ORCID Profile
0000-0002-5975-6051
Current Organisation
Southern Cross University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Turbulent Flows | Genomics | Quantum Chemistry | Interdisciplinary Engineering | Medicinal and Biomolecular Chemistry | Crop and Pasture Nutrition | Crop and Pasture Production | Genetics | Nanochemistry and Supramolecular Chemistry | Biologically Active Molecules | Chemical Characterisation of Materials | Agronomy | Nanophotonics | Cosmology and Extragalactic Astronomy
ANZSRC Socio-Economic Objective (SEO)
Education and Training not elsewhere classified | Information and Communication Services not elsewhere classified | Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Information and Computing Sciences | Winter Grains and Oilseeds not elsewhere classified | Expanding Knowledge in the Physical Sciences | Expanding Knowledge in the Biological Sciences | Expanding Knowledge in the Medical and Health Sciences |
Related Links
Publications
Resolution of quantitative trait loci for mechanical measures accounting for genetic variation in fruit texture of apple (Malus pumila Mill.)
Publisher: Springer Science and Business Media LLC
Date: 06-2001
Fitness of hybrids between rapeseed (Brassica napus) and wild Brassica rapa in natural habitats
Publisher: Wiley
Date: 14-03-2006
Maternal components of RNA ‐directed DNA methylation are required for seed development in Brassica rapa
Publisher: Wiley
Date: 23-04-2018
DOI: 10.1111/TPJ.13910
Abstract: Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction. Here we show that, unlike Arabidopsis, mutations in the Pol IV-dependent small RNA pathway cause severe and specific reproductive defects in Brassica rapa. High rates of abortion occur when seeds have RdDM mutant mothers, but not when they have mutant fathers. Although abortion occurs after fertilization, RdDM function is required in maternal somatic tissue, not in the female gametophyte or the developing zygote, suggesting that siRNAs from the maternal soma might function in filial tissues. We propose that recently outbreeding species such as B. rapa are key to understanding the role of RdDM during plant reproduction.
The distribution of BoCAL-a alleles in Brassica oleracea is consistent with a genetic model for curd development and domestication of the cauliflower.
Publisher: Springer Science and Business Media LLC
Date: 2000
Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa
Publisher: Wiley
Date: 18-03-2022
DOI: 10.1111/PBI.13807
Abstract: Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan‐genome analysis combined with population‐scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu‐401‐42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 erse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As ex les, four specific TIP‐containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of erse vegetable crops in B. rapa . Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.
Generation of nonvernal‐obligate, faster‐cycling Noccaea caerulescens lines through fast neutron mutagenesis
Publisher: Wiley
Date: 08-11-2010
DOI: 10.1111/J.1469-8137.2010.03554.X
Abstract: See also the Commentary by Frerot
A Systematic Approach to Defining Nutritional Quality of Underutilised Crops
Publisher: MDPI
Date: 07-04-2020
InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data
Publisher: Wiley
Date: 05-2012
DOI: 10.1111/J.1744-7909.2012.01120.X
Abstract: Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research. InterStoreDB is a suite of integrated databases designed to assist in this process. The in idual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. The databases include CropStoreDB, for management of population, genetic map, QTL and trait measurement data, SeqStoreDB for sequence-related data and AlignStoreDB, which stores sequence alignment information, and allows navigation between genetic and genomic datasets. Genetic maps are visualized and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser. This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal. We demonstrate the value of InterStoreDB as a tool for Brassica research. InterStoreDB is available from: www.interstoredb.org.
Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa-B. oleracea monosomic alien addition lines
Publisher: Oxford University Press (OUP)
Date: 24-05-2012
DOI: 10.1093/AOB/MCS052
Determination of starch lysophospholipids in rice using liquid chromatography-mass spectrometry (LC-MS)
Publisher: American Chemical Society (ACS)
Date: 03-07-2014
DOI: 10.1021/JF500585J
Abstract: Acquiring a complete understanding of rice starch lysophospholipids (LPLs), their biosynthetic pathways and genetic ersity, and the influence of genotype by environment interactions has been h ered by the lack of efficient high-throughput extraction and analysis methods. It was hypothesized a single-step aqueous n-propanol extraction combined with liquid chromatography-mass spectrometry (LC-MS) could be employed to analyze starch LPLs in white rice. The investigation found different grinding methods showed little effect on the final LPL detected, and a simple single-step extraction with 75% n-propanol (8 mL/0.15 g) heated at 100 °C for 2 h was as effective as an onerous multistep extraction method. A LC-MS method was optimized to simultaneously quantify 10 major LPLs in rice starch within 15 min. This method enables total and in idual starch LPL analysis of a large number of rice s les at little cost. This approach could be applied to starch LPLs in other cereals.
Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers
Publisher: Springer Science and Business Media LLC
Date: 07-1998
Resolving the aphid resistance locusSd-1 on a BAC contig within a sub-telomeric region ofMaluslinkage group 7
Publisher: Canadian Science Publishing
Date: 10-2002
DOI: 10.1139/G02-067
Abstract: Aphids cause serious physical and economic damage to most major crops throughout the world, and there is a pressing requirement to isolate genes conferring aphid resistance. The Sd-1 locus in Malus spp. (apple) confers resistance against the rosy leaf-curling aphid (Dysaphis devecta Wlk.), and was recently positioned within a 1.3-cM region on linkage group 7, flanked by molecular markers. These markers were used as a basis for development of a BAC contig spanning the locus, together with adapter-mediated lification of flanking sequences to obtain BAC insert-end sequences, and fingerprinting of BAC clones. Approximately 800 kb of the Sd-1 genomic region was covered by 19 overlapping BACs, with an average insert size of 75150 kb. The physical genetic distance ratio was estimated at 460 kb/cM, although the distribution of recombination events was irregular with respect to estimated physical distance. Recombinant analysis and development of new markers allowed Sd-1 to be positioned within an interval of approximately 180 kb located on either of two overlapping BACs. From one of these, an insert end sequence showed a significant degree of similarity to nucleotide binding site leucine rich repeat (NBSLRR) resistance genes. Fluorescent in situ hybridization (FISH) of BAC clones within the contig enabled positioning and orientation of the locus within a euchromatic region, very close to the telomere of linkage group 7.Key words: aphid, resistance gene, apple, Malus, physical map.
Complex Patterns of Cannabinoid Alkyl Side-Chain Inheritance in Cannabis
Publisher: Springer Science and Business Media LLC
Date: 06-08-2019
DOI: 10.1038/S41598-019-47812-2
Abstract: The cannabinoid alkyl side-chain represents an important pharmacophore, where genetic targeting of alkyl homologs has the potential to provide enhanced forms of Cannabis for biopharmaceutical manufacture. Delta(9)-tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA) synthase genes govern dicyclic (CBDA) and tricyclic (THCA) cannabinoid composition. However, the inheritance of alkyl side-chain length has not been resolved, and few studies have investigated the contributions and interactions between cannabinoid synthesis pathway loci. To examine the inheritance of chemical phenotype (chemotype), THCAS and CBDAS genotypes were scored and alkyl cannabinoid segregation analysed in 210 F 2 progeny derived from a cross between two Cannabis chemotypes ergent for alkyl and cyclic cannabinoids. Inheritance patterns of F 2 progeny were non-Gaussian and deviated from Mendelian expectations. However, discrete alkyl cannabinoid segregation patterns consistent with digenic as well as epistatic modes of inheritance were observed among F 2 THCAS and CBDAS genotypes. These results suggest linkage between cannabinoid pathway loci and highlight the need for further detailed characterisation of cannabinoid inheritance to facilitate metabolic engineering of chemically elite germplasm.
Phospholipids in rice: Significance in grain quality and health benefits: A review
Publisher: Elsevier BV
Date: 08-2013
DOI: 10.1016/J.FOODCHEM.2012.12.046
Abstract: Phospholipids (PLs) are a major class of lipid in rice grain. Although PLs are only a minor nutrient compared to starch and protein, they may have both nutritional and functional significance. We have systemically reviewed the literature on the class, distribution and variation of PLs in rice, their relation to rice end-use quality and human health, as well as available methods for analytical profiling. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI) and their lyso forms are the major PLs in rice. The deterioration of PC in rice bran during storage was considered as a trigger for the degradation of rice lipids with associated rancid flavour in paddy and brown rice. The lyso forms in rice endosperm represent the major starch lipid, and may form inclusion complexes with amylose, affecting the physicochemical properties and digestibility of starch, and hence its cooking and eating quality. Dietary PLs have a positive impact on several human diseases and reduce the side-effects of some drugs. As rice has long been consumed as a staple food in many Asian countries, rice PLs may have significant health benefits for those populations. Rice PLs may be influenced both by genetic (G) and environmental (E) factors, and resolving G×E interactions may allow future exploitation of PL composition and content, thus boosting rice eating quality and health benefits for consumers. We have identified and summarised the different methods used for rice PL analysis, and discussed the consequences of variation in reported PL values due to inconsistencies between methods. This review enhances the understanding of the nature and importance of PLs in rice and outlines potential approaches for manipulating PLs to improve the quality of rice grain and other cereals.
Pests, diseases, and aridity have shaped the genome of Corymbia citriodora
Publisher: Springer Science and Business Media LLC
Date: 10-05-2021
DOI: 10.1038/S42003-021-02009-0
Abstract: Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts ( Eucalyptus , Corymbia and Angophora ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora , anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although the two erged approximately 60 million years ago and have different genome sizes (408 vs 641 Mb), with few large intra-chromosomal rearrangements. C. citriodora shares an ancient whole-genome duplication event with E. grandis but has undergone tandem gene family expansions related to terpene biosynthesis, innate pathogen resistance, and leaf wax formation, enabling their successful adaptation to biotic/abiotic stresses and arid conditions of the Australian continent.
Generation and characterization of tribenuron-methyl herbicide-resistant rapeseed (Brasscia napus) for hybrid seed production using chemically induced male sterility
Publisher: Springer Science and Business Media LLC
Date: 14-12-2015
DOI: 10.1007/S00122-014-2415-7
Abstract: Identification and molecular analysis of four tribenuron-methyl resistant mutants in Brassica napus , which would be very useful in hybrid production using a Chemically induced male sterility system. Chemically induced male sterility (CIMS) systems dependent on chemical hybridization agents (CHAs) like tribenuron-methyl (TBM) represent an important approach for practical utilization of heterosis in rapeseed. However, when spraying the female parents with TBM to induce male sterility the male parents must be protected with a shield to avoid injury to the stamens, which would otherwise complicate the seed production protocol and increase the cost of hybrid seed production. Here we report the first proposed application of a herbicide-resistant cultivar in hybrid production, using a CIMS system based on identifying four TBM-resistant mutants in Brassica napus. Genetic analysis indicated that the TBM resistance was controlled by a single dominant nuclear gene. An in vitro enzyme activity assay for acetohydroxyacid synthase (AHAS) suggested that the herbicide resistance is caused by a gain-of-function mutation in a copy of AHAS genes. Comparative sequencing of the mutants and wild type BnaA.AHAS.a coding sequences identified a C-to-T transition at either position 535 or 536 from the translation start site, which resulted in a substitution of proline with serine or leucine at position 197 according to the Arabidopsis thaliana protein sequence. An allele-specific dCAPS marker developed from the C536T variation co-segregated with the herbicide resistance. Transgenic A. thaliana plants expressing BnaA.ahas3.a conferred herbicide resistance, which confirmed that the P197 substitution in BnaA.AHAS.a was responsible for the herbicide resistance. Moreover, the TBM-resistant lines maintain normal male fertility under TBM treatment and can be of practical value in hybrid seed production using CIMS.
Characterisation of disease resistance gene-like sequences in Brassica oleracea L.
Publisher: Springer Science and Business Media LLC
Date: 03-2001
Abundant expression of maternal siRNAs is a conserved feature of seed development
Publisher: Cold Spring Harbor Laboratory
Date: 06-12-2019
DOI: 10.1101/866806
Abstract: Small RNAs are abundant in plant reproductive tissues, especially 24-nt short interfering (si)RNAs. Most 24-nt siRNAs are dependent on RNA Pol IV and RDR2, and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa , RdDM is required in the maternal sporophyte for successful seed development. Here we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during B. rapa seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in erse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.
Quantitative genetic analysis and comparison of physical and sensory descriptors relating to fruit flesh firmness in apple (Malus pumila Mill.)
Publisher: Springer Science and Business Media LLC
Date: 05-2000
Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers
Publisher: Springer Science and Business Media LLC
Date: 2010
Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution
Publisher: Frontiers Media SA
Date: 09-10-2015
Rapeseed cytoplasm gives advantage in wild relatives and complicates genetically modified crop biocontainment
Publisher: Wiley
Date: 10-08-2009
DOI: 10.1111/J.1469-8137.2009.02877.X
Abstract: DOI: 10.1111/j.1469-8137.2009.02991.x Commentary p 925
Maximising recombination across macadamia populations to generate linkage maps for genome anchoring
Publisher: Springer Science and Business Media LLC
Date: 19-03-2020
DOI: 10.1038/S41598-020-61708-6
Abstract: The Proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of ,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of in idual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.
Characterisation of cannabinoid composition in a diverse Cannabis sativa L. germplasm collection
Publisher: Springer Science and Business Media LLC
Date: 30-10-2015
DOI: 10.1007/S10681-015-1585-Y
Abstract: The ability to characterise cannabinoid chemical phenotype (chemotype) accurately is important for the development of Cannabis sativa L. cultivars specific for pharmacological, hemp fibre, or seed end use. Although a number of chemotyping and genotyping methods have previously been developed to predict and characterise cannabinoid composition, only a subset of the gene pool has been examined. A representative survey from a wide range of geographically and genetically erse C. sativa accessions using liquid chromatography–mass spectrometry (LC–MS) cannabinoid profiling together with dominant and co-dominant DNA marker assays was performed. Overall variability of chemotype across the gene pool was found to be three-fold greater within heterozygote genotypes than previously reported. Interestingly, an in idual plant of East Asian origin was found to exhibit a rare propyl alkyl cannabinoid homologue and a chemotype inconsistent with the predicted genotype. We propose that in order to carry out comprehensive screening of genetic resource collections and to identify chemotypic variants specific for end-use pharmacological applications, a strategy which adopts both cannabinoid profiling and the co-dominant DNA marker assay is required. Further research with consideration of propyl-alkyl-cannabinoid homologues should explore the relationship between chemotype and genotype in greater detail.
Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed
Publisher: Wiley
Date: 17-04-2019
DOI: 10.1111/PBI.13115
Stability, structure and complexity of yeast chromosome III
Publisher: Oxford University Press (OUP)
Date: 1993
Abstract: The complete sequence of yeast chromosome III provides a model for studies relating DNA sequence and structure at different levels of organisation in eukaryotic chromosomes. DNA helical stability, intrinsic curvature and sequence complexity have been calculated for the complete chromosome. These features are compartmentalised at different levels of organisation. Compartmentalisation of thermal stability is observed from the level delineating coding/non-coding sequences, to higher levels of organisation which correspond to regions varying in G + C content. The three-dimensional path reveals a symmetrical structure for the chromosome, with a densely packed central region and more diffuse and linear subtelomeric regions. This interspersion of regions of high and low curvature is reflected at lower levels of organisation. Complexity of n-tuplets (n = 1 to 6) also reveals compartmentalisation of the chromosome at different levels of organisation, in many cases corresponding to the structural features. DNA stability, conformation and complexity delineate telomeres, centromere, autonomous replication sequences (ARS), transposition hotspots, recombination hotspots and the mating-type loci.
A sequence-tagged linkage map of Brassica rapa
Publisher: Oxford University Press (OUP)
Date: 09-2006
DOI: 10.1534/GENETICS.106.060152
Abstract: A detailed genetic linkage map of Brassica rapa has been constructed containing 545 sequence-tagged loci covering 1287 cM, with an average mapping interval of 2.4 cM. The loci were identified using a combination of 520 RFLP and 25 PCR-based markers. RFLP probes were derived from 359 B. rapa EST clones and lification products of 11 B. rapa and 26 Arabidopsis. Including 21 SSR markers provided anchors to previously published linkage maps for B. rapa and B. napus and is followed as the referenced mapping of R1–R10. The sequence-tagged markers allowed interpretation of the pattern of chromosome duplications within the B. rapa genome and comparison with Arabidopsis. A total of 62 EST markers showing a single RFLP band were mapped through 10 linkage groups, indicating that these can be valuable anchoring markers for chromosome-based genome sequencing of B. rapa. Other RFLP probes gave rise to 2–5 loci, inferring that B. rapa genome duplication is a general phenomenon through 10 chromosomes. The map includes five loci of FLC paralogues, which represent the previously reported BrFLC-1, -2, -3, and -5 and additionally identified BrFLC3 paralogues derived from local segmental duplication on R3.
Identification of environmentally stable QTL for resistance against Leptosphaeria maculans in oilseed rape (Brassica napus)
Publisher: Springer Science and Business Media LLC
Date: 30-10-2016
Genetic analysis and FISH mapping of the Colourless non-ripening locus of tomato
Publisher: Springer Science and Business Media LLC
Date: 02-2002
Abstract: Cnr ( Colourless non-ripening) is a dominant pleiotropic ripening mutation of tomato ( Lycopersicon esculentum) which has previously been mapped to the proximal region of tomato chromosome 2. We describe the fine mapping of the Cnr locus using both linkage analysis and fluorescence in situ hybridisation (FISH). Restriction fragment length polymorphism (RFLP)-, lified restriction fragment polymorphism (AFLP)-, and cleaved lified polymorphic sequence (CAPS)-based markers, linked to the Cnrlocus were mapped onto the long arm of chromosome 2. Detailed linkage analysis indicated that the Cnr locus was likely to lie further away from the top of the long arm than previously thought. This was confirmed by FISH, which was applied to tomato pachytene chromosomes in order to gain an insight into the organisation of hetero- and euchromatin and its relationship to the physical and genetic distances in the Cnr region. Three molecular markers linked to Cnr were unambiguously located by FISH to the long arm of chromosome 2 using in idual BAC probes containing these single-copy sequences. The physical order of the markers coincided with that established by genetic analysis. The two AFLP markers most-closely linked to the Cnr locus were located in the euchromatic region 2.7-cM apart. The physical distance between these markers was measured on the pachytene spreads and estimated to be approximately 900 kb, suggesting a bp:cM relationship in this region of chromosome 2 of about 330 kb/cM. This is less than half the average value of 750 kb/cM for the tomato genome. The relationship between genetic and physical distances on chromosome 2 is discussed.
Detection and resolution of genetic loci affecting circadian period in Brassica oleracea
Publisher: Springer Science and Business Media LLC
Date: 13-12-2006
DOI: 10.1007/S00122-006-0468-Y
Abstract: Circadian rhythms regulate many aspects of plant growth, fitness and vigour. The components and detailed mechanism of circadian regulation to date have been dissected in the reference species Arabidopsis thaliana. To determine the genetic basis and range of natural allelic variation for intrinsic circadian period in the closest crop relatives, we used an accurate and high throughput data capture system to record rhythmic cotyledon movement in two immortal segregating populations of Brassica oleracea, derived from parent lines representing different crop types. Periods varied between 24.4 and 26.1 h between the parent lines, with transgressive segregation between extreme recombinant lines in both populations of approximately 3.5 h. The additive effect of in idual QTL identified in each population varied from 0.17 to 0.36 h. QTL detected in one doubled haploid population were verified and the mapping intervals further resolved by determining circadian period in genomic substitution lines derived from the parental lines. Comparative genomic analysis based on collinearity between Brassica and Arabidopsis also allowed identification of candidate orthologous genes known to regulate period in Arabidopsis, that may account for the additive circadian effects of specific QTL. The distinct QTL positions detected in the two populations, and the extent of transgressive segregation suggest that there is likely to be considerable scope for modulating the range of available circadian periods in natural populations and crop species of Brassica. This may provide adaptive advantage for optimising growth and development in different latitudes, seasons or climate conditions.
A taxometric analysis of seed proteins in the genus Briza s. l. (Poaceae)
Publisher: Springer Science and Business Media LLC
Date: 02-1986
DOI: 10.1007/BF02430272
Brassica GLABRA2 genes: analysis of function related to seed oil content and development of functional markers
Publisher: Springer Science and Business Media LLC
Date: 17-02-2010
DOI: 10.1007/S00122-010-1279-8
Abstract: Regulation of seed oil accumulation in oilseed rape (Brassica napus) has important economic significance. However, few genes have been characterized that affect final seed oil content. Through a mutant identification, the class IV homeodomain-ZIP transcription factor GLABRA2 (GL2) has been found to regulate seed oil accumulation in Arabidopsis, in addition to its role in trichome development. In this study, we isolated four distinct orthologues of GL2 from B. napus (AC-genome), B. rapa (A) and B. oleracea (C), using an overlapping-PCR strategy. The four GL2 orthologues were very similar, with 96.10-99.69% identity in exon regions, 75.45-93.84% in intron regions, 97.34-99.87% in amino acid sequences. Alignments of the four genes revealed that the A-genome sequences of BnaA.GL2.a from B. napus and BraA.GL2.a from B. rapa are more similar than the others, and likewise the C-genome sequences of BnaC.GL2.b from B. napus and BolC.GL2.a from B. oleracea are more similar. BnaA.GL2.a and BraA.GL2.a from the A-genome are highly expressed in roots, whilst BnaC.GL2.b and BolC.GL2.a from the C-genome are preferentially expressed in seeds. Transgenic ectopic overexpression and suppression of BnaC.GL2.b in Arabidopsis allowed further investigation of the effect on seed oil content. Overexpression generated two phenotypes: the wild-type-like and the gl2-mutant-like (an Arabidopsis glabrous mutant of gl2-2), with increases in seed oil content of 3.5-5.0% in the gl2-mutant-like transgenic plants. Suppression resulted in increases of 2.5-6.1% in seed oil content, and reduced trichome number at the leaf margins. These results suggest that BnaC.GL2.b can negatively regulate oil accumulation in Arabidopsis seeds. As a result of comparing the four GL2 genes, three A/C-genome-specific primer sets were developed and a C-genome-specific EcoRV cleavage site was identified, which can be used as functional markers to distinguish these orthologues within Brassica species. The genes identified and their molecular markers developed in this study will be valuable both for oilseed rape breeding focusing on improvement of seed oil content, and for detecting gene flow between populations.
Exploring and exploiting epigenetic variation in crops
Publisher: Canadian Science Publishing
Date: 11-2010
DOI: 10.1139/G10-059
Abstract: This review addresses the mechanisms by which epigenetic variation modulates plant gene regulation and phenotype. In particular we explore the scope for harnessing such processes within the context of crop genetic improvement. We focus on the role of DNA methylation as an epigenetic mark that contributes to epiallelic ersity and modulation of gene regulation. We outline the prevalence and distribution of epigenetic marks in relation to eukaryote developmental processes, and in particular identify where this may be relevant to crop traits both in terms of specific developmental stages and in relation to physiological responses to environmental change. Recent whole genome surveys have identified specific characteristics of the distribution of DNA methylation within plant genomes. Together with greater understanding of the mode of action of different maintenance and de novo methyltransferases, this provides an opportunity to modulate DNA methylation status at specific loci as an intervention strategy in crop genetic improvement. We discuss alternative approaches that may be suitable for harnessing such induced epiallelic variation. Most of the discussion is associated with Brassica crops, which demonstrate considerable morphological plasticity, segmental chromosomal duplication, and polyploidy.
Genetical and Comparative Genomics of Brassica under Altered Ca Supply Identifies Arabidopsis Ca-Transporter Orthologs
Publisher: Oxford University Press (OUP)
Date: 07-2014
Abstract: Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca2+ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500) 23 cis- and 948 trans- eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca2+ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification rioritization.
Introgression of the Vf source of scab resistance and distribution of linked marker alleles within the Malus gene pool
Publisher: Springer Science and Business Media LLC
Date: 10-1999
A molecular approach to the identification of S-alleles in Brassica oleracea
Publisher: Springer Science and Business Media LLC
Date: 07-1994
DOI: 10.1007/BF00232738
Crop epigenetics and the molecular hardware of genotype × environment interactions
Publisher: Frontiers Media SA
Date: 06-11-2015
Shoot Calcium and Magnesium Concentrations Differ between Subtaxa, Are Highly Heritable, and Associate with Potentially Pleiotropic Loci in Brassica oleracea
Publisher: Oxford University Press (OUP)
Date: 15-02-2008
Abstract: Calcium (Ca) and magnesium (Mg) are the most abundant group II elements in both plants and animals. Genetic variation in shoot Ca and shoot Mg concentration (shoot Ca and Mg) in plants can be exploited to biofortify food crops and thereby increase dietary Ca and Mg intake for humans and livestock. We present a comprehensive analysis of within-species genetic variation for shoot Ca and Mg, demonstrating that shoot mineral concentration differs significantly between subtaxa (varietas). We established a structured ersity foundation set of 376 accessions to capture a high proportion of species-wide allelic ersity within domesticated Brassica oleracea, including representation of wild relatives (C genome, 1n = 9) from natural populations. These accessions and 74 modern F1 hybrid cultivars were grown in glasshouse and field environments. Shoot Ca and Mg varied 2- and 2.3-fold, respectively, and was typically not inversely correlated with shoot biomass, within most subtaxa. The closely related capitata (cabbage) and sabauda (Savoy cabbage) subtaxa consistently had the highest mean shoot Ca and Mg. Shoot Ca and Mg in glasshouse-grown plants was highly correlated with data from the field. To understand and dissect the genetic basis of variation in shoot Ca and Mg, we studied homozygous lines from a segregating B. oleracea mapping population. Shoot Ca and Mg was highly heritable (up to 40%). Quantitative trait loci (QTL) for shoot Ca and Mg were detected on chromosomes C2, C6, C7, C8, and, in particular, C9, where QTL accounted for 14% to 55% of the total genetic variance. The presence of QTL on C9 was substantiated by scoring recurrent backcross substitution lines, derived from the same parents. This also greatly increased the map resolution, with strong evidence that a 4-cM region on C9 influences shoot Ca. This region corresponds to a 0.41-Mb region on Arabidopsis (Arabidopsis thaliana) chromosome 5 that includes 106 genes. There is also evidence that pleiotropic loci on C8 and C9 affect shoot Ca and Mg. Map-based cloning of these loci will reveal how shoot-level phenotypes relate to Ca2+ and Mg2+ uptake and homeostasis at the molecular level.
Three-point appraisal of genetic linkage maps
Publisher: Springer Science and Business Media LLC
Date: 29-06-2012
DOI: 10.1007/S00122-012-1920-9
Abstract: This paper develops a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure. The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders. Simulation and two case studies were used to illustrate the method. In the first case study, the diagnostic revealed conflicts in map ordering for short inter-marker distances that were resolved at a distance of 8-12 cM, except for a set of markers at the end of the linkage group. In the second case study, the ordering did not resolve as distances increase, which could be attributed to regions of the map where many in iduals were untyped.
RFLP and RAPD markers linked to the rosy leaf curling aphid resistance gene (Sd1) in apple
Publisher: Springer Science and Business Media LLC
Date: 03-1997
Assessing Quantitative Resistance against Leptosphaeria maculans (Phoma Stem Canker) in Brassica napus (Oilseed Rape) in Young Plants
Publisher: Public Library of Science (PLoS)
Date: 15-01-2014
Quantitative resistance to symptomless growth of Leptosphaeria maculans (phoma stem canker) in Brassica napus (oilseed rape)
Publisher: Wiley
Date: 11-03-2009
A rich TILLING resource for studying gene function in Brassica rapa
Publisher: Springer Science and Business Media LLC
Date: 09-04-2010
Abstract: The Brassicaceae family includes the model plant Arabidopsis thaliana as well as a number of agronomically important species such as oilseed crops (in particular Brassica napus, B. juncea and B. rapa ) and vegetables ( eg. B. rapa and B. oleracea ). Separated by only 10-20 million years, Brassica species and Arabidopsis thaliana are closely related, and it is expected that knowledge obtained relating to Arabidopsis growth and development can be translated into Brassicas for crop improvement. Moreover, certain aspects of plant development are sufficiently different between Brassica and Arabidopsis to warrant studies to be carried out directly in the crop species. However, mutating in idual genes in the hidiploid Brassicas such as B. napus and B. juncea may, on the other hand, not give rise to expected phenotypes as the genomes of these species can contain up to six orthologues per single-copy Arabidopsis gene. In order to elucidate and possibly exploit the function of redundant genes for oilseed rape crop improvement, it may therefore be more efficient to study the effects in one of the diploid Brassica species such as B. rapa . Moreover, the ongoing sequencing of the B. rapa genome makes this species a highly attractive model for Brassica research and genetic resource development. Seeds from the diploid Brassica A genome species, B. rapa were treated with ethyl methane sulfonate (EMS) to produce a TILLING (Targeting Induced Local Lesions In Genomes) population for reverse genetics studies. We used the B. rapa genotype, R-o-18, which has a similar developmental ontogeny to an oilseed rape crop. Hence this resource is expected to be well suited for studying traits with relevance to yield and quality of oilseed rape. DNA was isolated from a total of 9,216 M 2 plants and pooled to form the basis of the TILLING platform. Analysis of six genes revealed a high level of mutations with a density of about one per 60 kb. This analysis also demonstrated that screening a 1 kb licon in just one third of the population (3072 M 2 plants) will provide an average of 68 mutations and a 97% probability of obtaining a stop-codon mutation resulting in a truncated protein. We furthermore calculated that each plant contains on average ~10,000 mutations and due to the large number of plants, it is predicted that mutations in approximately half of the GC base pairs in the genome exist within this population. We have developed the first EMS TILLING resource in the diploid Brassica species, B. rapa . The mutation density in this population is ~1 per 60 kb, which makes it the most densely mutated diploid organism for which a TILLING population has been published. This resource is publicly available through the RevGen UK reverse genetics platform revgenuk.jic.ac.uk .
The potential of the underutilized pulse bambara groundnut (Vigna subterranea (L.) Verdc.) for nutritional food security
Publisher: Elsevier BV
Date: 04-2019
Standardized gene nomenclature for the Brassica genus
Publisher: Springer Science and Business Media LLC
Date: 2008
Genetics and epigenetics of fruit development and ripening
Publisher: Elsevier BV
Date: 02-2008
DOI: 10.1016/J.PBI.2007.09.003
Abstract: Fruits come in a vast variety of forms with both dry and fleshy types being essential components of the human diet. Elegant studies on the dry fruits of Arabidopsis have identified a suite of transcription factors involved in their development and dehiscence. Recent discoveries in tomato have revealed a hitherto unsuspected regulatory network involved in the developmental regulation of ripening in these fleshy fruits. Intriguingly it has become apparent that tomato shares some elements of its regulatory network in common with those involved in fruit development in Arabidopsis. Furthermore epigenetic variation has been shown to influence tomato ripening. These discoveries are likely to have a major impact on strategies for crop improvement in fruit bearing species.
Evaluation of linkage disequilibrium pattern and association study on seed oil content in Brassica napus using ddRAD sequencing
Publisher: Public Library of Science (PLoS)
Date: 05-01-2016
A functional genomics resource for Brassica napus: Development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING
Publisher: Wiley
Date: 06-11-2008
DOI: 10.1111/J.1469-8137.2008.02619.X
Abstract: Two ethylmethanesulfonate (EMS) mutant populations of the semi-winter rapeseed cv. Ningyou7 were constructed with high mutant load, to provide a TILLING platform for functional genomics in Brassica napus, and for introduction of novel allelic variation in rapeseed breeding. Forward genetic screening of mutants from the M2 populations resulted in identification of a large number of novel phenotypes. Reverse genetic screening focused on the potentially multi-paralogous gene FAE1 (fatty acid elongase1), which controls seed erucic acid synthesis in rapeseed. A B. napus BAC library was screened, and loci in a reference mapping population (TNDH) were mapped to conclude that there are two paralogous copies of FAE1, one on each of the B. napus A and C genomes. A new procedure is demonstrated to identify novel mutations in situations where two or more very similar paralogous gene copies exist in a genome. The procedure involves TILLING of single plants, using existing SNPs as a positive control, and is able to distinguish novel mutations based on primer pairs designed to lify both FAE1 paralogues simultaneously. The procedure was applied to 1344 M2 plants, with 19 mutations identified, of which three were functionally compromised with reduced seed erucic acid content.
Regulatory Hotspots Are Associated with Plant Gene Expression under Varying Soil Phosphorus Supply in Brassica rapa
Publisher: Oxford University Press (OUP)
Date: 28-04-2011
Abstract: Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.
Constraints on mutability in a multiallelic gene family
Publisher: Springer Science and Business Media LLC
Date: 12-1995
DOI: 10.1007/BF00173153
A SQUAMOSA MADS Box Gene Involved in the Regulation of Anthocyanin Accumulation in Bilberry Fruits
Publisher: Oxford University Press (OUP)
Date: 21-06-2010
Abstract: Anthocyanins are important health-promoting phytochemicals that are abundant in many fleshy fruits. Bilberry (Vaccinium myrtillus) is one of the best sources of these compounds. Here, we report on the expression pattern and functional analysis of a SQUAMOSA-class MADS box transcription factor, VmTDR4, associated with anthocyanin biosynthesis in bilberry. Levels of VmTDR4 expression were spatially and temporally linked with color development and anthocyanin-related gene expression. Virus-induced gene silencing was used to suppress VmTDR4 expression in bilberry, resulting in substantial reduction in anthocyanin levels in fully ripe fruits. Chalcone synthase was used as a positive control in the virus-induced gene silencing experiments. Additionally, in sectors of fruit tissue in which the expression of the VmTDR4 gene was silenced, the expression of R2R3 MYB family transcription factors related to the biosynthesis of flavonoids was also altered. We conclude that VmTDR4 plays an important role in the accumulation of anthocyanins during normal ripening in bilberry, probably through direct or indirect control of transcription factors belonging to the R2R3 MYB family.
Abundant expression of maternal siRNAs is a conserved feature of seed development
Publisher: Proceedings of the National Academy of Sciences
Date: 15-06-2020
Abstract: Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa , RdDM is required in the maternal sporophyte for successful seed development. Here, we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during B. rapa seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in erse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together, these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.
Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa
Publisher: Springer Science and Business Media LLC
Date: 22-10-2010
Abstract: The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa . An integrated linkage map between the hidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus . Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa , although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus . The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus , and for comparative analysis of the A genome within Brassica species.
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.
The first meiosis of resynthesized Brassica napus, a genome blender
Publisher: Wiley
Date: 03-03-2010
DOI: 10.1111/J.1469-8137.2010.03182.X
Abstract: Polyploidy promotes the restructuring of merged genomes within initial generations of resynthesized Brassica napus, possibly caused by homoeologous recombination at meiosis. However, little is known about the impact of the first confrontation of two genomes at the first meiosis which could lead to genome exchanges in progeny. Here, we assessed the role of the first meiosis in the genome instability of synthetic B. napus. We used three different newly resynthesized B. napus plants and established meiotic pairing frequencies for the A and C genomes. We genotyped the three corresponding progenies in a cross to a natural B. napus on the two homoeologous A1 and C1 chromosomes. Pairing at meiosis in a set of progenies with various rearrangements was scored. Here, we confirmed that the very first meiosis of resynthesized plants of B. napus acts as a genome blender, with many of the meiotic-driven genetic changes transmitted to the progenies, in proportions that depend significantly on the cytoplasm background inherited from the progenitors. We conclude that the first meiosis generates rearrangements on both genomes and promotes subsequent restructuring in further generations. Our study advances the knowledge on the timing of genetic changes and the mechanisms that may bias their transmission.
Remobilisation and Fate of Sulphur in Indian Mustard (Brassica juncea. L)
Publisher: MDPI
Date: 31-12-2019
Magnesium and calcium overaccumulate in the leaves of aschengen3mutant ofBrassica rapa
Publisher: Oxford University Press (OUP)
Date: 08-04-2021
Abstract: Magnesium (Mg) and calcium (Ca) are essential mineral nutrients poorly supplied in many human food systems. In grazing livestock, Mg and Ca deficiencies are costly welfare issues. Here, we report a Brassica rapa loss-of-function schengen3 (sgn3) mutant, braA.sgn3.a-1, which accumulates twice as much Mg and a third more Ca in its leaves. We mapped braA.sgn3.a to a single recessive locus using a forward ionomic screen of chemically mutagenized lines with subsequent backcrossing and linked-read sequencing of second back-crossed, second filial generation (BC2F2) segregants. Confocal imaging revealed a disrupted root endodermal diffusion barrier, consistent with SGN3 encoding a receptor-like kinase required for normal formation of Casparian strips, as reported in thale cress (Arabidopsis thaliana). Analysis of the spatial distribution of elements showed elevated extracellular Mg concentrations in leaves of braA.sgn3.a-1, hypothesized to result from preferential export of excessive Mg from cells to ensure suitable cellular concentrations. This work confirms a conserved role of SGN3 in controlling nutrient homeostasis in B. rapa, and reveals mechanisms by which plants are able to deal with perturbed shoot element concentrations resulting from a “leaky” root endodermal barrier. Characterization of variation in leaf Mg and Ca accumulation across a mutagenized population of B. rapa shows promise for using such populations in breeding programs to increase edible concentrations of essential human and animal nutrients.
Identification of genetic factors controlling the efficiency of Agrobacterium rhizogenes-mediated transformation in Brassica oleracea by QTL analysis
Publisher: Springer Science and Business Media LLC
Date: 09-2002
DOI: 10.1007/S00122-002-0905-5
Abstract: We have identified quantitative trait loci (QTL) for transgenic and adventitious root production using an Agrobacterium rhizogenes-mediated co-transformation system in conjunction with a Brassica oleracea double haploid (DH) mapping population. Three QTL for green fluorescent protein (GFP)-fluorescent root production and four QTL for adventitious root production were identified as accounting for 26% and 32% of the genetic variation in the population, respectively. Two of the QTL regions identified were common to both transgenic and adventitious root production. Two different methods of QTL analysis were employed (marker regression and interval mapping) and with the exception of one region on linkage group O7 for transgenic root production, both techniques detected the same regions of the genome. The regions we identified to be associated with the control of transgenic root production following A. rhizogenes-mediated transformation are the first to be detected using a QTL mapping approach. In addition, this is the first study to identify genetic regions that co-regulate both transgenic and adventitious root production within the constraints of an A. rhizogenes-mediated transformation process. We have identified plant genotypes that do not produce any transgenic roots that may be deficient for T-DNA integration via illegitimate recombination and that may also be potentially important for the development of homologous recombination protocols. Conversely, we have also identified plant genotypes with high rates of transgenic root production that will be critical in the development of high throughput transformation systems.
Bridging the food security gap: an information-led approach to connect dietary nutrition, food composition and crop production
Publisher: Wiley
Date: 31-12-2020
DOI: 10.1002/JSFA.10157
Abstract: Food security is recognized as a major global challenge, yet human food-chain systems are inherently not geared towards nutrition, with decisions on crop and cultivar choice not informed by dietary composition. Currently, food compositional tables and databases (FCT/FCDB) are the primary information sources for decisions relating to dietary intake. However, these only present single mean values representing major components. Establishment of a systematic controlled vocabulary to fill this gap requires representation of a more complex set of semantic relationships between terms used to describe nutritional composition and dietary function. We carried out a survey of 11 FCT/FCDB and 177 peer-reviewed papers describing variation in nutritional composition and dietary function for food crops to identify a comprehensive set of terms to construct a controlled vocabulary. We used this information to generate a Crop Dietary Nutrition Data Framework (CDN-DF), which incorporates controlled vocabularies systematically organized into major classes representing nutritional components and dietary functions. We demonstrate the value of the CDN-DF for comparison of equivalent components between crop species or cultivars, for identifying data gaps and potential for formal meta-analysis. The CDN-DF also enabled us to explore relationships between nutritional components and the functional attributes of food. We have generated a structured crop dietary nutrition data framework, which is generally applicable to the collation and comparison of data relevant to crop researchers, breeders, and other stakeholders, and will facilitate dialogue with nutritionists. It is currently guiding the establishment of a more robust formal ontology. © 2019 Society of Chemical Industry.
Strategy and techniques for mapping horticultural genomes
Publisher: Springer Science and Business Media LLC
Date: 03-1992
DOI: 10.1007/BF02980416
Through a genome, darkly: Comparative analysis of plant chromosomal DNA
Publisher: Springer Science and Business Media LLC
Date: 2002
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.
Genetic analysis of the bracting trait in cauliflower and broccoli
Publisher: Elsevier BV
Date: 05-2003
Distribution of calcium (Ca) and magnesium (Mg) in the leaves of Brassica rapa under varying exogenous Ca and Mg supply
Publisher: Oxford University Press (OUP)
Date: 23-02-2012
DOI: 10.1093/AOB/MCS029
Complete chloroplast genome of Macadamia integrifolia confirms the position of the Gondwanan early-diverging eudicot family Proteaceae
Publisher: Springer Science and Business Media LLC
Date: 12-2014
Relationships between water‐use traits and photosynthesis in Brassica oleracea resolved by quantitative genetic analysis
Publisher: Wiley
Date: 15-11-2005
Progress in mapping agronomic genes in apple (The European Apple Genome Mapping Project)
Publisher: Springer Science and Business Media LLC
Date: 02-1994
DOI: 10.1007/BF02551463
Identification of quantitative trait loci controlling developmental characteristics of Brassica oleracea L.
Publisher: Springer Science and Business Media LLC
Date: 03-2002
Abstract: A segregating population of F(1)-derived doubled haploid (DH) lines of Brassica oleracea was used to detect and locate QTLs controlling 27 morphological and developmental traits, including leaf, flowering, axillary bud and stem characters. The population resulted from a cross between two very different B. oleracea crop types, an annual cauliflower and a biennial Brussels sprout. A principal component analysis (PCA), based on line means, allowed all the traits to be grouped into distinct categories according to the first five Principal Components. These were: leaf traits (PC1), flowering traits (PC2), axillary bud traits (PC3 and 5) and stem traits (PC4). Between zero and four putative QTL were located per trait, which in idually explained between 6% and 43% of the additive genetic variation, using the multiple-marker regression approach to QTL mapping. For lamina width, bare petiole length and stem length two QTL with opposite effects were detected on the same linkage groups. Intra- and inter-specific comparative mapping using RFLP markers identified a QTL on linkage group O8 accounting for variation in vernalisation, which is probably synonymous with a QTL detected on linkage group N19 of Brassica napus. In addition, a QTL for petiole length detected on O3 of this study appeared to be homologous to a QTL detected on another B. oleracea genetic map (Camargo et al. 1995).
Effects of R gene‐mediated resistance in Brassica napus (oilseed rape) on asexual and sexual sporulation of Pyrenopeziza brassicae (light leaf spot)
Publisher: Wiley
Date: 31-08-2011
A Brassica Exon Array for Whole-Transcript Gene Expression Profiling
Publisher: Public Library of Science (PLoS)
Date: 16-09-2010
High-Throughput Sequencing and Mutagenesis to Accelerate the Domestication of Microlaena stipoides as a New Food Crop
Publisher: Public Library of Science (PLoS)
Date: 18-12-2013
Genotypic variation in lysophospholipids of milled rice
Publisher: American Chemical Society (ACS)
Date: 12-09-2014
DOI: 10.1021/JF503213P
Abstract: Phospholipids (PLs) play a prominent role in both grain cellular structure and nutritional function of cereal crops. Their lyso forms (lysophospholipids, LPLs) often combine with cereal starch to form an amylose-lipid complex (ALC), which may influence starch properties. In this study, 20 rice accessions were grown over two seasons at the same location to explore ersity in LPLs of milled rice. Levels of specific LPLs differed significantly among rice genotypes, demonstrating there is a wide ersity in LPLs in rice grain. The main LPL components were lysophosphatidylcholine (LPC) 16:0 (ranging from 3009.7 to 4697.8 μg/g), LPC18:2 (836.6-2182.3 μg/g), lysophosphatidylethanolamine (LPE) 16:0 (625.7-1139.8 μg/g), and LPE18:2 (170.6-481.6 μg/g). Total LPC, total LPE, and total LPL ranged from 4727.1 to 7685.2 μg/g, from 882.8 to 1809.5 μg/g, and from 5609.8 to 9401.1 μg/g, respectively. Although significant (P < 0.001) environment and genotype × environment (G × E) interactions were detected by analysis of variance (ANOVA), these effects accounted for only 0.7-38.9 and 1.8-6.6% of the total variance, respectively. Correlation analysis between LPL components provided insight into the possible LPL biosynthesis pathway in plants. Hierarchical cluster analysis suggested that the 20 rice accessions could be classified into three groups, whereas principal component analysis also identified three groups, with the first two components explaining 57.7 and 16.2% of the total variance. Further genetic studies are needed to identify genes or quantitative trait loci (QTLs) underlying the genetic control of LPLs in rice grain.
The evolution of Brassica napus FLOWERING LOCUST paralogues in the context of inverted chromosomal duplication blocks
Publisher: Springer Science and Business Media LLC
Date: 25-11-2009
Abstract: The gene FLOWERING LOCUS T ( FT ) and its orthologues play a central role in the integration of flowering signals within Arabidopsis and other erse species. Multiple copies of FT , with different cis -intronic sequence, exist and appear to operate harmoniously within polyploid crop species such as Brassica napus (AACC), a member of the same plant family as Arabidopsis . We have identified six BnFT paralogues from the genome of B. napus and mapped them to six distinct regions, each of which is homologous to a common ancestral block (E) of Arabidopsis chromosome 1. Four of the six regions were present within inverted duplicated regions of chromosomes A7 and C6. The coding sequences of BnFT paralogues showed 92-99% identities to each other and 85-87% identity with that of Arabidopsis . However, two of the paralogues on chromosomes A2 and C2, BnA2.FT and BnC2.FT , were found to lack the distinctive CArG box that is located within intron 1 that has been shown in Arabidopsis to be the binding site for theFLC protein. Three BnFT paralogues ( BnA2.FT , BnC6.FT.a and BnC6.FT.b ) were associated with two major QTL clusters for flowering time. One of the QTLs encompassing two BnFT paralogues ( BnC6.FT.a and BnC6.FT.b ) on chromosome C6 was resolved further using near isogenic lines, specific alleles of which were both shown to promote flowering. Association analysis of the three BnFT paralogues across 55 cultivars of B. napus showed that the alleles detected in the original parents of the mapping population used to detect QTL (NY7 and Tapidor) were ubiquitous amongst spring and winter type cultivars of rapeseed. It was inferred that the ancestral FT homologues in Brassica evolved from two distinct copies, one of which was duplicated along with inversion of the associated chromosomal segment prior to the ergence of B. rapa (AA) and B. oleracea (CC). At least ten such inverted duplicated blocks (IDBs) were identified covering a quarter of the whole B. napus genome. Six orthologues of Arabidopsis FT were identified and mapped in the genome of B. napus which sheds new light on the evolution of paralogues in polyploidy species. The allelic variation of BnFT paralogues results in functional differences affecting flowering time between winter and spring type cultivars of oilseed Brassica . The prevalent inverted duplicated blocks, two of which were located by four of the six BnFT paralogues, contributed to gene duplications and might represent predominant pathway of evolution in Brassica .
Contrasting genome organisation: two regions of the <i>Brassica oleracea</i> genome compared with collinear regions of the <i>Arabidopsis</i> <i>thaliana</i> genome
Publisher: Canadian Science Publishing
Date: 2001
DOI: 10.1139/GEN-44-5-808
Development of Selection Indices for Improvement of Seed Yield and Lipid Composition in Bambara Groundnut (Vigna subterranea (L.) Verdc.)
Publisher: MDPI AG
Date: 29-12-2021
Abstract: The underutilised grain legume bambara groundnut (Vigna subterranea) has the potential to contribute significantly to nutritional security. However, the lack of commercial cultivars has hindered its wider adoption and utilisation as a food source. The development of competitive cultivars is impeded by (1) lack of systematic data describing variation in nutritional composition within the gene pool, and (2) a poor understanding of how concentrations of different nutritional components interact. In this study, we analysed seed lipid and protein concentration and lipid composition within a collection of 100 lines representing the global gene pool. Seed protein and lipid varied over twofold with a normal distribution, but no significant statistical correlation was detected between the two components. Seed lipid concentration (4.2–8.8 g/100 g) is primarily determined by the proportion of oleic acid (r2 = 0.45). Yield and composition data for a subset of 40 lines were then used to test selection parameters for high yielding, high lipid breeding lines. From five selection indices tested using 15 scenarios, an index based on the seed number, seed weight, and oleic acid yielded a % expected increase in each of the mean values of seed number, pod dry weight, seed dry weight, and seed size, as well as an expected 7% increase in seed lipid concentration.
Sustainable harvest: Managing plasticity for resilient crops
Publisher: Wiley
Date: 29-05-2014
DOI: 10.1111/PBI.12198
Epigenetic QTL mapping in Brassica napus
Publisher: Oxford University Press (OUP)
Date: 11-2011
DOI: 10.1534/GENETICS.111.131615
Abstract: There is increasing evidence that epigenetic marks such as DNA methylation contribute to phenotypic variation by regulating gene transcription, developmental plasticity, and interactions with the environment. However, relatively little is known about the relationship between the stability and distribution of DNA methylation within chromosomes and the ability to detect trait loci. Plant genomes have a distinct range of target sites and more extensive DNA methylation than animals. We analyzed the stability and distribution of epialleles within the complex genome of the oilseed crop plant Brassica napus. For methylation sensitive AFLP (MSAP) and retrotransposon (RT) epimarkers, we found a high degree of stability, with 90% of mapped markers retaining their allelic pattern in contrasting environments and developmental stages. Moreover, for two distinct parental lines 97% of epialleles were transmitted through five meioses and segregated in a mapping population. For the first time we have established the genetic position for 17 of the 19 centromeres within this hidiploid species. Epiloci and genetic loci were distributed within distinct clusters, indicating differential detection of recombination events. This enabled us to identify additional significant QTL associated with seven important agronomic traits in the centromeric regions of five linkage groups.
Parental genome imbalance in Brassica oleracea causes asymmetric triploid block
Publisher: Wiley
Date: 08-06-2012
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-08-2014
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
Simple sequence repeats reveal uneven distribution of genetic diversity in chloroplast genomes of Brassica oleracea L. and (n = 9) wild relatives
Publisher: Springer Science and Business Media LLC
Date: 02-12-2007
DOI: 10.1007/S00122-006-0461-5
Abstract: Diversity in the chloroplast genome of 171 accessions representing the Brassica 'C' (n = 9) genome, including domesticated and wild B. oleracea and nine inter-fertile related wild species, was investigated using six chloroplast SSR (microsatellite) markers. The lack of ersity detected among 105 cultivated and wild accessions of B. oleracea contrasted starkly with that found within its wild relatives. The vast majority of B. oleracea accessions shared a single haplotype, whereas as many as six haplotypes were detected in two wild species, B. villosa Biv. and B. cretica Lam.. The SSRs proved to be highly polymorphic across haplotypes, with calculated genetic ersity values (H) of 0.23-0.87. In total, 23 different haplotypes were detected in C genome species, with an additional five haplotypes detected in B. rapa L. (A genome n = 10) and another in B. nigra L. (B genome, n = 8). The low chloroplast ersity of B. oleracea is not suggestive of multiple domestication events. The predominant B. oleracea haplotype was also common in B. incana Ten. and present in low frequencies in B. villosa, B. macrocarpa Guss, B. rupestris Raf. and B. cretica. The chloroplast SSRs reveal a wealth of ersity within wild Brassica species that will facilitate further evolutionary and phylogeographic studies of this important crop genus.
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
Publisher: Springer Science and Business Media LLC
Date: 2014
Promoter Variation and Transcript Divergence in Brassicaceae Lineages of FLOWERING LOCUS T
Publisher: Public Library of Science (PLoS)
Date: 11-10-2012
Multiple field and glasshouse assessments increase the reliability of linkage mapping of the Vf source of scab resistance in apple
Publisher: Springer Science and Business Media LLC
Date: 04-1998
Tandem Quadruplication of HMA4 in the Zinc (Zn) and Cadmium (Cd) Hyperaccumulator Noccaea caerulescens
Publisher: Public Library of Science (PLoS)
Date: 10-03-2011
Disruption of a CAROTENOID CLEAVAGE DIOXYGENASE 4 gene converts flower colour from white to yellow in Brassica species
Publisher: Wiley
Date: 17-02-2015
DOI: 10.1111/NPH.13335
Abstract: In Brassica napus , yellow petals had a much higher content of carotenoids than white petals present in a small number of lines, with violaxanthin identified as the major carotenoid compound in yellow petals of rapeseed lines. Using positional cloning we identified a carotenoid cleavage dioxygenase 4 gene, BnaC3 . CCD 4 , responsible for the formation of flower colour, with preferential expression in petals of white‐flowered B. napus lines. Insertion of a CACTA ‐like transposable element 1 ( TE 1) into the coding region of BnaC3 . CCD 4 had disrupted its expression in yellow‐flowered rapeseed lines. α‐Ionone was identified as the major volatile apocarotenoid released from white petals but not from yellow petals. We speculate that BnaC3. CCD 4 may use δ‐ and/or α‐carotene as substrates. Four variations, including two CACTA ‐like TE s (alleles M1 and M4) and two insertion/deletions ( INDEL s, alleles M2 and M3), were identified in yellow‐flowered Brassica oleracea lines. The two CACTA ‐like TE s were also identified in the coding region of BcaC3 . CCD 4 in Brassica carinata . However, the two INDEL s were not detected in B. napus and B. carinata . We demonstrate that the insertions of TE s in BolC3 . CCD 4 predated the formation of the two allotetraploids.
Double haploids, markers and QTL analysis in vegetable brassicas
Publisher: Springer Science and Business Media LLC
Date: 20-06-2008
An auxin signaling gene BnaA3.IAA7 contributes to improved plant architecture and yield heterosis in rapeseed.
Publisher: Wiley
Date: 05-01-2019
DOI: 10.1111/NPH.15632
Abstract: Plant architecture is the key factor affecting overall yield in many crops. The genetic basis underlying plant architecture in rapeseed (Brassica napus), a key global oil crop, is elusive. We characterized an ethyl methanesulfonate (EMS)-mutagenized rapeseed mutant, sca, which had multiple phenotypic alterations, including crinkled leaves, semi-dwarf stature, narrow branch angles and upward-standing siliques. We identified the underlying gene, which encodes an Aux/IAA protein (BnaA3.IAA7). A G-to-A mutation changed the glycine at the 84
Development of a method for the identification of S alleles in Brassica oleracea based on digestion of PCR-amplified DNA with restriction endonucleases
Publisher: Springer Science and Business Media LLC
Date: 05-1993
DOI: 10.1007/BF00227658
High-resolution genetic analysis of the Sd-1 aphid resistance locus in Malus spp.
Publisher: Springer Science and Business Media LLC
Date: 08-2002
DOI: 10.1007/S00122-002-0904-6
Abstract: Aphids cause serious physical and economic damage to most major crops throughout the world through feeding damage, with consequent symptom development and virus transmission. The rosy leaf-curling aphid ( Dysaphis devecta Wlk.) is a pest of apple ( Malus spp.) which displays an exceptionally clear phenotype with respect to susceptible and resistant symptoms. The Sd-1 locus for resistance to D. devecta biotypes 1 and 2 is present in Cox's Orange Pippin and its progeny and had previously been mapped to the top of linkage group 7. Detailed fine mapping of the locus was initiated with AFLP bulked segregant analysis of both pedigree and segregating bulks, which identified three new marker loci. Preliminary marker order in the Sd-1 region was established through mapping in a family derived from Prima x Fiesta, with additional segregation analysis on a Fiesta x Golden Delicious family. Previous recombinant data was re-evaluated and corrected. Two co-segregating AFLP fragments were found to contain a common (GA)(23) repeat, from which a PCR-based simple sequence repeat (SSR) assay was developed. A high-resolution map around the Sd-1 region was established by analysing a large meta-population of Sd-1 recombinants using 759 additional in iduals from different families. The Sd-1 gene has been located within a 1.3-cM interval flanked by the molecular markers SdSSRa and 2B12a and co-locates with the RFLP marker MC064. Allelism between Sd-1 and Sd-2 resistant sources was tested. Molecular markers tightly linked to Sd-1 were shown to be co-segregating with the Sd-2 locus, which indicated that Sd-1 and Sd-2 loci are at least tightly linked and, probably, allelic.
A and C genome distinction and chromosome identification in Brassica napus by sequential fluorescence in situ hybridization and genomic in situ hybridization
Publisher: Oxford University Press (OUP)
Date: 12-2008
DOI: 10.1534/GENETICS.108.095893
Abstract: The two genomes (A and C) of the allopolyploid Brassica napus have been clearly distinguished using genomic in situ hybridization (GISH) despite the fact that the two extant diploids, B. rapa (A, n = 10) and B. oleracea (C, n = 9), representing the progenitor genomes, are closely related. Using DNA from B. oleracea as the probe, with B. rapa DNA and the intergenic spacer of the B. oleracea 45S rDNA as the block, hybridization occurred on 9 of the 19 chromosome pairs along the majority of their length. The pattern of hybridization confirms that the two genomes have remained distinct in B. napus line DH12075, with no significant genome homogenization and no large-scale translocations between the genomes. Fluorescence in situ hybridization (FISH)—with 45S rDNA and a BAC that hybridizes to the pericentromeric heterochromatin of several chromosomes—followed by GISH allowed identification of six chromosomes and also three chromosome groups. Our procedure was used on the B. napus cultivar Westar, which has an interstitial reciprocal translocation. Two translocated segments were detected in pollen mother cells at the pachytene stage of meiosis. Using B. oleracea chromosome-specific BACs as FISH probes followed by GISH, the chromosomes involved were confirmed to be A7 and C6.
Effects of fungicide on growth of Leptosphaeria maculans and L. biglobosa in relation to development of phoma stem canker on oilseed rape (Brassica napus)
Publisher: Wiley
Date: 11-01-2011
A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening
Publisher: Springer Science and Business Media LLC
Date: 09-07-2006
DOI: 10.1038/NG1841
Abstract: A major component in the regulatory network controlling fruit ripening is likely to be the gene at the tomato Colorless non-ripening (Cnr) locus. The Cnr mutation results in colorless fruits with a substantial loss of cell-to-cell adhesion. The nature of the mutation and the identity of the Cnr gene were previously unknown. Using positional cloning and virus-induced gene silencing, here we demonstrate that an SBP-box (SQUAMOSA promoter binding protein-like) gene resides at the Cnr locus. Furthermore, the Cnr phenotype results from a spontaneous epigenetic change in the SBP-box promoter. The discovery that Cnr is an epimutation was unexpected, as very few spontaneous epimutations have been described in plants. This study demonstrates that an SBP-box gene is critical for normal ripening and highlights the likely importance of epialleles in plant development and the generation of natural variation.
Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741)
Publisher: Cold Spring Harbor Laboratory
Date: 27-05-2020
DOI: 10.1101/2020.05.25.114009
Abstract: Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 92% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics.
Breeding histories and selection criteria for oilseed rape in Europe and China identified by genome wide pedigree dissection
Publisher: Springer Science and Business Media LLC
Date: 15-05-2017
DOI: 10.1038/S41598-017-02188-Z
Abstract: Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape ( Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor- bzh . Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees. IBD number and length were greater in the Ningyou7 pedigree than in the Tapidor pedigree. Seventy nine QTLs for flowering time, seed quality and root morphology traits were identified in the IBDs of Tapidor and Ningyou7. Many more candidate genes had been selected within the Ningyou7 pedigree than within the Tapidor pedigree. These results highlight differences in the transfer of favorable gene clusters controlling key traits during selection breeding in Europe and China.
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.
Molecular genetics and breeding of vegetable brassicas
Publisher: Springer Science and Business Media LLC
Date: 10-1990
DOI: 10.1007/BF00023632
Quick on the Uptake: Characterization of a Family of Plant Auxin Influx Carriers
Publisher: Springer Science and Business Media LLC
Date: 09-2001
Shoot yield drives phosphorus use efficiency in Brassica oleracea and correlates with root architecture traits
Publisher: Oxford University Press (OUP)
Date: 03-04-2009
DOI: 10.1093/JXB/ERP083
Abstract: The environmental and financial costs of using inorganic phosphate fertilizers to maintain crop yield and quality are high. Breeding crops that acquire and use phosphorus (P) more efficiently could reduce these costs. The variation in shoot P concentration (shoot-P) and various measures of P use efficiency (PUE) were quantified among 355 Brassica oleracea L. accessions, 74 current commercial cultivars, and 90 doubled haploid (DH) mapping lines from a reference genetic mapping population. Accessions were grown at two or more external P concentrations in glasshouse experiments commercial and DH accessions were also grown in replicated field experiments. Within the substantial species-wide ersity observed for shoot-P and various measures of PUE in B. oleracea, current commercial cultivars have greater PUE than would be expected by chance. This may be a consequence of breeding for increased yield, which is a significant component of most measures of PUE, or early establishment. Root development and architecture correlate with PUE in particular, lateral root number, length, and growth rate. Significant quantitative trait loci associated with shoot-P and PUE occur on chromosomes C3 and C7. These data provide information to initiate breeding programmes to improve PUE in B. oleracea.
Sinapis genomes provide insights into whole‐genome triplication and divergence patterns within tribe Brassiceae
Publisher: Wiley
Date: 16-12-2022
DOI: 10.1111/TPJ.16043
Abstract: Sinapis alba and Sinapis arvensis are mustard crops within the Brassiceae tribe of the Brassicaceae family, and represent an important genetic resource for crop improvement. We performed the de novo assembly of Brassica nigra , S. alba , and S. arvensis , and conducted comparative genomics to investigate the pattern of genomic evolution since an ancient whole‐genome triplication event. Both Sinapis species retained evidence of the Brassiceae whole‐genome triplication approximately 20.5 million years ago (Mya), with subgenome dominance observed in gene density, gene expression, and selective constraint. While S. alba erged from the ancestor of Brassica and Raphanus at approximately 12.5 Mya, the ergence time of S. arvensis and B. nigra was approximately 6.5 Mya. S. arvensis and B. nigra had greater collinearity compared with their relationship to either Brassica rapa or Brassica oleracea . Two chromosomes of S. alba (Sal03 and Sal08) were completely collinear with two ancestral chromosomes proposed in the Ancestral Crucifer Karyotype (ACK) genomic block model, the first time this has been observed in the Brassiceae. These results are consistent with S. alba representing a relatively ancient lineage of the species evolved from the common ancestor of tribe Brassiceae, and suggest that the phylogeny of the Brassica and Sinapis genera requires some revision. Our study provides new insights into the genome evolution and phylogenetic relationships of Brassiceae and provides genomic information for genetic improvement of these plants.
Genetic analysis of potassium use efficiency in Brassica oleracea
Publisher: Oxford University Press (OUP)
Date: 08-10-2010
DOI: 10.1093/AOB/MCP253
Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa
Publisher: Springer Science and Business Media LLC
Date: 09-02-2011
Abstract: The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae . However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available. We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used hidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis , including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa . Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.
Genotypic variation in wheat flour lysophospholipids
Publisher: MDPI AG
Date: 31-05-2017
Characteristics of the Underutilised Pulse Bambara Groundnut (Vigna subterranea (L.) Verdc.) Relevant to Food & Nutritional Security
Publisher: MDPI
Date: 08-04-2020
Realistic image synthesis of plant structures for genetic analysis
Publisher: Elsevier BV
Date: 05-2001
Genetic Elucidation of Glucosinolates in a Diverse Collection of Indian Mustard (Brassica juncea L.)
Publisher: MDPI
Date: 08-04-2020
Genome-wide investigation of genetic changes during modern breeding of Brassica napus
Publisher: Springer Science and Business Media LLC
Date: 20-06-2014
DOI: 10.1007/S00122-014-2343-6
Abstract: Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide ersity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic ersity varied in different sub-groups. Moreover, the genetic ersity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.
Quantitative genetic analysis of seed vigour and pre-emergence seedling growth traits in Brassica oleracea
Publisher: Wiley
Date: 27-11-2000
DOI: 10.1046/J.1469-8137.2000.00760.X
Abstract: The ability of seeds to germinate and establish seedlings in a predictable manner under a range of conditions has a direct contribution to the economic success of commercial crops, and should therefore be considered in crop improvement. We measured traits associated with seed vigour and pre‐emergence seedling growth in a segregating population of 105 doubled haploid Brassica oleracea lines. The germination traits measured were: mean germination times for unstressed germination germination under water stress or germination after a heat treatment and conductivity of seed leachate. The seedling growth traits measured were: seed weight seedling growth rate and seedling size at the end of the exponential growth phase. There were some correlations, notably among germination traits, and between seed weight and pre‐emergence seedling growth. Heritability of the various traits was typically in the 10–15% range, with heritability of conductivity and mean germination time under water stress 25 and 24% respectively. Collectively the results indicate that germination and pre‐emergence seedling growth are under separate genetic control. Quantitative trait loci analyses were carried out on all measurements and revealed significant loci on linkage groups O1, O3, O6, O7 and O9. We suggest that genes at these loci are important in determining predictable seed germination and seedling establishment in practice.
High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus
Publisher: Oxford University Press (OUP)
Date: 08-06-2012
Abstract: Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Firs.p.QTL2.1 to Firs.p.QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Firs.p.QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Firs.p.QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.
High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes
Publisher: Springer Science and Business Media LLC
Date: 12-2011
Abstract: Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa . Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of s les. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA . MET1.a in Brassica rapa . We analysed 12 mutations in BraA.CAX1.a and five in BraA . MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M 3 seed of Brassica rapa from the RevGenUK TILLING service.
Assessing the risk of epidemic dropsy from black salve use
Publisher: Wiley
Date: 30-03-2018
DOI: 10.1002/JAT.3619
Abstract: Epidemic dropsy is a potentially life-threatening condition resulting from the ingestion of argemone oil derived from the seeds of Argemone mexicana Linn. Exposure to argemone oil is usually inadvertent, arising from mustard cooking oil adulteration. Sanguinarine, an alkaloid present in argemone oil, has been postulated as a causative agent with the severity of epidemic dropsy correlating with plasma sanguinarine levels. Cases of epidemic dropsy have also been reported following the topical application of argemone containing massage oil. Black salve, a topical skin cancer therapy also contains sanguinarine, but at significantly higher concentrations than that reported for contaminated massage oil. Although not reported to date, a theoretical risk therefore exists of black salve inducing epidemic dropsy. This literature review explores the presentation and pathophysiology of epidemic dropsy and assesses the risk of it being induced by black salve.
Novel Insights into Seed Fatty Acid Synthesis and Modification Pathways from Genetic Diversity and Quantitative Trait Loci Analysis of the Brassica C Genome
Publisher: Oxford University Press (OUP)
Date: 15-06-2007
Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data
Publisher: F1000 Research Ltd
Date: 15-11-2017
DOI: 10.12688/F1000RESEARCH.11301.2
Abstract: The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users. BIP opens up the opportunity to apply integrative, cross-project analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.
Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data
Publisher: F1000 Research Ltd
Date: 12-04-2017
DOI: 10.12688/F1000RESEARCH.11301.1
Abstract: The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for scientists and breeders. BIP opens up the opportunity to apply big data analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.
Complementing model species with model clades
Publisher: Oxford University Press (OUP)
Date: 12-10-2023
A Hypomethylated population of Brassica rapa for forward and reverse Epi-genetics
Publisher: Springer Science and Business Media LLC
Date: 20-10-2012
Abstract: Epigenetic marks superimposed on the DNA sequence of eukaryote chromosomes provide agility and plasticity in terms of modulating gene expression, ontology, and response to the environment. Modulating the methylation status of cytosine can generate epialleles, which have been detected and characterised at specific loci in several plant systems, and have the potential to generate novel and relatively stable phenotypes. There have been no systematic attempts to explore and utilise epiallelic variation, and so extend the range of phenotypes available for selection in crop improvement. We developed an approach for generating novel epialleles by perturbation of the DNA methylation status. 5- Azacytidine (5-AzaC) provides selective targeting of 5m CG, which in plants is associated with exonic DNA. Targeted chemical intervention using 5-AzaC has advantages over transgenic or mutant modulation of methyltransferases, allowing stochastic generation of epialleles across the genome. We demonstrate the potential of stochastic chemically-induced hypomethylation to generate novel and valuable variation for crop improvement. Systematic analysis of dose–response to 5-AzaC in B. rapa guided generation of a selfed stochastically hypomethylated population, used for forward screening of several agronomic traits. Dose–response was sigmoidal for several traits, similar to that observed for chemical mutagens such as EMS. We demonstrated transgenerational inheritance of some phenotypes. BraRoAZ is a unique hypomethylated population of 1000 E2 sib lines. When compared to untreated controls, 5-Aza C-treated lines exhibited reduced immuno-staining of 5m C on pachytene chromosomes, and Methylation Sensitive Amplified Polymorphism (MSAP) profiles that were both ergent and more variable. There was coincident phenotypic variation among these lines for a range of seed yield and composition traits, including increased seed protein content and decreased oil content, as well as decreased erucic acid and corresponding increases in linoleic and/or palmitic acid. Each 5-AzaC-treated line represents a unique combination of hypomethylated epialleles. The approach and populations developed are available for forward and reverse screening of epiallelic variation and subsequent functional and inheritance studies. The generation of stochastically hypomethylated populations has utility in epiallele discovery for a wide range of crop plants, and has considerable potential as an intervention strategy for crop improvement.
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.
Whole genome shotgun sequences for microsatellite discovery and application in cultivated and wild Macadamia (Proteaceae)
Publisher: Wiley
Date: 31-03-2014
DOI: 10.3732/APPS.1300089
Seed glucosinolate yield is maximized by higher rates of sulfur nutrition than required for seed yield in condiment mustard (Brassica juncea L.)
Publisher: Public Library of Science (PLoS)
Date: 02-04-2019
Perturbation of nutrient source-sink relationships by post-anthesis stresses results in differential accumulation of nutrients in wheat grain
Publisher: Wiley
Date: 14-01-2015
Universal endogenous gene controls for bisulphite conversion in analysis of plant DNA methylation
Publisher: Springer Science and Business Media LLC
Date: 12-2011
Abstract: Accurate analysis of DNA methylation by bisulphite sequencing depends on the complete conversion of all cytosines into uracil. Until now there has been no standard or universal gene identified as an endogenous control to monitor the conversion frequency in plants. Here, we report the development of PCR based assays for one nuclear gene IND ( INDEHISCENT ) and two mitochondrial genes, NAD ( NICOTINAMIDE ADENINE DINUCLEOTIDE ) and ATP1 ( ATPase SUBUNIT 1 ). We demonstrated their efficacy as bisulphite conversion controls in Brassica and other plant taxa. The target regions lified by four primer pairs were found to be consistently free from DNA methylation. Primer pairs for IND.a and NAD were effective within Brassica species, whereas two primer pairs for ATP1 provided reliable controls across a representative range of dicot and monocot angiosperm species. These primer sets may therefore be adopted as controls in plant methylation analysis for a wide range of studies.
Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate
Publisher: Oxford University Press (OUP)
Date: 03-09-2021
Abstract: Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, a panel of 505 erse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 × 106 single-nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27 kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low-phytate variety (LPA20) was significantly elevated compared with a high-phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favourable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.
Enabling reusability of plant phenomic datasets with MIAPPE 1.1
Publisher: Wiley
Date: 25-04-2020
DOI: 10.1111/NPH.16544
Related Organisations
University Of Manchester
Location: United Kingdom of Great Britain and Northern Ireland
University Of Warwick
Location: United Kingdom of Great Britain and Northern Ireland
University Of London
Location: United Kingdom of Great Britain and Northern Ireland
Institute Of Horticultural Research
Location: United Kingdom of Great Britain and Northern Ireland
Rothamsted Research
Location: United Kingdom of Great Britain and Northern Ireland
Horticulture Research International
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
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Start Date: 01-2019
End Date: 03-2022
Amount: $360,000.00
Funder: Australian Research Council
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End Date: 06-2018
Amount: $900,000.00
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View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE140100002
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End Date: 12-2016
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Start Date: 05-2017
End Date: 12-2018
Amount: $1,040,000.00
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View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE140100119
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End Date: 12-2015
Amount: $2,000,000.00
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