and sunflower oil, sending food prices soaring with other adverse consequences in the food supply chain. This detrimental effect is particularly prominent for low-income countries relying on grain imports, with record-high food prices and inflation affecting their livelihoods. This review discusses the role of Russia and Ukraine in the global food system and the impact of the Russia–Ukraine conflict on food security. It also highlights how ersifying four areas of agrifood systems—markets, production, crops, and technology can contribute to achieving food supply chain resilience for future food security and sustainability.

The pangenome of hexaploid bread wheat

Publisher: Wiley

Date: 05-04-2017

DOI: 10.1111/TPJ.13515

Abstract: There is an increasing understanding that variation in gene presence-absence plays an important role in the heritability of agronomic traits however, there have been relatively few studies on variation in gene presence-absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic ersity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome ersity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene ersity across 18 wheat cultivars. We predict a pangenome size of 140 500 ± 102 genes, a core genome of 81 070 ± 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal single nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome ersity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at appliedbioinformatics.com.au/cgi-bin/gb2/gbrowse/WheatPan/, and data are available to download from heat_genome_databases.php.

Sequencing the Chickpea Genome

Publisher: Springer International Publishing

Date: 2017

DOI: 10.1007/978-3-319-66117-9_10

Dispersion and domestication shaped the genome of bread wheat

Publisher: Wiley

Date: 24-01-2013

DOI: 10.1111/PBI.12044

Abstract: Despite the international significance of wheat, its large and complex genome hinders genome sequencing efforts. To assess the impact of selection on this genome, we have assembled genomic regions representing genes for chromosomes 7A, 7B and 7D. We demonstrate that the dispersion of wheat to new environments has shaped the modern wheat genome. Most genes are conserved between the three homoeologous chromosomes. We found differential gene loss that supports current theories on the evolution of wheat, with greater loss observed in the A and B genomes compared with the D. Analysis of intervarietal polymorphisms identified fewer polymorphisms in the D genome, supporting the hypothesis of early gene flow between the tetraploid and hexaploid. The enrichment for genes on the D genome that confer environmental adaptation may be associated with dispersion following wheat domestication. Our results demonstrate the value of applying next-generation sequencing technologies to assemble gene-rich regions of complex genomes and investigate polyploid genome evolution. We anticipate the genome-wide application of this reduced-complexity syntenic assembly approach will accelerate crop improvement efforts not only in wheat, but also in other polyploid crops of significance.

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

Publisher: Springer Science and Business Media LLC

Date: 17-09-2018

DOI: 10.1007/S00122-018-3171-X

Genomic databases for crop improvement

Publisher: MDPI AG

Date: 20-03-2012

DOI: 10.3390/AGRONOMY2010062

Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome

Publisher: Wiley

Date: 15-10-2019

DOI: 10.1111/PBI.13015

AutoSNPdb: An annotated single nucleotide polymorphism database for crop plants

Publisher: Oxford University Press (OUP)

Date: 2009

DOI: 10.1093/NAR/GKN650

Wheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes

Publisher: Cold Spring Harbor Laboratory

Date: 25-02-2022

DOI: 10.1101/2022.02.23.481560

Abstract: Bread wheat is one of humanity’s most important staple crops, characterized by a large and complex genome with a high level of gene presence/absence variation between cultivars, h ering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a erse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate due to the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess presence/absence variation between bread wheat genomes. Database URL: www.appliedbioinformatics.com.au/wheat_panache

SNP discovery and applications in Brassica napus

Publisher: The Korean Society for Plant Biotechnology

Date: 31-03-2012

DOI: 10.5010/JPB.2012.39.1.049

Virulence/avirulence patterns among Leptosphaeria maculans isolates determines expression of resistance, senescence and yellowing in cotyledons of Brassica napus

Publisher: Springer Science and Business Media LLC

Date: 13-03-2020

DOI: 10.1007/S10658-020-01963-5

Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate

Publisher: Springer Science and Business Media LLC

Date: 12-05-2020

DOI: 10.1038/S42003-020-0932-2

Abstract: Genomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes. They are partitioned into topologically associated domains (TADs), defined as regions of high chromatin inter-connectivity. While TADs are not a prominent feature of A. thaliana genome organization, they have been reported for other plants including rice, maize, tomato and cotton and for which TAD formation appears to be linked to transcription and chromatin epigenetic status. Here we show that in the rice genome, sequence variation and meiotic recombination rate correlate with the 3D genome structure. TADs display increased SNP and SV density and higher recombination rate compared to inter-TAD regions. We associate the observed differences with the TAD epigenetic landscape, TE composition and an increased incidence of meiotic crossovers.

Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L.var. capitata L.)

Publisher: Springer Science and Business Media LLC

Date: 05-2015

DOI: 10.1007/S11032-015-0318-1

Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree

Publisher: Humana Press

Date: 2009

DOI: 10.1007/978-1-59745-251-9_15

Abstract: Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and the association of heritable traits with underlying genetic variation. The development of high-throughput methods for the detection of single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) has led to a revolution in their use as molecular markers. The availability of large sequence data sets permits mining for these molecular markers, which may then be used for applications such as genetic trait mapping, ersity analysis and marker assisted selection in agriculture. Here we describe web-based automated methods for the discovery of SSRs using SSR taxonomy tree, the discovery of SNPs from sequence data using SNPServer and the identification of validated SNPs from within the dbSNP database. SSR taxonomy tree identifies pre-determined SSR lification primers for virtually all species represented within the GenBank database. SNPServer uses a redundancy based approach to identify SNPs within DNA sequences. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms. The NCBI dbSNP database is a catalogue of molecular variation, hosting validated SNPs for several species within a public-domain archive.

DNA sequence databases

Publisher: Springer New York

Date: 2007

DOI: 10.1007/978-0-387-92738-1_1

Induced methylation in plants as a crop improvement tool

Publisher: MDPI AG

Date: 28-09-2020

DOI: 10.3390/AGRONOMY10101484

Abstract: The methylation of gene promoters is an epigenetic process that can have a major impact on plant phenotypes through its control of gene expression. This phenomenon can be observed as a response to stress, such as drought, cold/heat stress or pathogen infection. The transgenerational heritability of DNA methylation marks could enable breeders to fix beneficial methylation patterns in crops over successive generations. These properties of DNA methylation, its impact on the phenotype and its heritability, could be used to support the accelerated breeding of improved crop varieties. Induced DNA methylation has the potential to complement the existing plant breeding process, supporting the introduction of desirable characteristics in crops within a single generation that persist in its progeny. Therefore, it is important to understand the underlying mechanisms involved in the regulation of gene expression through DNA methylation and to develop methods for precisely modulating methylation patterns for crop improvement. Here we describe the currently available epigenetic editing tools and their advantages and limitations in the domain of crop breeding. Finally, we discuss the biological and legislative limitations currently restricting the development of epigenetic modification as a crop improvement tool.

Genome analysis identified novel candidate genes for ascochyta blight resistance in chickpea using whole genome re-sequencing data

Publisher: Frontiers Media SA

Date: 17-03-2017

DOI: 10.3389/FPLS.2017.00359

A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference

Publisher: Springer Science and Business Media LLC

Date: 27-11-2019

DOI: 10.1007/S10142-018-0647-3

Abstract: Next-generation DNA sequencing technologies, such as RNA-Seq, currently dominate genome-wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies, a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the high cost of generating high-coverage data for de novo assembly hinders this approach and more importantly the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences. As an alternative to the standard reference mapping approach, we have developed a k-mer-based analysis pipeline (DiffKAP) to identify differentially expressed reads between RNA-Seq datasets without the requirement for a reference. We compared the DiffKAP approach with the traditional Tophat/Cuffdiff method using RNA-Seq data from soybean, which has a suitable reference genome. We subsequently examined differential gene expression for a coral meta-transcriptome where no reference is available, and validated the results using qRT-PCR. We conclude that DiffKAP is an accurate method to study differential gene expression in complex meta-transcriptomes without the requirement of a reference genome.

Characterization of simple sequence repeat markers derived in silico from Brassica rapa bacterial artificial chromosome sequences and their application inBrassica napus

Publisher: Wiley

Date: 20-12-2007

DOI: 10.1111/J.1471-8286.2006.01578.X

Molecular marker discovery and genetic map visualisation

Publisher: Springer New York

Date: 2007

DOI: 10.1007/978-0-387-92738-1_8

Supporting crop plant resilience during climate change

Publisher: Wiley

Date: 04-06-2023

DOI: 10.1002/CSC2.21019

Abstract: The changing climate poses significant threats to agriculture and the ability to ensure sufficient global food production. With the expanding population, there is an urgent demand to increase crop productivity to meet the rising food demand. Producing climate‐smart crop varieties together with developing new agronomic management strategies are strategies that may help address this issue. Recent advances in genomics‐assistant breeding, the use of high‐throughput DNA sequencing, high‐resolution phenotyping, and advanced genome engineering can support the development of advanced, climate resilient crops. Here, we assess the potential to enhance the resilience of crops under the changing climate. Through the use of big data, advanced breeding strategies, and advanced agriculture practices, crop varieties could be produced with enhanced resilience and increased productivity and nutrition, supporting future global food security.

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Publisher: Wiley

Date: 18-09-2019

DOI: 10.1111/PBI.13240

Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics

Publisher: Springer Science and Business Media LLC

Date: 14-04-2021

DOI: 10.1007/S00122-021-03820-3

Plant genome resequencing and population genomics

Publisher: Elsevier BV

Date: 08-2023

DOI: 10.1016/J.MOLP.2023.07.009

Plant Bioinformatics

Publisher: Springer New York

Date: 2016

DOI: 10.1007/978-1-4939-3167-5

Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL.

Publisher: Wiley

Date: 28-12-2022

DOI: 10.1002/TPG2.20184

Abstract: In the last decade, more than 70 quantitative trait loci (QTL) related to soybean [Glycine max (L.) Merr.] partial resistance (PR) against Phytophthora sojae have been identified by genome-wide association studies (GWAS). However, most of them have either a minor effect on the resistance level or are specific to a single phenotypic variable or one isolate, thereby limiting their use in breeding programs. In this study, we have used an analytical approach combining (a) the phenotypic characterization of a erse panel of 357 soybean accessions for resistance to P. sojae captured through a single variable, corrected dry weight (b) a new hydroponic assay allowing the inoculation of a combination of P. sojae isolates covering the spectrum of commercially relevant Rps genes and (c) exhaustive genotyping through whole-genome resequencing (WGS). This led to the identification of a novel P. sojae resistance QTL with a relatively major effect compared with the previously reported QTL. The QTL interval, spanning ∼500 kb on chromosome (Chr) 15, does not colocalize with previously reported QTL for P. sojae resistance. Plants carrying the favorable allele at this QTL were 60% more resistant. Eight genes were found to reside in the linkage disequilibrium (LD) block containing the peak single-nucleotide polymorphism (SNP) including Glyma.15G217100, which encodes a major latex protein (MLP)-like protein, with a functional annotation related to pathogen resistance. Expression analysis of Glyma.15G217100 indicated that it was nearly eight times more highly expressed in a group of plant introductions (PIs) carrying the resistant (R) allele compared with those carrying the susceptible (S) allele within a short period after inoculation. These results offer new and valuable options to develop improved soybean cultivars with broad resistance to P. sojae through marker-assisted selection.

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Publisher: Springer Science and Business Media LLC

Date: 17-05-2019

DOI: 10.1186/S12864-019-5774-2

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

Publisher: Wiley

Date: 11-11-2021

DOI: 10.1002/TPG2.20060

Abstract: The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub‐genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.

Updated guidelines for gene nomenclature in wheat

Publisher: Springer Science and Business Media LLC

Date: 23-03-2023

DOI: 10.1007/S00122-023-04253-W

Abstract: Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

Copy number variation and disease resistance in plants

Publisher: Springer Science and Business Media LLC

Date: 17-10-2017

DOI: 10.1007/S00122-017-2993-2

Abstract: Plant genome ersity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs their importance, role and function, as well as their association with disease resistance in plants.

Construction and characterisation of a yeast artificial chromosome library containing three haploid maize genome equivalents

Publisher: Springer Science and Business Media LLC

Date: 05-1992

DOI: 10.1007/BF00027351

Towards a more predictable plant breeding pipeline with CRISPR/Cas-induced allelic series to optimize quantitative and qualitative traits

Publisher: Elsevier BV

Date: 10-2018

DOI: 10.1016/J.PBI.2018.04.013

Abstract: The rate of crop improvement must increase to meet rising global demand for food. Crop breeding pipelines can be h ered by the imprecision and multi-generational timeframe of methods such as intercrossing and stochastic mutagenesis used to generate variation. Genome editing can generate targeted allelic series of trait-related genes and regulatory elements, creating a series of variable phenotypes for breeding within a single generation. Disrupting genic and regulatory regions is particularly effective for engineering quantitative traits. Although qualitative traits can be more difficult to engineer using disruption, precise base editing may allow an efficient path to rationally improve qualitative traits if protein function can be accurately modelled. As functional understanding of genes and regulatory elements increases, genome editing can enhance the predictability of plant breeding outcomes and will ensure food security.

Toward haplotype studies in polyploid plants to assist breeding

Publisher: Elsevier BV

Date: 12-2021

DOI: 10.1016/J.MOLP.2021.11.004

Pangenomics and Crop Genome Adaptation in a Changing Climate

Publisher: MDPI AG

Date: 27-07-2022

DOI: 10.3390/PLANTS11151949

Abstract: During crop domestication and breeding, wild plant species have been shaped into modern high-yield crops and adapted to the main agro-ecological regions. However, climate change will impact crop productivity in these regions, and agriculture needs to adapt to support future food production. On a global scale, crop wild relatives grow in more erse environments than crop species, and so may host genes that could support the adaptation of crops to new and variable environments. Through identification of in iduals with increased climate resilience we may gain a greater understanding of the genomic basis for this resilience and transfer this to crops. Pangenome analysis can help to identify the genes underlying stress responses in in iduals harbouring untapped genomic ersity in crop wild relatives. The information gained from the analysis of these pangenomes can then be applied towards breeding climate resilience into existing crops or to re-domesticating crops, combining environmental adaptation traits with crop productivity.

Using genomics to adapt crops to climate change

Publisher: Springer International Publishing

Date: 2019

DOI: 10.1007/978-3-319-77878-5_5

Identification and characterization of simple sequence repeat markers from Brassica napus expressed sequences

Publisher: Wiley

Date: 26-03-2007

DOI: 10.1111/J.1471-8286.2007.01738.X

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Publisher: American Association for the Advancement of Science (AAAS)

Date: 17-08-2018

DOI: 10.1126/SCIENCE.AAR7191

Abstract: Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Ex les of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science , this issue p. eaar7191 see also p. eaar6089

Maize Yield Prediction at an Early Developmental Stage Using Multispectral Images and Genotype Data for Preliminary Hybrid Selection

Publisher: MDPI AG

Date: 04-10-2021

DOI: 10.3390/RS13193976

Abstract: Assessing crop production in the field often requires breeders to wait until the end of the season to collect yield-related measurements, limiting the pace of the breeding cycle. Early prediction of crop performance can reduce this constraint by allowing breeders more time to focus on the highest-performing varieties. Here, we present a multimodal deep learning model for predicting the performance of maize (Zea mays) at an early developmental stage, offering the potential to accelerate crop breeding. We employed multispectral images and eight vegetation indices, collected by an uncrewed aerial vehicle approximately 60 days after sowing, over three consecutive growing cycles (2017, 2018 and 2019). The multimodal deep learning approach was used to integrate field management and genotype information with the multispectral data, providing context to the conditions that the plants experienced during the trial. Model performance was assessed using holdout data, in which the model accurately predicted the yield (RMSE 1.07 t/ha, a relative RMSE of 7.60% of 16 t/ha, and R2 score 0.73) and identified the majority of high-yielding varieties, outperforming previously published models for early yield prediction. The inclusion of vegetation indices was important for model performance, with a normalized difference vegetation index and green with normalized difference vegetation index contributing the most to model performance. The model provides a decision support tool, identifying promising lines early in the field trial.

Draft Genome Assembly and Transcriptome Dataset for European Turnip (Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance

Publisher: Frontiers Media SA

Date: 02-07-2021

DOI: 10.3389/FGENE.2021.651298

Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP

Publisher: MDPI AG

Date: 27-08-2012

DOI: 10.3390/BIOLOGY1020370

Scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis

Publisher: Oxford University Press (OUP)

Date: 04-2015

DOI: 10.1534/G3.114.014571

Abstract: Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second-generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakojima, was chemically mutated with alkylating ethyl methanesulfonate (EMS) for the scanning of DNA lesions throughout the genome. Using second-generation sequencing, two in idually mutated third-generation progeny (M3, named AM and AS) were sequenced and analyzed to identify single nucleotide polymorphisms and reveal the effects of EMS on nucleotide sequences in these mutant genomes. Single-nucleotide polymorphisms were found in every 208 kb (AS) and 202 kb (AM) with a bias mutation of G/C-to-A/T changes at low percentage. Most mutations were intergenic. The mutation spectrum of the genomes was comparable in their in idual chromosomes however, each mutated genome has unique alterations, which are useful to identify causal mutations for their phenotypic changes. The data obtained demonstrate that whole genomic sequencing is applicable as a high-throughput tool to investigate genomic changes due to mutagenesis. The identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm.

Trait associations in the pangenome of pigeon pea (Cajanus cajan)

Publisher: Wiley

Date: 12-03-2020

DOI: 10.1111/PBI.13354

Construction and comparison of three reference‐quality genome assemblies for soybean

Publisher: Wiley

Date: 28-10-2019

DOI: 10.1111/TPJ.14500

Abstract: We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean ersity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

Approaches to increase the validity of gene family identification using manual homology search tools

Publisher: Springer Science and Business Media LLC

Date: 10-10-2023

DOI: 10.1007/S10709-023-00196-8

Plant bioinformatics: from genome to phenome

Publisher: Elsevier BV

Date: 05-2004

DOI: 10.1016/J.TIBTECH.2004.03.002

Identification and characterization of candidate Rlm4 blackleg resistance genes in Brassica napus using next-generation sequencing

Publisher: Wiley

Date: 23-06-2012

DOI: 10.1111/J.1467-7652.2012.00716.X

Abstract: A thorough understanding of the relationships between plants and pathogens is essential if we are to continue to meet the agricultural needs of the world's growing population. The identification of genes underlying important quantitative trait loci is extremely challenging in complex genomes such as Brassica napus (canola, oilseed rape or rapeseed). However, recent advances in next-generation sequencing (NGS) enable much quicker identification of candidate genes for traits of interest. Here, we demonstrate this with the identification of candidate disease resistance genes from B. napus for its most devastating fungal pathogen, Leptosphaeria maculans (blackleg fungus). These two species are locked in an evolutionary arms race whereby a gene-for-gene interaction confers either resistance or susceptibility in the plant depending on the genotype of the plant and pathogen. Preliminary analysis of the complete genome sequence of Brassica rapa, the diploid progenitor of B. napus, identified numerous candidate genes with disease resistance characteristics, several of which were clustered around a region syntenic with a major locus (Rlm4) for blackleg resistance on A7 of B. napus. Molecular analyses of the candidate genes using B. napus NGS data are presented, and the difficulties associated with identifying functional gene copies within the highly duplicated Brassica genome are discussed.

Resources for image-based high-throughput phenotyping in crops and data sharing challenges

Publisher: Oxford University Press (OUP)

Date: 28-06-2021

DOI: 10.1093/PLPHYS/KIAB301

Abstract: High-throughput phenotyping (HTP) platforms are capable of monitoring the phenotypic variation of plants through multiple types of sensors, such as red green and blue (RGB) cameras, hyperspectral sensors, and computed tomography, which can be associated with environmental and genotypic data. Because of the wide range of information provided, HTP datasets represent a valuable asset to characterize crop phenotypes. As HTP becomes widely employed with more tools and data being released, it is important that researchers are aware of these resources and how they can be applied to accelerate crop improvement. Researchers may exploit these datasets either for phenotype comparison or employ them as a benchmark to assess tool performance and to support the development of tools that are better at generalizing between different crops and environments. In this review, we describe the use of image-based HTP for yield prediction, root phenotyping, development of climate-resilient crops, detecting pathogen and pest infestation, and quantitative trait measurement. We emphasize the need for researchers to share phenotypic data, and offer a comprehensive list of available datasets to assist crop breeders and tool developers to leverage these resources in order to accelerate crop breeding.

Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation

Publisher: Frontiers Media SA

Date: 05-09-2017

DOI: 10.3389/FPLS.2017.01463

A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats

Publisher: Springer Science and Business Media LLC

Date: 2003

DOI: 10.1023/A:1022446021230

Skim-based genotyping by sequencing

Publisher: Springer New York

Date: 03-10-2015

DOI: 10.1007/978-1-4939-1966-6_19

Abstract: Genotyping by sequencing (GBS) is a relatively new method used to determine the differences in the genetic makeup of in iduals. Its novelty stems from a combination of two already available methods: genotyping and next-generation sequencing. Depending on the in idual study design GBS protocols can take multiple forms, however most share a sequence of core steps that have to be undertaken. These include: sequencing of the DNA from the in iduals of interest (usually two parents of a mapping population and their progeny), mapping of the sequencing reads to the reference sequence, SNP calling and filtering, SNP genotyping and imputation, followed by haplotype identification and downstream analysis. GBS has a range of applications from general marker discovery, haplotype identification, and recombination characterization to quantitative trait locus (QTL) analysis, genome-wide association studies (GWAS), and genomic selection (GS). It has already been applied to a range of plant species including: rice, maize, artichoke, and Arabidopsis thaliana. It is a promising approach which is likely to provide new and important insights into plant biology.

Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars

Publisher: Springer Science and Business Media LLC

Date: 11-10-2009

DOI: 10.1007/S00122-009-1160-9

Abstract: Genetic map construction and identification of quantitative trait loci (QTLs) for blackleg resistance were performed for four mapping populations derived from five different canola source cultivars. Three of the populations were generated from crosses between single genotypes from the blackleg-resistant cultivars Caiman, Camberra and (AV)Sapphire and the blackleg-susceptible cultivar Westar(10). The fourth population was derived from a cross between genotypes from two blackleg resistant varieties (Rainbow and (AV)Sapphire). Different types of DNA-based markers were designed and characterised from a collection of 20,000 EST sequences generated from multiple Brassica species, including a new set of 445 EST-SSR markers of high value to the international community. Multiple molecular genetic marker systems were used to construct linkage maps with locus numbers varying between 219 and 468, and coverage ranging from 1173 to 1800 cM. The proportion of polymorphic markers assigned to map locations varied from 70 to 89% across the four populations. Publicly available simple sequence repeat markers were used to assign linkage groups to reference nomenclature, and a sub-set of mapped markers were also screened on the Tapidor x Ningyou (T x N) reference population to assist this process. QTL analysis was performed based on percentage survival at low and high disease pressure sites. Multiple QTLs were identified across the four mapping populations, accounting for 13-33% of phenotypic variance (V (p)). QTL-linked marker data are suitable for implementation in breeding for disease resistance in Australian canola cultivars. However, the likelihood of shifts in pathogen race structure across different geographical locations may have implications for the long-term durability of such associations.

Producing High-Quality Single Nucleotide Polymorphism Data for Genome-Wide Association Studies

Publisher: Springer US

Date: 2022

DOI: 10.1007/978-1-0716-2237-7_9

Abstract: Single-nucleotide polymorphisms (SNPs) have become the primary type of molecular genetic marker used in a erse range of genetic and genomic studies. SNPs can be used to identify genomic regions linked to traits such as disease in genome-wide association studies, to understand population structure and ersity, or to understand mechanisms of genome evolution. One of the first steps of any SNP-based workflow, following SNP discovery, is quality control of SNP data. The protocol described here details how to perform quality control on SNP data to minimise errors in downstream analysis.

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

Publisher: Frontiers Media SA

Date: 29-08-2017

DOI: 10.3389/FPLS.2017.01461

Future tools for association mapping in crop plants

Publisher: Canadian Science Publishing

Date: 11-2010

DOI: 10.1139/G10-057

Abstract: Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data TAGdb for the identification of gene specific paired read Illumina GAII data CMap3D for the comparison of mapped genetic and physical markers and BAC and Gene Annotator for the online annotation of genes and genomic sequences.

Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation

Publisher: Springer Science and Business Media LLC

Date: 15-10-2012

DOI: 10.1007/S00122-011-1717-2

Abstract: Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestivum chromosome arm 7BS, followed by the construction of a syntenic build based on gene order in Brachypodium. We have delimited the position of a previously reported translocation between 7BS and 4AL with a resolution of one or a few genes and report approximately 13% genes from 7BS having been translocated to 4AL. An additional 13 genes are found on 7BS which appear to have originated from 4AL. The gene content of the 7DS and 7BS syntenic builds indicate a total of ~77,000 genes in wheat. Within wheat syntenic regions, 7BS and 7DS share 740 genes and a common gene conservation rate of ~39% of the genes from the corresponding regions in Brachypodium, as well as a common rate of colinearity with Brachypodium of ~60%. Comparison of wheat homoeologues revealed ~84% of genes previously identified in 7DS have a homoeologue on 7BS or 4AL. The conservation rates we have identified among wheat homoeologues and with Brachypodium provide a benchmark of homoeologous gene conservation levels for future comparative genomic analysis. The syntenic build of 7BS is publicly available at www.wheatgenome.info.

Identification of a Major QTL-Controlling Resistance to the Subtropical Race 4 of Fusarium oxysporum f. sp. cubense in Musa acuminata ssp. malaccensis

Publisher: MDPI AG

Date: 09-02-2023

DOI: 10.3390/PATHOGENS12020289

Abstract: Vascular wilt caused by the ascomycete fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a major constraint of banana production around the world. The virulent race, namely Tropical Race 4, can infect all Cavendish-type banana plants and is now widespread across the globe, causing devastating losses to global banana production. In this study, we characterized Foc Subtropical Race 4 (STR4) resistance in a wild banana relative which, through estimated genome size and ancestry analysis, was confirmed to be Musa acuminata ssp. malaccensis. Using a self-derived F2 population segregating for STR4 resistance, quantitative trait loci sequencing (QTL-seq) was performed on bulks consisting of resistant and susceptible in iduals. Changes in SNP index between the bulks revealed a major QTL located on the distal end of the long arm of chromosome 3. Multiple resistance genes are present in this region. Identification of chromosome regions conferring resistance to Foc can facilitate marker assisted selection in breeding programs and paves the way towards identifying genes underpinning resistance.

Speed breeding is a powerful tool to accelerate crop research and breeding.

Publisher: Springer Science and Business Media LLC

Date: 2018

DOI: 10.1038/S41477-017-0083-8

Abstract: The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia

Publisher: Oxford University Press (OUP)

Date: 30-06-2017

DOI: 10.1093/BIB/BBX071

Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)

Publisher: Springer Science and Business Media LLC

Date: 07-09-2013

DOI: 10.1007/S00122-012-1966-8

Abstract: We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related lified polymorphism, sequence characterised lified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.

Understanding R Gene Evolution in Brassica

Publisher: MDPI AG

Date: 30-06-2022

DOI: 10.3390/AGRONOMY12071591

Abstract: Brassica crop diseases caused by various pathogens, including viruses, bacteria, fungi and oomycetes, have devastating effects on the plants, leading to significant yield loss. This effect is worsened by the impact of climate change and the pressure to increase cultivation worldwide to feed the burgeoning population. As such, managing Brassica diseases has become a challenge demanding a rapid solution. In this review, we provide a detailed introduction of the plant immune system, discuss the evolutionary pattern of both dominant and recessive disease resistance (R) genes in Brassica and discuss the role of epigenetics in R gene evolution. Reviewing the current findings of how R genes evolve in Brassica spp. provides further insight for the development of creative ideas for crop improvement in relation to breeding sustainable, high quality, disease-resistant Brassica crops.

Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea

Publisher: Springer Science and Business Media LLC

Date: 19-03-2018

DOI: 10.1038/S41598-018-23116-9

Abstract: Salinity is a major constraint for intrinsically salt sensitive grain legume chickpea. Chickpea exhibits large genetic variation amongst cultivars, which show better yields in saline conditions but still need to be improved further for sustainable crop production. Based on previous multi-location physiological screening, JG 11 (salt tolerant) and ICCV 2 (salt sensitive) were subjected to salt stress to evaluate their physiological and transcriptional responses. A total of ~480 million RNA-Seq reads were sequenced from root tissues which resulted in identification of 3,053 differentially expressed genes (DEGs) in response to salt stress. Reproductive stage shows high number of DEGs suggesting major transcriptional reorganization in response to salt to enable tolerance. Importantly, cationic peroxidase, Aspartic ase, NRT1/PTR , phosphatidylinositol phosphate kinase, DREB1E and ERF genes were significantly up-regulated in tolerant genotype. In addition, we identified a suite of important genes involved in cell wall modification and root morphogenesis such as dirigent proteins, expansin and casparian strip membrane proteins that could potentially confer salt tolerance. Further, phytohormonal cross-talk between ERF and PIN-FORMED genes which modulate the root growth was observed. The gene set enrichment analysis and functional annotation of these genes suggests they may be utilised as potential candidates for improving chickpea salt tolerance.

Towards plant pangenomics

Publisher: Wiley

Date: 23-11-2016

DOI: 10.1111/PBI.12499

Abstract: As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single in idual is insufficient to represent the gene ersity within a whole species. Many studies examine the sequence ersity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.

Plant Bioinformatics

Publisher: Springer US

Date: 2022

DOI: 10.1007/978-1-0716-2067-0

Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification

Publisher: Wiley

Date: 24-01-2007

DOI: 10.1111/J.1471-8286.2007.01681.X

The genome of a southern hemisphere seagrass species (Zostera muelleri)

Publisher: Oxford University Press (OUP)

Date: 03-07-2016

DOI: 10.1104/PP.16.00868

In silico prediction and analysis of transmembrane‐coiled‐coil resistance gene analogues in 27 Brassicaceae species

Publisher: Wiley

Date: 18-08-2023

DOI: 10.1111/PPA.13794

Abstract: The Brassicaceae family is composed of a broad range of species, including the economically important crops from Brassica , Raphanus , Camelina and Sinapis genera. The production of Brassicaceae species, particularly the crop members, is threatened by major diseases. However, the impact of diseases can be minimized or even negated by improving disease resistance. Transmembrane‐coiled‐coil (TM‐CC) genes are a type of resistance gene analogue (RGA) that have been proven to play specific roles in resistance to several diseases. Here, TM‐CCs have been predicted in 27 genomes from Brassicaceae genera including Arabidopsis , Arabis , Barbarea , Boechera , Brassica , Camelina , Capsella , Cardamine , Eutrema , Leavenworthia , Lepidium , Raphanus , Sinapis , Sisymbrium , Schrenkiella and Thlaspi . The number of TM‐CCs varies throughout the studied genomes, as well as between genera, diploids and polyploids, and Brassica genomes and subgenomes. In total, 6788 TM‐CCs were identified, with 708 of them predicted with signalling function, 172 colocalized with previously known disease resistance regions and 70 phylogenetically related to cloned resistance genes, indicating the possible functional involvement of TM‐CCs in resistance. This study provides a resource for the identification of functional Brassicaceae TM‐CCs along with their clustering and duplication patterns and provides a benchmark for further studies investigating TM‐CCs.

Not all pathways are the same – unique adaptations to submerged environments emerge from comparative seagrass genomics

Publisher: Cold Spring Harbor Laboratory

Date: 24-11-2022

DOI: 10.1101/2022.11.22.517588

Abstract: Seagrasses are an ecologically important group of plants that have returned to the sea from terrestrial ancestors on at least three occasions (Cymodoceaceae, Posidoniaceae, Zosteraceae). Seagrass-specific genomic adaptations to marine life are known from the Zosteraceae. However, independent lineages may have devised different solutions to life underwater. Here, we present two new genome assemblies from endemic Australian seagrasses, Amphibolis antarctica (Cymodoceaceae) and Posidonia australis (Posidoniaceae). We found large differences in genome size between Amphibolis and Posidonia driven by repeat expansion in Posidonia . We show that parts of ethylene pathways known to be lost in Zosteraceae are partially retained in older seagrass lineages (Cymodoceaeceae and Posidoniaceae). We describe adaptations within salinity, disease resistance, cell wall, and photosynthesis-related pathways not shared with other seagrasses. These findings provide insight into the impact of recolonising marine environments on formerly terrestrial plant genomes, with some adaptations previously thought to be universal to marine living not having occurred in A. antarctica and P. australis .

Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense Using Musa acuminata ssp. malaccensis

Publisher: MDPI AG

Date: 09-06-2023

DOI: 10.3390/PATHOGENS12060820

Abstract: Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on chromosome 3 of ‘DH-Pahang’ reference assembly v4. Within this region, there was a cluster of pattern recognition receptors, namely leucine-rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell-wall-associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins, positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant progenies but not in the susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent ‘Ma850’ and a susceptible line ‘Ma848’, to show that the STR4 resistance co-segregated with marker ‘28820’ at this locus. Finally, an informative SNP marker 29730 allowed the locus-specific resistance to be assessed in a collection of diploid and polyploid banana plants. Of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4-resistant, such as ‘Pahang’, ‘SH-3362’, ‘SH-3217’, ‘Ma-ITC0250’, and ‘DH-Pahang/CIRAD 930’. Additional screening in the International Institute for Tropical Agriculture’s collection suggests that the dominant allele is common among the elite ‘Matooke’ NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine mapping and candidate gene identification will allow characterization of molecular mechanisms underlying the TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.

Plant pan-genomes are the new reference

Publisher: Springer Science and Business Media LLC

Date: 20-07-2020

DOI: 10.1038/S41477-020-0733-0

Genome-Wide Identification, Expression and Functional Analysis Reveal the Involvement of FCS-Like Zinc Finger Gene Family in Submergence Response in Rice

Publisher: Springer Science and Business Media LLC

Date: 21-08-2021

DOI: 10.1186/S12284-021-00519-3

Abstract: Direct seeding is an efficient rice cultivation practice. However, its application is often limited due to O 2 deficiency following submergence, leading to poor seed germination, seedling establishment, and consequently yield loss. Identification of genes associated with tolerance to submergence and understanding their regulatory mechanisms is the fundamental way to address this problem. Unfortunately, the molecular mechanism of rice response to submergence stress is still not well understood. Here, we have performed a genome-wide identification of FCS-like zinc finger (FLZ) proteins and assessed their involvement in submergence response in rice. We identified 29 FLZ genes in rice, and the expression analysis revealed that several genes actively responded to submergence stress. Eight OsFLZ proteins interact with SnRK1A. As a case study, we demonstrated that OsFLZ18 interacted with SnRK1A and inhibited the transcriptional activation activity of SnRK1A in modulating the expression of its target gene αAmy3 , a positive regulator in rice flooding tolerance. In line with this, OsFLZ18 -overexpression lines displayed retarded early seedling growth and shorter coleoptile following submergence. These data provide the most comprehensive information of OsFLZ genes in rice, and highlight their roles in rice submergence response.

The genome of the mesopolyploid crop species Brassica rapa

Publisher: Springer Science and Business Media LLC

Date: 28-08-2011

DOI: 10.1038/NG.919

Abstract: We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

A reference genome for pea provides insight into legume genome evolution

Publisher: Springer Science and Business Media LLC

Date: 09-2019

DOI: 10.1038/S41588-019-0480-1

Abstract: We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae erged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

In silico integration of disease resistance QTL, genes and markers with the Brassica juncea physical map

Publisher: Springer Science and Business Media LLC

Date: 27-06-2022

DOI: 10.1007/S11032-022-01309-5

Abstract: Brassica juncea (AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences for B. juncea has made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be identified by co-localization with genetically mapped disease resistance quantitative trait loci (QTL). Here we identify and characterise disease resistance gene analogs (RGAs), including nucleotide-binding site–leucine-rich repeat (NLR), receptor-like kinase (RLK) and receptor-like protein (RLP) classes, and investigate their association with disease resistance QTL intervals. The molecular genetic marker sequences for four white rust ( Albugo candida ) disease resistance QTL, six blackleg ( Leptosphaeria maculans ) disease resistance QTL and BjCHI1 , a gene cloned from B. juncea for hypocotyl rot disease, were extracted from previously published studies and used to compare with candidate RGAs. Our results highlight the complications for the identification of functional resistance genes, including the duplicated appearance of genetic markers for several resistance loci, including Ac2(t) , AcB1-A4.1, AcB1-A5.1, Rlm6 and PhR2 in both the A and B genomes, due to the presence of homoeologous regions. Furthermore, the white rust loci, Ac2(t) and AcB1-A4.1, mapped to the same position on chromosome A04 and may be different alleles of the same gene. Despite these challenges, a total of nine candidate genomic regions hosting 14 RLPs, 28 NLRs and 115 RLKs were identified. This study facilitates the mapping and cloning of functional resistance genes for applications in crop improvement programs.

Plant Bioinformatics

Publisher: Humana Press

Date: 2007

DOI: 10.1007/978-1-59745-535-0

Erratum for the Report: “Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome” by B. Chalhoub, F. Denoeud, S. Liu, I. A. P. Parkin, H. Tang,

Publisher: American Association for the Advancement of Science (AAAS)

Date: 12-09-2014

DOI: 10.1126/SCIENCE.1260782

DNABERT-based explainable lncRNA identification in plant genome assemblies

Publisher: Cold Spring Harbor Laboratory

Date: 10-02-2022

DOI: 10.1101/2022.02.09.479647

Abstract: Long non-coding ribonucleic acids (lncRNAs) have been shown to play an important role in plant gene regulation, being involved in both epigenetic and transcript regulation. LncRNAs are transcripts longer than 200 nucleotides that are not translated into functional proteins but can be translated into small peptides. Machine learning and deep learning models have predominantly used transcriptome data with manually defined features to detect lncRNAs, however, they often underrepresent the abundance of lncRNAs and can be biased in their detection. Here we present a study using Natural Language Processing (NLP) models to identify plant lncRNAs from genomic sequences rather than transcriptomic data. The NLP models were trained to predict lncRNAs for seven model and crop species ( Zea mays, Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max and Oryza sativa ) using publicly available genomic references. We demonstrated that lncRNAs can be accurately predicted from genomic sequences, and that genome assembly quality affects the accuracy of lncRNA identification. Furthermore, we demonstrated that the NLP models are applicable for cross-species prediction as they could predict lncRNAs from a species not used to train the model, with an average of 61% accuracy. Finally, we show that the models can be interpreted using explainable artificial intelligence to identify motifs important for lncRNA prediction and that these motifs were frequently present flanking the lncRNA sequence. We demonstrate for the first time the identification of lncRNAs from genomic sequences, instead of transcriptome sequences, allowing the identification of lowly expressed lncRNAs. A deep learning model (natural language processing) was employed for the prediction of lncRNAs in two monocot and five dicot plant species. We used explainable machine learning to extract the genomic motifs associated with lncRNA identification, highlighting potentially conserved structures present in more than one plant species.

Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP

Publisher: Oxford University Press (OUP)

Date: 12-02-2003

DOI: 10.1093/BIOINFORMATICS/BTF881

Abstract: Summary: AutoSNP is a program to detect single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) in expressed sequence tag (EST) data. The program uses d2cluster and cap3 to cluster and align EST sequences, and uses redundancy to differentiate between candidate SNPs and sequence errors. Candidate polymorphisms are identified as occurring in multiple reads within an alignment. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co segregation of the candidate SNP with other SNPs in the alignment. Availability: The program was written in PERL and is freely available to non-commercial users by request from the authors. Contact: dave.edwards@nre.vic.gov.au * To whom correspondence should be addressed.

Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus

Publisher: Frontiers Media SA

Date: 14-02-2023

DOI: 10.3389/FPLS.2023.1051994

Abstract: Utilising resistance ( R ) genes, such as LepR1 , against Leptosphaeria maculans , the causal agent of blackleg in canola ( Brassica napus ), could help manage the disease in the field and increase crop yield. Here we present a genome wide association study (GWAS) in B. napus to identify LepR1 candidate genes. Disease phenotyping of 104 B. napus genotypes revealed 30 resistant and 74 susceptible lines. Whole genome re-sequencing of these cultivars yielded over 3 million high quality single nucleotide polymorphisms (SNPs). GWAS in mixed linear model (MLM) revealed a total of 2,166 significant SNPs associated with LepR1 resistance. Of these SNPs, 2108 (97%) were found on chromosome A02 of B. napus cv. Darmor bzh v9 with a delineated LepR1 _mlm1 QTL at 15.11-26.08 Mb. In LepR1 _mlm1, there are 30 resistance gene analogs (RGAs) (13 nucleotide-binding site-leucine rich repeats (NLRs), 12 receptor-like kinases (RLKs), and 5 transmembrane-coiled-coil (TM-CCs)). Sequence analysis of alleles in resistant and susceptible lines was undertaken to identify candidate genes. This research provides insights into blackleg resistance in B. napus and assists identification of the functional LepR1 blackleg resistance gene.

The reference genetic linkage map for the multinational Brassica rapa genome sequencing project

Publisher: Springer Science and Business Media LLC

Date: 24-07-2007

DOI: 10.1007/S00122-007-0608-Z

Abstract: We describe the construction of a reference genetic linkage map for the Brassica A genome, which will form the backbone for anchoring sequence contigs for the Multinational Brassica rapa Genome Sequencing Project. Seventy-eight doubled haploid lines derived from anther culture of the F(1) of a cross between two erse Chinese cabbage (B. rapa ssp. pekinensis) inbred lines, 'Chiifu-401-42' (C) and 'Kenshin-402-43' (K) were used to construct the map. The map comprises a total of 556 markers, including 278 AFLP, 235 SSR, 25 RAPD and 18 ESTP, STS and CAPS markers. Ten linkage groups were identified and designated as R1-R10 through alignment and orientation using SSR markers in common with existing B. napus reference linkage maps. The total length of the linkage map was 1,182 cM with an average interval of 2.83 cM between adjacent loci. The length of linkage groups ranged from 81 to 161 cM for R04 and R06, respectively. The use of 235 SSR markers allowed us to align the A-genome chromosomes of B. napus with those of B. rapa ssp. pekinensis. The development of this map is vital to the integration of genome sequence and genetic information and will enable the international research community to share resources and data for the improvement of B. rapa and other cultivated Brassica species.

Analytical and Decision Support Tools for Genomics-Assisted Breeding

Publisher: Elsevier BV

Date: 04-2016

DOI: 10.1016/J.TPLANTS.2015.10.018

Abstract: To successfully implement genomics-assisted breeding (GAB) in crop improvement programs, efficient and effective analytical and decision support tools (ADSTs) are 'must haves' to evaluate and select plants for developing next-generation crops. Here we review the applications and deployment of appropriate ADSTs for GAB, in the context of next-generation sequencing (NGS), an emerging source of massive genomic information. We discuss suitable software tools and pipelines for marker-based approaches (markers/haplotypes), including large-scale genotypic and phenotypic, data management, and molecular breeding approaches. Although phenotyping remains expensive and time consuming, prediction of allelic effects on phenotypes opens new doors to enhance genetic gain across crop cycles, building on reliable phenotyping approaches and good crop information systems, including pedigree information and target haplotypes.

Genotyping-by-sequencing approaches to characterize crop genomes

Publisher: Wiley

Date: 24-01-2017

DOI: 10.1111/PBI.12645

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Publisher: Springer Science and Business Media LLC

Date: 09-02-2022

DOI: 10.1007/S00122-022-04045-8

Abstract: The major soy protein QTL, cqProt-003, was analysed for haplotype ersity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein in iduals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.

De novo sequencing of plant genomes using second-generation technologies

Publisher: Oxford University Press (OUP)

Date: 11-2009

DOI: 10.1093/BIB/BBP039

Abstract: The ability to sequence the DNA of an organism has become one of the most important tools in modern biological research. Until recently, the sequencing of even small model genomes required substantial funds and international collaboration. The development of 'second-generation' sequencing technology has increased the throughput and reduced the cost of sequence generation by several orders of magnitude. These new methods produce vast numbers of relatively short reads, usually at the expense of read accuracy. Since the first commercial second-generation sequencing system was produced by 454 Technologies and commercialised by Roche, several other companies including Illumina, Applied Biosystems, Helicos Biosciences and Pacific Biosciences have joined the competition. Because of the relatively high error rate and lack of assembly tools, short-read sequence technology has mainly been applied to the re-sequencing of genomes. However, some recent applications have focused on the de novo assembly of these data. De novo assembly remains the greatest challenge for DNA sequencing and there are specific problems for second generation sequencing which produces short reads with a high error rate. However, a number of different approaches for short-read assembly have been proposed and some have been implemented in working software. In this review, we compare the current approaches for second-generation genome sequencing, explore the future direction of this technology and the implications for plant genome research.

Identification and characterization of simple sequence repeat (SSR) markers from Fragaria x ananassa expressed sequences

Publisher: Wiley

Date: 05-05-2006

DOI: 10.1111/J.1471-8286.2005.01215.X

Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP

Publisher: Future Science Ltd

Date: 05-2002

DOI: 10.2144/02325RR04

Abstract: The lification of transposon insertion flanking sequences is the basis of a variety of techniques used for the detection and characterization of specific transposon insertion events. We have developed a method for the efficient size determination and quantification of lified genomic sequences that flank Mutator (Mu) transposon insertions in maize. Using this detection method, we have been able to optimize Mu insertion site lification and to assess lification from increasingly complex templates representing increasing numbers of Mu-active maize plants. This detection method should be applicable for the characterization of transposon or transgene insertion events in a wide variety of organisms.

Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence

Publisher: Frontiers Media SA

Date: 25-02-2022

DOI: 10.3389/FPLS.2022.811152

Abstract: Guava wilt disease is caused by the fungus Nalanthamala psidii . The wilt disease results in large-scale destruction of orchards in South Africa, Taiwan, and several Southeast Asian countries. De novo assembly, annotation, and in-depth analysis of the N. psidii genome were carried out to facilitate the identification of characteristics associated with pathogenicity and pathogen evolution. The predicted secretome revealed a range of CAZymes, proteases, lipases and peroxidases associated with plant cell wall degradation, nutrient acquisition, and disease development. Further analysis of the N. psidii carbohydrate-active enzyme profile exposed the broad-spectrum necrotrophic lifestyle of the pathogen, which was corroborated by the identification of putative effectors and secondary metabolites with the potential to induce tissue necrosis and cell surface-dependent immune responses. Putative regulatory proteins including transcription factors and kinases were identified in addition to transporters potentially involved in the secretion of secondary metabolites. Transporters identified included important ABC and MFS transporters involved in the efflux of fungicides. Analysis of the repetitive landscape and the detection of mechanisms linked to reproduction such as het and mating genes rendered insights into the biological complexity and evolutionary potential of N. psidii as guava pathogen. Hence, the assembly and annotation of the N. psidii genome provided a valuable platform to explore the pathogenic potential and necrotrophic lifestyle of the guava wilt pathogen.

Quantitative Trait Locus Mapping of Resistance to Turnip Yellows Virus in Brassica rapa and Brassica oleracea and Introgression of These Resistances by Resynthesis Into Allotetraploid Plants for Deployment in Brassica napus

Publisher: Frontiers Media SA

Date: 10-12-2021

DOI: 10.3389/FPLS.2021.781385

Abstract: Turnip yellows virus (TuYV) is aphid-transmitted and causes considerable yield losses in oilseed rape (OSR, Brassica napus , genome: AACC) and vegetable brassicas. Insecticide control of the aphid vector is limited due to insecticide resistance and the banning of the most effective active ingredients in the EU. There is only one source of TuYV resistance in current commercial OSR varieties, which has been mapped to a single dominant quantitative trait locus (QTL) on chromosome A04. We report the identification, characterisation, and mapping of TuYV resistance in the diploid progenitor species of OSR, Brassica rapa (genome: AA), and Brassica oleracea (genome: CC). Phenotyping of F 1 populations, produced from within-species crosses between resistant and susceptible in iduals, revealed the resistances were quantitative and partially dominant. QTL mapping of segregating backcross populations showed that the B. rapa resistance was controlled by at least two additive QTLs, one on chromosome A02 and the other on chromosome A06. Together, they explained 40.3% of the phenotypic variation. In B. oleracea , a single QTL on chromosome C05 explained 22.1% of the phenotypic variation. The TuYV resistance QTLs detected in this study are different from those in the extant commercial resistant varieties. To exploit these resistances, an allotetraploid (genome: AACC) plant line was resynthesised from the interspecific cross between the TuYV-resistant B. rapa and B. oleracea lines. Flow cytometry confirmed that plantlets regenerated from the interspecific cross had both A and C genomes and were mixoploid. To stabilise ploidy, a fertile plantlet was self-pollinated to produce seed that had the desired resynthesised, allotetraploid genome AACC. Phenotyping of the resynthesised plants confirmed their resistance to TuYV. Genotyping with resistance-linked markers identified during the mapping in the progenitors confirmed the presence of all TuYV resistance QTLs from B. rapa and B. oleracea . This is the first report of TuYV resistance mapped in the Brassica C genome and of an allotetraploid AACC line possessing dual resistance to TuYV originating from both of its progenitors. The introgression into OSR can now be accelerated, utilising marker-assisted selection, and this may reduce selection pressure for TuYV isolates that are able to overcome existing sources of resistance to TuYV.

Plant genome sequencing: Applications for crop improvement

Publisher: Wiley

Date: 09-12-2010

DOI: 10.1111/J.1467-7652.2009.00459.X

Abstract: DNA sequencing technology is undergoing a revolution with the commercialization of second generation technologies capable of sequencing thousands of millions of nucleotide bases in each run. The data explosion resulting from this technology is likely to continue to increase with the further development of second generation sequencing and the introduction of third generation single-molecule sequencing methods over the coming years. The question is no longer whether we can sequence crop genomes which are often large and complex, but how soon can we sequence them? Even cereal genomes such as wheat and barley which were once considered intractable are coming under the spotlight of the new sequencing technologies and an array of new projects and approaches are being established. The increasing availability of DNA sequence information enables the discovery of genes and molecular markers associated with erse agronomic traits creating new opportunities for crop improvement. However, the challenge remains to convert this mass of data into knowledge that can be applied in crop breeding programs.

De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Publisher: MDPI AG

Date: 30-06-2021

DOI: 10.3390/AGRONOMY11071342

Abstract: The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome

Publisher: American Association for the Advancement of Science (AAAS)

Date: 18-07-2014

DOI: 10.1126/SCIENCE.1251788

Abstract: An ordered draft sequence of the 17-gigabase hexaploid bread wheat ( Triticum aestivum ) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the ergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Comparative analysis of Stowaway‐like miniature inverted repeat transposable elements in wheat group 7 chromosomes: Abundance, composition, and evolution

Publisher: Wiley

Date: 19-08-2014

DOI: 10.1111/JSE.12113

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Publisher: Cold Spring Harbor Laboratory

Date: 13-10-2021

DOI: 10.1101/2021.10.12.464159

Abstract: Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait associated region within a 173 kb linkage block was identified and variants in the region were characterised, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the third exon of gene 20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304bp deletion and have identified additional nested variation present in high-protein in iduals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximise protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterisation and modification. The major soy protein QTL, cqProt-003, was analysed for haplotype ersity and global distribution, results indicate 304bp deletion and variable tandem repeats in protein coding regions are likely causal candidates.

Segmentation of Sandplain Lupin Weeds from Morphologically Similar Narrow-Leafed Lupins in the Field

Publisher: MDPI AG

Date: 29-03-2023

DOI: 10.3390/RS15071817

Abstract: Narrow-leafed lupin (Lupinus angustifolius) is an important dryland crop, providing a protein source in global grain markets. While agronomic practices have successfully controlled many dicot weeds among narrow-leafed lupins, the closely related sandplain lupin (Lupinus cosentinii) has proven difficult to control, reducing yield and harvest quality. Here, we successfully trained a segmentation model to detect sandplain lupins and differentiate them from narrow-leafed lupins under field conditions. The deep learning model was trained using 9171 images collected from a field site in the Western Australian grain belt. Images were collected using an unoccupied aerial vehicle at heights of 4, 10, and 20 m. The dataset was supplemented with images sourced from the WeedAI database, which were collected at 1.5 m. The resultant model had an average precision of 0.86, intersection over union of 0.60, and F1 score of 0.70 for segmenting the narrow-leafed and sandplain lupins across the multiple datasets. Images collected at a closer range and showing plants at an early developmental stage had significantly higher precision and recall scores (p-value 0.05), indicating image collection methods and plant developmental stages play a substantial role in the model performance. Nonetheless, the model identified 80.3% of the sandplain lupins on average, with a low variation (±6.13%) in performance across the 5 datasets. The results presented in this study contribute to the development of precision weed management systems within morphologically similar crops, particularly for sandplain lupin detection, supporting future narrow-leafed lupin grain yield and quality.

Pangenomics Comes of Age

Publisher: Elsevier BV

Date: 02-2020

DOI: 10.1016/J.TIG.2019.11.006

Abstract: The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single in idual the sequence can be core, present in all in iduals, or accessory (variable or dispensable), found in a subset of in iduals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from ergent evolutionary histories, but also surprising similarities.

Improvements in Genomic Technologies

Publisher: Elsevier BV

Date: 06-2017

DOI: 10.1016/J.TIBTECH.2017.02.009

Abstract: Second-generation sequencing (SGS) has advanced the study of crop genomes and has provided insights into ersity and evolution. However, repetitive DNA sequences in crops often lead to incomplete or erroneous assemblies because SGS reads are too short to fully resolve these repeats. To overcome some of these challenges, long-read sequencing and optical mapping have been developed to produce high-quality assemblies for complex genomes. Previously, high error rates, low throughput, and high costs have limited the adoption of long-read sequencing and optical mapping. However, with recent improvements and the development of novel algorithms, the application of these technologies is increasing. We review the development of long-read sequencing and optical mapping, and assess their application in crop genomics for breeding improved crops.

Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species

Publisher: Scientific Societies

Date: 05-2023

DOI: 10.1094/PHYTO-08-22-0289-FI

Abstract: Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.

The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment

Publisher: Springer Science and Business Media LLC

Date: 09-2014

DOI: 10.1186/S13059-014-0468-1

Wild origins of macadamia domestication identified through intraspecific chloroplast genome sequencing

Publisher: Frontiers Media SA

Date: 21-03-2019

DOI: 10.3389/FPLS.2019.00334

QTL Genetic Mapping Study for Traits Affecting Meal Quality in Winter Oilseed Rape (Brassica Napus L.)

Publisher: MDPI AG

Date: 11-08-2021

DOI: 10.3390/GENES12081235

Abstract: Rapeseed (Brassica napus L.) meal is an important source of protein, but the presence of anti-nutritional compounds, such as fibre and glucosinolates, still limits its use as a livestock feed. Understanding the genetic basis of seed fibre biosynthesis would help to manipulate its content in seeds of oilseed rape. Here, we applied high-resolution skim genotyping by sequencing (SkimGBS) and characterised 187,835 single-nucleotide polymorphism (SNP) markers across a mapping population subsequently used for a genetic mapping study (R/qtl). This approach allowed the identification of 11 stable QTL related to seed quality traits and led to the identification of potential functional genes underlying these traits. Among these, key genes with a known role in carbohydrate metabolic process, cell wall, lignin, and flavonoid biosynthesis, including cellulase GH5, TT10/LAC15, TT4, and SUC2, were found. This study furthers the understanding of the molecular mechanisms underlying seed fibre content and provides new markers for molecular breeding in B. napus.

The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size

Publisher: Oxford University Press (OUP)

Date: 30-07-2021

DOI: 10.1093/MOLBEV/MSAB231

Abstract: Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 in iduals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra s les. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome ersity and provides materials to unveil the evolution history of chicken domestication.

Prioritization of candidate genes in QTL-hotspot region for drought tolerance in chickpea (Cicer arietinum L.)

Publisher: Springer Science and Business Media LLC

Date: 19-10-2015

DOI: 10.1038/SREP15296

Abstract: A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “ QTL-hotspot ” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “ QTL-hotspot ” region into two subregions namely “ QTL-hotspot_a ” (15 genes) and “ QTL-hotspot_b ” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data and the candidate genes from the refined “ QTL-hotspot ” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “ QTL-hotspot ” for drought tolerance in chickpea.

Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Publisher: MDPI AG

Date: 05-05-2023

DOI: 10.20944/PREPRINTS202305.0339.V1

Abstract: Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. malaccensis segregating populations segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on Chromosome 3 of & lsquo DH-Pahang& rsquo reference assembly v4. Within this region, there is a cluster of pattern recognition receptors, namely leucine rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell wall associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant but not in susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent & lsquo Ma850& rsquo and a susceptible line & lsquo Ma848& rsquo , to show that the STR4 resistance co-segregated with marker & lsquo & rsquo at this locus. Finally, an informative SNP marker 29730 allowed the locus specific resistance to be assessed in a collection of diploid and polyploid banana plants. Out of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4 resistant, such as & lsquo Pahang& rsquo , & lsquo SH-3362& rsquo , & lsquo SH-3217& rsquo , & lsquo Ma-ITC0250& rsquo , and & lsquo DH-Pahang/CIRAD 930& rsquo . Additional screening in the International Institute for Tropical Agriculture& rsquo s collection suggests that the dominant allele is common among in the elite & lsquo Matooke& rsquo NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine-mapping and candidate gene identification will allow characterization of molecular mechanisms underlying TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.

An assessment of genetic diversity within and between Brassica napus and Brassica juncealines from international germplasm collections

Publisher: International Society for Horticultural Science (ISHS)

Date: 04-2006

DOI: 10.17660/ACTAHORTIC.2006.706.11

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

Publisher: Wiley

Date: 23-01-2016

DOI: 10.1111/PBI.12513

Plant Genotype to Phenotype Prediction Using Machine Learning

Publisher: Frontiers Media SA

Date: 18-05-2022

DOI: 10.3389/FGENE.2022.822173

Abstract: Genomic prediction tools support crop breeding based on statistical methods, such as the genomic best linear unbiased prediction (GBLUP). However, these tools are not designed to capture non-linear relationships within multi-dimensional datasets, or deal with high dimension datasets such as imagery collected by unmanned aerial vehicles. Machine learning (ML) algorithms have the potential to surpass the prediction accuracy of current tools used for genotype to phenotype prediction, due to their capacity to autonomously extract data features and represent their relationships at multiple levels of abstraction. This review addresses the challenges of applying statistical and machine learning methods for predicting phenotypic traits based on genetic markers, environment data, and imagery for crop breeding. We present the advantages and disadvantages of explainable model structures, discuss the potential of machine learning models for genotype to phenotype prediction in crop breeding, and the challenges, including the scarcity of high-quality datasets, inconsistent metadata annotation and the requirements of ML models.

Candidate Rlm6 resistance genes against Leptosphaeria. maculans identified through a genome-wide association study in Brassica juncea (L.) Czern

Publisher: Springer Science and Business Media LLC

Date: 25-03-2021

DOI: 10.1007/S00122-021-03803-4

Abstract: One hundred and sixty-seven B. juncea varieties were genotyped on the 90K Brassica assay (42,914 SNPs), which led to the identification of sixteen candidate genes for Rlm6. Brassica species are at high risk of severe crop loss due to pathogens, especially Leptosphaeria maculans (the causal agent of blackleg). Brassica juncea (L.) Czern is an important germplasm resource for canola improvement, due to its good agronomic traits, such as heat and drought tolerance and high blackleg resistance. The present study is the first using genome-wide association studies to identify candidate genes for blackleg resistance in B. juncea based on genome-wide SNPs obtained from the Illumina Infinium 90 K Brassica SNP array. The verification of Rlm6 in B. juncea was performed through a cotyledon infection test. Genotyping 42,914 single nucleotide polymorphisms (SNPs) in a panel of 167 B. juncea lines revealed a total of seven SNPs significantly associated with Rlm6 on chromosomes A07 and B04 in B. juncea. Furthermore, 16 candidate Rlm6 genes were found in these regions, defined as nucleotide binding site leucine-rich-repeat (NLR), leucine-rich repeat RLK (LRR-RLK) and LRR-RLP genes. This study will give insights into the blackleg resistance in B. juncea and facilitate identification of functional blackleg resistance genes which can be used in Brassica breeding.

Bioinformatics tools to assist breeding for climate change

Publisher: Springer Berlin Heidelberg

Date: 2013

DOI: 10.1007/978-3-642-37045-8_10

Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation

Publisher: Wiley

Date: 19-08-2022

DOI: 10.1111/NPH.17658

Comparison of transcription of multiple genes at three developmental stages of the plant pathogen Sclerotinia sclerotiorum

Publisher: Oxford University Press (OUP)

Date: 05-2006

DOI: 10.1111/J.1574-6968.2006.00212.X

Abstract: The ascomycete Sclerotinia sclerotiorum is a plant pathogen with a very broad host range. In order to identify and characterize genes involved in S. sclerotiorum infection of Brassica napus (canola), expressed sequence tags (ESTs) were examined from libraries prepared from three tissues: complex appressorium (infection cushions), mycelia grown on agar and lesions formed on leaves of B. napus. A high proportion of genes (68%) had not been previously reported for S. sclerotiorum in public gene or EST databases. The types of novel genes identified in the infection cushion library highlights the functional specificity of these structures and similarities to appressoria in other fungal pathogens. Quantitative real-time PCR was used to analyse tissue specificity and timing of transcription of genes with best matches to MAS3 (appressoria-associated protein from Magnaporthe grisea), cellobiohydrolase I, oxaloacetate acetylhydrolase, metallothionein, pisatin demethylase, and an unknown gene with orthologs in fungal pathogens but not in saprophytic fungi.

The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses

Publisher: Springer Science and Business Media LLC

Date: 21-07-2016

DOI: 10.1007/S10142-016-0501-4

Abstract: Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

Publisher: Wiley

Date: 10-01-2018

DOI: 10.1111/PBI.12867

Fast-forward breeding for a food-secure world

Publisher: Elsevier BV

Date: 12-2021

DOI: 10.1016/J.TIG.2021.08.002

Abstract: Crop production systems need to expand their outputs sustainably to feed a burgeoning human population. Advances in genome sequencing technologies combined with efficient trait mapping procedures accelerate the availability of beneficial alleles for breeding and research. Enhanced interoperability between different omics and phenotyping platforms, leveraged by evolving machine learning tools, will help provide mechanistic explanations for complex plant traits. Targeted and rapid assembly of beneficial alleles using optimized breeding strategies and precise genome editing techniques could deliver ideal crops for the future. Realizing desired productivity gains in the field is imperative for securing an adequate future food supply for 10 billion people.

Investigating Pangenome Graphs Using Wheat Panache

Publisher: Springer US

Date: 2023

DOI: 10.1007/978-1-0716-3389-2_2

Single-cell genomic analysis in plants

Publisher: MDPI AG

Date: 22-01-2018

DOI: 10.3390/GENES9010050

Towards CRISPR/Cas crops - bringing together genomics and genome editing

Publisher: Wiley

Date: 08-2017

DOI: 10.1111/NPH.14702

Abstract: Contents 682 I. 682 II. 683 III. 684 IV. 685 V. 685 VI. 688 VII. 690 VIII. 694 694 References 694 SUMMARY: With the rapid increase in the global population and the impact of climate change on agriculture, there is a need for crops with higher yields and greater tolerance to abiotic stress. However, traditional crop improvement via genetic recombination or random mutagenesis is a laborious process and cannot keep pace with increasing crop demand. Genome editing technologies such as clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) allow targeted modification of almost any crop genome sequence to generate novel variation and accelerate breeding efforts. We expect a gradual shift in crop improvement away from traditional breeding towards cycles of targeted genome editing. Crop improvement using genome editing is not constrained by limited existing variation or the requirement to select alleles over multiple breeding generations. However, current applications of crop genome editing are limited by the lack of complete reference genomes, the sparse knowledge of potential modification targets, and the unclear legal status of edited crops. We argue that overcoming technical and social barriers to the application of genome editing will allow this technology to produce a new generation of high-yielding, climate ready crops.

The impact of genomics technology on adapting plants to climate change

Publisher: Springer New York

Date: 2016

DOI: 10.1007/978-1-4939-3536-9_8

SC-CAN: Spectral Convolution and Channel Attention Network for Wheat Stress Classification

Publisher: MDPI AG

Date: 30-08-2022

DOI: 10.3390/RS14174288

Abstract: Biotic and abiotic plant stress (e.g., frost, fungi, diseases) can significantly impact crop production. It is thus essential to detect such stress at an early stage before visual symptoms and damage become apparent. To this end, this paper proposes a novel deep learning method, called Spectral Convolution and Channel Attention Network (SC-CAN), which exploits the difference in spectral responses of healthy and stressed crops. The proposed SC-CAN method comprises two main modules: (i) a spectral convolution module, which consists of dilated causal convolutional layers stacked in a residual manner to capture the spectral features (ii) a channel attention module, which consists of a global pooling layer and fully connected layers that compute inter-relationship between feature map channels before scaling them based on their importance level (attention score). Unlike standard convolution, which focuses on learning local features, the dilated convolution layers can learn both local and global features. These layers also have long receptive fields, making them suitable for capturing long dependency patterns in hyperspectral data. However, because not all feature maps produced by the dilated convolutional layers are important, we propose a channel attention module that weights the feature maps according to their importance level. We used SC-CAN to classify salt stress (i.e., abiotic stress) on four datasets (Chinese Spring (CS), Aegilops columnaris (co(CS)), Ae. speltoides auchery (sp(CS)), and Kharchia datasets) and Fusarium head blight disease (i.e., biotic stress) on Fusarium dataset. Reported experimental results show that the proposed method outperforms existing state-of-the-art techniques with an overall accuracy of 83.08%, 88.90%, 82.44%, 82.10%, and 82.78% on CS, co(CS), sp(CS), Kharchia, and Fusarium datasets, respectively.

Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress

Publisher: Springer Science and Business Media LLC

Date: 2014

DOI: 10.1186/1471-2164-15-1052

SNP discovery using a pangenome

Publisher: MDPI AG

Date: 11-03-2017

DOI: 10.3390/BIOLOGY6010021

Accessing complex crop genomes with next-generation sequencing

Publisher: Springer Science and Business Media LLC

Date: 05-09-2012

DOI: 10.1007/S00122-012-1964-X

Abstract: Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and lification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading ex les of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic ersity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence-absence variations and other structural chromosomal variants in erse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding.

Karyology and Genome Size Analyses of Iranian Endemic Pimpinella (Apiaceae) Species

Publisher: Frontiers Media SA

Date: 15-06-2022

DOI: 10.3389/FPLS.2022.898881

Abstract: Pimpinella species are annual, biennial, and perennial semibushy aromatic plants cultivated for folk medicine, pharmaceuticals, food, and spices. The karyology and genome size of 17 populations of 16 different Pimpinella species collected from different locations in Iran were analyzed for inter-specific karyotypic and genome size variations. For karyological studies, root tips were squashed and painted with a DAPI solution (1 mg/ml). For flow cytometric measurements, fresh leaves of the standard reference ( Solanum lycopersicum cv. Stupick, 2C DNA = 1.96 pg) and the Pimpinella s les were stained with propidium iodide. We identified two ploidy levels: diploid (2 x ) and tetraploid (4 x ), as well as five metaphase chromosomal counts of 18, 20, 22, 24, and 40. 2 n = 24 is reported for the first time in the Pimpinella genus, and the presence of a B-chromosome is reported for one species. The nuclear DNA content ranged from 2C = 2.48 to 2C = 5.50 pg, along with a wide range of genome sizes between 1212.72 and 2689.50 Mbp. The average monoploid genome size and the average value of 2C DNA/chromosome were not proportional to ploidy. There were considerable positive correlations between 2C DNA and total chromatin length and total chromosomal volume. The present study results enable us to classify the genus Pimpinella with a high degree of morphological variation in Iran. In addition, cytological studies demonstrate karyotypic differences between P. anthriscoides and other species of Pimpinella , which may be utilized as a novel identification key to affiliate into a distinct, new genus – Pseudopimpinella .

The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics

Publisher: MDPI AG

Date: 17-10-2022

DOI: 10.3390/PLANTS11202740

Abstract: The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.

SNP markers-based map construction and genome-wide linkage analysis in Brassica napus

Publisher: Wiley

Date: 03-04-2014

DOI: 10.1111/PBI.12186

Abstract: An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 in iduals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

Publisher: Elsevier BV

Date: 2019

DOI: 10.1016/J.NBT.2018.03.003

Abstract: Bread wheat (Triticum aestivum L.) is a staple food for a significant part of the world's population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere.

Evaluating Plant Gene Models Using Machine Learning

Publisher: MDPI AG

Date: 20-06-2022

DOI: 10.3390/PLANTS11121619

Abstract: Gene models are regions of the genome that can be transcribed into RNA and translated to proteins, or belong to a class of non-coding RNA genes. The prediction of gene models is a complex process that can be unreliable, leading to false positive annotations. To help support the calling of confident conserved gene models and minimize false positives arising during gene model prediction we have developed Truegene, a machine learning approach to classify potential low confidence gene models using 14 gene and 41 protein-based characteristics. Amino acid and nucleotide sequence-based features were calculated for conserved (high confidence) and non-conserved (low confidence) annotated genes from the published Pisum sativum Cameor genome. These features were used to train eXtreme Gradient Boost (XGBoost) classifier models to predict whether a gene model is likely to be real. The optimized models demonstrated a prediction accuracy ranging from 87% to 90% and an F-1 score of 0.91–0.94. We used SHapley Additive exPlanations (SHAP) and feature importance plots to identify the features that contribute to the model predictions, and we show that protein and gene-based features can be used to build accurate models for gene prediction that have applications in supporting future gene annotation processes.

Legume‐wide comparative analysis of pod shatter locus PDH1 reveals phaseoloid specificity, high cowpea expression, and stress responsive genomic context

Publisher: Wiley

Date: 13-04-2023

DOI: 10.1111/TPJ.16209

Abstract: Pod dehiscence is a major source of yield loss in legumes, which is exacerbated by aridity. Disruptive mutations in “ Pod indehiscent 1 ” ( PDH1 ), a pod sclerenchyma‐specific lignin biosynthesis gene, has been linked to significant reductions in dehiscence in several legume species. We compared syntenic PDH1 regions across 12 legumes and two outgroups to uncover key historical evolutionary trends at this important locus. Our results clarified the extent to which PDH1 orthologs are present in legumes, showing the typical genomic context surrounding PDH1 has only arisen relatively recently in certain phaseoloid species ( Vigna , Phaseolus , Glycine ). The notable absence of PDH1 in Cajanus cajan may be a major contributor to its indehiscent phenotype compared with other phaseoloids. In addition, we identified a novel PDH1 ortholog in Vigna angularis and detected remarkable increases in PDH1 transcript abundance during Vigna unguiculata pod development. Investigation of the shared genomic context of PDH1 revealed it lies in a hotspot of transcription factors and signaling gene families that respond to abscisic acid and drought stress, which we hypothesize may be an additional factor influencing expression of PDH1 under specific environmental conditions. Our findings provide key insights into the evolutionary history of PDH1 and lay the foundation for optimizing the pod dehiscence role of PDH1 in major and understudied legume species.

Assembly and comparison of two closely related Brassica napus genomes

Publisher: Wiley

Date: 14-06-2017

DOI: 10.1111/PBI.12742

Genomic advances will herald new insights into the Brassica: Leptosphaeria maculans pathosystem

Publisher: Wiley

Date: 25-05-2012

DOI: 10.1111/J.1438-8677.2011.00481.X

Abstract: The study of the relationship between plants and phytopathogenic fungi is one of the most rapidly moving fields in the plant sciences, the findings of which have contributed to the development of new strategies and technologies to protect crops. Plants employ sophisticated mechanisms to perceive and appropriately defend themselves against pathogens. A good ex le of plant and pathogen evolution is the gene-for-gene interaction between the fungal pathogen Leptosphaeria maculans, the causal agent of blackleg disease, and Brassica crops. This interaction has been studied at the genetic and physiological level due to its agro-economic importance. The newly available genome sequence for Brassica spp. and L. maculans will provide the resources to study the co-evolution of this plant and pathogen. Particularly, an understanding of the co-evolution of genes responsible for virulence and resistance will lead to improved plant protection strategies for Brassica canola and provide a model to understand plant-pathogen interactions in other major crops. This review summarises the research-to-date in the study of the Brassica-L. maculans gene-for-gene interaction, with a focus on the genetics of resistance in Brassica and the wealth of information to be gained from genome sequencing efforts.

crosshap

Publisher: Oxford University Press (OUP)

Date: 08-2023

DOI: 10.1093/BIOINFORMATICS/BTAD518

Abstract: GWAS excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present ‘crosshap’, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture haplotype structures in a local genomic region of interest. Following this, ‘crosshap’ is equipped with visualization tools for choosing optimal clustering parameters (ɛ) before producing an intuitive figure that provides an overview of the complex relationships between linked variants, haplotype combinations, phenotype and metadata traits. The ‘crosshap’ package is freely available under the MIT license and can be downloaded directly from CRAN with R & 4.0.0. The development version is available on GitHub alongside issue support (acobimarsh/crosshap). Tutorial vignettes and documentation are available (jacobimarsh.github.io/crosshap/). Supplementary data are available at Bioinformatics online.

Development and Validation of –Expressed Molecular Markers Specific for the Long Arm of Chromosome 7E

Publisher: Wiley

Date: 2016

DOI: 10.2135/CROPSCI2015.03.0184

SNP analysis of Macadamia integrifolia chloroplast genomes to determine the genetic structure of wild populations

Publisher: International Society for Horticultural Science (ISHS)

Date: 02-2016

DOI: 10.17660/ACTAHORTIC.2016.1109.29

Next generation characterisation of cereal genomes for marker discovery

Publisher: MDPI AG

Date: 25-11-2013

DOI: 10.3390/BIOLOGY2041357

Resistance gene analogs in the Brassicaceae

Publisher: Oxford University Press (OUP)

Date: 12-08-2020

DOI: 10.1104/PP.20.00835

Single nucleotide polymorphism discovery from wheat next-generation sequence data

Publisher: Wiley

Date: 03-07-2012

DOI: 10.1111/J.1467-7652.2012.00718.X

Abstract: Single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and can be used for producing high-resolution genetic maps, marker-trait association studies and marker-assisted breeding. Large polyploid genomes such as wheat present a challenge for SNP discovery because of the potential presence of multiple homoeologs for each gene. AutoSNPdb has been successfully applied to identify SNPs from Sanger sequence data for several species, including barley, rice and Brassica, but the volume of data required to accurately call SNPs in the complex genome of wheat has prevented its application to this important crop. DNA sequencing technology has been revolutionized by the introduction of next-generation sequencing, and it is now possible to generate several million sequence reads in a timely and cost-effective manner. We have produced wheat transcriptome sequence data using 454 sequencing technology and applied this for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer. A total of 4,694,141 sequence reads from three bread wheat varieties were assembled to identify a total of 38 928 candidate SNPs. Each SNP is within an assembly complete with annotation, enabling the selection of polymorphism within genes of interest.

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution

Publisher: Wiley

Date: 23-09-2017

DOI: 10.1111/PBI.12615

Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers

Publisher: Humana Press

Date: 2007

DOI: 10.1007/978-1-59745-535-0_23

Abstract: Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data. SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR lification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR lification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

Publisher: Cold Spring Harbor Laboratory

Date: 26-06-2020

DOI: 10.1101/2020.06.26.162966

Abstract: Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus , flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus . An F 2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. Flowering time in the mapping population differed by up to 25 days between in iduals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ∼12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3,605.70 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trail locus (QTL) on chromosome C2 was detected in the vicinity of flowering time genes including FT and FLC . These findings demonstrate the effectiveness of the ddRAD approach to s le the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F 2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.

Editorial overview

Publisher: Elsevier BV

Date: 08-2020

DOI: 10.1016/J.PBI.2020.08.001

High-Throughput Genotyping Technologies in Plant Taxonomy

Publisher: Springer US

Date: 11-12-2020

DOI: 10.1007/978-1-0716-0997-2_9

The pangenome of an agronomically important crop plant Brassica oleracea

Publisher: Springer Science and Business Media LLC

Date: 11-11-2016

DOI: 10.1038/NCOMMS13390

Abstract: There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single in idual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait ersity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Publisher: Wiley

Date: 10-10-2020

DOI: 10.1111/PBI.13262

Structural variations in plant genomes

Publisher: Oxford University Press (OUP)

Date: 06-06-2014

DOI: 10.1093/BFGP/ELU016

Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars

Publisher: Wiley

Date: 08-12-2019

DOI: 10.1111/PBI.13022

Copy Number Variation among Resistance Genes Analogues in Brassica napus

Publisher: MDPI AG

Date: 04-11-2022

DOI: 10.3390/GENES13112037

Abstract: Copy number variations (CNVs) are defined as deletions, duplications and insertions among in iduals of a species. There is growing evidence that CNV is a major factor underlining various autoimmune disorders and diseases in humans however, in plants, especially oilseed crops, the role of CNVs in disease resistance is not well studied. Here, we investigate the genome-wide ersity and genetic properties of CNVs in resistance gene analogues (RGAs) across eight Brassica napus lines. A total of 1137 CNV events (704 deletions and 433 duplications) were detected across 563 RGAs. The results show CNVs are more likely to occur across clustered RGAs compared to singletons. In addition, 112 RGAs were linked to a blackleg resistance QTL, of which 25 were affected by CNV. Overall, we show that the presence and abundance of CNVs differ between lines, suggesting that in B. napus, the distribution of CNVs depends on genetic background. Our findings advance the understanding of CNV as an important type of genomic structural variation in B. napus and provide a resource to support breeding of advanced canola lines.

Molecular genetic markers: Discovery, applications, data storage and visualisation

Publisher: Bentham Science Publishers Ltd.

Date: 2009

DOI: 10.2174/157489309787158198

Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)

Publisher: Wiley

Date: 11-07-2023

DOI: 10.1111/PBI.14116

Abstract: Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield‐limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa , these were mainly based on a single genome reference and do not represent the full range of RGA ersity in B. rapa . In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa . We show that 309 RGAs were affected by presence‐absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine‐rich repeat (TM‐LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide‐binding site leucine‐rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa . This further clarifies the genetic relationship of these loci, which may be useful in narrowing‐down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.

Sequence and structure of Brassica rapa chromosome A3

Publisher: Springer Science and Business Media LLC

Date: 2010

DOI: 10.1186/GB-2010-11-9-R94

Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea

Publisher: Wiley

Date: 13-05-2022

DOI: 10.1111/PBI.13822

Abstract: Salinity severely affects the yield of chickpea. Understanding the role of lncRNAs can shed light on chickpea salt tolerance mechanisms. However, because lncRNAs are encoded by multiple sites within the genome, their classification to reveal functional versatility at the transcriptional and the post‐transcriptional levels is challenging. To address this, we deep sequenced 24 salt‐challenged flower transcriptomes from two parental genotypes of a RIL population that significantly differ in salt tolerance ability. The transcriptomes for the first time included 12 polyadenylated and 12 non‐polyadenylated RNA libraries to a sequencing depth of ~50 million reads. The ab initio transcriptome assembly comprised ~34 082 transcripts from three biological replicates of salt‐tolerant (JG11) and salt‐sensitive (ICCV2) flowers. A total of 9419 lncRNAs responding to salt stress were identified, 2345 of which were novel lncRNAs specific to chickpea. The expression of poly(A+) lncRNAs and naturally antisense transcribed RNAs suggest their role in post‐transcriptional modification and gene silencing. Notably, 178 differentially expressed lncRNAs were induced in the tolerant genotype but repressed in the sensitive genotype. Co‐expression network analysis revealed that the induced lncRNAs interacted with the FLOWERING LOCUS ( FLC ), chromatin remodelling and DNA methylation genes, thus inducing flowering during salt stress. Furthermore, 26 lncRNAs showed homology with reported lncRNAs such as COOLAIR , IPS1 and AT4 , thus confirming the role of chickpea lncRNAs in controlling flowering time as a crucial salt tolerance mechanism in tolerant chickpea genotype. These robust set of differentially expressed lncRNAs provide a deeper insight into the regulatory mechanisms controlled by lncRNAs under salt stress.

Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.)

Publisher: Springer Science and Business Media LLC

Date: 28-03-2012

DOI: 10.1007/S00122-012-1842-6

Abstract: Blackleg, caused by Leptosphaeria maculans, is one of the most important diseases of oilseed and vegetable crucifiers worldwide. The present study describes (1) the construction of a genetic linkage map, comprising 255 markers, based upon simple sequence repeats (SSR), sequence-related lified polymorphism, sequence tagged sites, and EST-SSRs and (2) the localization of qualitative (race-specific) and quantitative (race non-specific) trait loci controlling blackleg resistance in a doubled-haploid population derived from the Australian canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum using the whole-genome average interval mapping approach. Marker regression analyses revealed that at least 14 genomic regions with LOD ≥ 2.0 were associated with qualitative and quantitative blackleg resistance, explaining 4.6-88.9 % of genotypic variation. A major qualitative locus, designated RlmSkipton (Rlm4), was mapped on chromosome A7, within 0.8 cM of the SSR marker Xbrms075. Alignment of the molecular markers underlying this QTL region with the genome sequence data of B. rapa L. suggests that RlmSkipton is located approximately 80 kb from the Xbrms075 locus. Molecular marker-RlmSkipton linkage was further validated in an F(2) population from Skipton/Ag-Spectrum. Our results show that SSR markers linked to consistent genomic regions are suitable for enrichment of favourable alleles for blackleg resistance in canola breeding programs.

Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

Publisher: Springer Science and Business Media LLC

Date: 08-02-2021

DOI: 10.1038/S41597-021-00834-W

Abstract: We report characteristics of soybean genetic ersity and structure from the resequencing of 481 erse soybean accessions, comprising 52 wild ( Glycine soja ) selections and 429 cultivated ( Glycine max ) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

The application of genomics and bioinformatics to accelerate crop improvement in a changing climate

Publisher: Elsevier BV

Date: 04-2016

DOI: 10.1016/J.PBI.2016.02.002

Abstract: The changing climate and growing global population will increase pressure on our ability to produce sufficient food. The breeding of novel crops and the adaptation of current crops to the new environment are required to ensure continued food production. Advances in genomics offer the potential to accelerate the genomics based breeding of crop plants. However, relating genomic data to climate related agronomic traits for use in breeding remains a huge challenge, and one which will require coordination of erse skills and expertise. Bioinformatics, when combined with genomics has the potential to help maintain food security in the face of climate change through the accelerated production of climate ready crops.

High-throughput genotyping for species identification and diversity assessment in germplasm collections

Publisher: Wiley

Date: 21-02-2015

DOI: 10.1111/1755-0998.12379

Abstract: Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic ersity data. We genotyped 180 Brassicaceae s les sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea s les into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of s les (32/180) were misclassified on the basis of species. Within these 180 s les, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the s les randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several in iduals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic ersity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.

Brassica napus genes Rlm4 and Rlm7, conferring resistance to Leptosphaeria maculans, are alleles of the Rlm9 wall‐associated kinase‐like resistance locus

Publisher: Wiley

Date: 05-05-2022

DOI: 10.1111/PBI.13818

Preface

Publisher: Springer New York

Date: 2016

DOI: 10.1007/978-1-4939-3536-9

Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway

Publisher: Wiley

Date: 24-05-2012

DOI: 10.1111/J.1467-7652.2012.00706.X

Abstract: Establishment of the nitrogen-fixing nodulation symbiosis between legumes and rhizobia requires plant-wide reprogramming to allow infection and development of nodules. Nodulation is regulated principally via a mechanism called autoregulation of nodulation (AON). AON is dependent on shoot and root factors and is maintained by the nodulation autoregulation receptor kinase (NARK) in soybean. We developed a bioassay to detect root-derived signalling molecules in xylem sap of soybean plants which may function in AON. The bioassay involves feeding of xylem extracts via the cut hypocotyl of soybean seedlings and monitoring of molecular markers of AON in the leaf. Transcript abundance changes occurring in the leaf in response to feeding were used to determine the biological activity of the extracts. To identify transcript abundance changes that occur during AON, which may also be used in the bioassay, we used an RNA-seq-based transcriptomics approach. We identified changes in the leaves of bioassay plants fed with xylem extracts derived from either Bradyrhizobium japonicum-inoculated or uninoculated plants. Differential expression responses were detected for genes involved in jasmonic acid metabolism, pathogenesis and receptor kinase signalling. We identified an inoculation- and NARK-dependent candidate gene (GmUFD1a) that responds in both the bioassay and intact, inoculated plants. GmUFD1a is a component of the ubiquitin-dependent protein degradation pathway and provides new insight into the molecular responses occurring during AON. It may now also be used in our feeding bioassay as a molecular marker to assist in identifying the factors contributing to the systemic regulation of nodulation.

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain

Publisher: Frontiers Media SA

Date: 06-2021

DOI: 10.3389/FPLS.2021.666342

Abstract: Sorghum ( Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome ersity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically erse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic ersity resources in sorghum which can be used in genome assisted crop improvement.

Transient Nod factor-dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots

Publisher: Wiley

Date: 02-08-2012

DOI: 10.1111/J.1467-7652.2012.00729.X

Abstract: All lateral organ development in plants, such as nodulation in legumes, requires the temporal and spatial regulation of genes and gene networks. A total mRNA profiling approach using RNA-seq to target the specific soybean (Glycine max) root tissues responding to compatible rhizobia [i.e. the Zone Of Nodulation (ZON)] revealed a large number of novel, often transient, mRNA changes occurring during the early stages of nodulation. Focusing on the ZON enabled us to discard the majority of root tissues and their developmentally erse gene transcripts, thereby highlighting the lowly and transiently expressed nodulation-specific genes. It also enabled us to concentrate on a precise moment in early nodule development at each s ling time. We focused on discovering genes regulated specifically by the Bradyrhizobium-produced Nod factor signal, by inoculating roots with either a competent wild-type or incompetent mutant (nodC(-) ) strain of Bradyrhizobium japonicum. Collectively, 2915 genes were identified as being differentially expressed, including many known soybean nodulation genes. A number of unknown nodulation gene candidates and soybean orthologues of nodulation genes previously reported in other legume species were also identified. The differential expression of several candidates was confirmed and further characterized via inoculation time-course studies and qRT-PCR. The expression of many genes, including an endo-1,4-β-glucanase, a cytochrome P450 and a TIR-LRR-NBS receptor kinase, was transient, peaking quickly during the initiation of nodule ontogeny. Additional genes were found to be down-regulated. Significantly, a set of differentially regulated genes acting in the gibberellic acid (GA) biosynthesis pathway was discovered, suggesting a novel role of GAs in nodulation.

Expanding Gene-Editing Potential in Crop Improvement with Pangenomes

Publisher: MDPI AG

Date: 18-02-2022

DOI: 10.3390/IJMS23042276

Abstract: Pangenomes aim to represent the complete repertoire of the genome ersity present within a species or cohort of species, capturing the genomic structural variance between in iduals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.