ORCID Profile
0000-0001-5868-559X
Current Organisation
University of Queensland
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Conservation and Biodiversity | Horticultural Production not elsewhere classified | Horticultural Production | Agricultural Biotechnology not elsewhere classified | Environmental Science and Management |
Urban and Industrial Flora, Fauna and Biodiversity | Ornamentals, Natives, Flowers and Nursery Plants | Environmentally Sustainable Plant Production not elsewhere classified | Macadamias | Forest and Woodlands Flora, Fauna and Biodiversity
Publisher: Springer Science and Business Media LLC
Date: 08-07-2015
Publisher: Frontiers Media SA
Date: 25-09-2015
Publisher: Public Library of Science (PLoS)
Date: 14-10-2014
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/HR/UHAC157
Abstract: Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80% of the world’s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48 915 avocado genes of which 39 207 could be ascribed functions. The genome contained 62.6% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species erged near or prior to the ergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.
Publisher: Springer Science and Business Media LLC
Date: 19-01-2023
Publisher: MDPI AG
Date: 15-06-2023
Abstract: Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a ‘cadmium-enriched’ parent, ‘P1’, with high cadmium transport and accumulation in the shoot (cadmium root: shoot transfer ratio of 153.75%), and a low-cadmium-accumulation parent, ‘P2’, (with a cadmium transfer ratio of 48.72%) were assessed for Cd concentration using inductively coupled plasma mass spectrometry (ICP-MS). An F2 genetic population was constructed by crossing ‘P1’ with ‘P2’ to map QTL intervals and underlying genes associated with cadmium enrichment. Fifty extremely cadmium-enriched F2 in iduals and fifty extremely low-accumulation F2 in iduals were selected based on cadmium content and cadmium transfer ratio and used for bulk segregant analysis (BSA) in combination with whole genome resequencing. This generated a total of 3,660,999 SNPs and 787,034 InDels between these two segregated phenotypic groups. Based on the delta SNP index (the difference in SNP frequency between the two bulked pools), nine candidate Quantitative trait loci (QTLs) from five chromosomes were identified, and four intervals were validated. RNA sequencing of ‘P1’ and ‘P2’ in response to cadmium was also performed and identified 3502 differentially expressed genes (DEGs) between ‘P1’ and ‘P2’ under Cd treatment. Finally, 32 candidate DEGs were identified within 9 significant mapping intervals, including genes encoding a glutathione S-transferase (GST), a molecular chaperone (DnaJ), and a phosphoglycerate kinase (PGK), among others. These genes are strong candidates for playing an active role in helping rapeseed cope with cadmium stress. Therefore, this study not only sheds new light on the molecular mechanisms of Cd accumulation in rapeseed but could also be useful for rapeseed breeding programs targeting this trait.
Publisher: The Korean Society for Plant Biotechnology
Date: 31-03-2012
Publisher: Isaac Scientific Publishing Co., Ltd.
Date: 05-2020
Publisher: International Society for Horticultural Science (ISHS)
Date: 06-2018
Publisher: Springer Science and Business Media LLC
Date: 05-08-2022
DOI: 10.1007/S13659-022-00351-2
Abstract: Neptunia lexicaulis is an herbaceous legume endemic to the Richmond area in central Queensland, Australia and is one of the strongest known Selenium hyperaccumulators on earth, showing significant potential to be utilised in Se phytoextraction applications. Here a protocol was established for in vitro micropropagation of Se hyperaccumulator N. lexicaulis using nodal segments from in vitro-germinated seedlings. Shoot multiplication was achieved on Murashige and Skoog (MS) basal media supplemented with various concentrations of 6-Benzylaminopurine (BA) (1.0, 2.0, 3.0 mg L −1 ) alone or in combination with low levels of Naphthaleneacetic acid (NAA) (0.1, 0.2, 0.3 mg L −1 ), with 2.0 mg L −1 BA + 0.2 mg L −1 NAA found to be most effective. Elongated shoots were rooted in vitro using NAA, with highest root induction rate of 30% observed at 0.2 mg L −1 NAA. About 95% of the in vitro rooted shoots survived acclimatization. Clonally propagated plantlets were dosed with selenate/selenite solution and assessed for Se tissue concentrations using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES) and found to retain their ability to hyperaccumulate. The protocol developed for this study has potential to be optimised for generating clonal plants of N. lexicaulis for use in research and phytoextraction industry applications.
Publisher: International Society for Horticultural Science (ISHS)
Date: 11-2018
Publisher: Elsevier BV
Date: 12-2019
Publisher: Elsevier BV
Date: 12-2022
Publisher: MDPI
Date: 16-01-2020
Publisher: Elsevier BV
Date: 10-2012
DOI: 10.1016/J.YGENO.2012.07.004
Abstract: The movement of transposable elements (TE) in eukaryotic genomes can often result in the occurrence of nested TEs (the insertion of TEs into pre-existing TEs). We performed a general TE assessment using available databases to detect nested TEs and analyze their characteristics and putative functions in eukaryote genomes. A total of 802 TEs were found to be inserted into 690 host TEs from a total number of 11,329 TEs. We reveal that repetitive sequences are associated with an increased occurrence of nested TEs and sequence biased of TE insertion. A high proportion of the genes which were associated with nested TEs are predicted to localize to organelles and participate in nucleic acid and protein binding. Many of these function in metabolic processes, and encode important enzymes for transposition and integration. Therefore, nested TEs in eukaryotic genomes may negatively influence genome expansion, and enrich the ersity of gene expression or regulation.
Publisher: Wiley
Date: 06-07-2012
DOI: 10.1111/J.1467-7652.2012.00719.X
Abstract: The Brassicaceae contains the most erse collection of agriculturally important crop species of all plant families. Yet, this is one of the few families that do not form functional symbiotic associations with mycorrhizal fungi in the soil for improved nutrient acquisition. The genes involved in this symbiosis were more recently recruited by legumes for symbiotic association with nitrogen-fixing rhizobia bacteria. This study applied second-generation sequencing (SGS) and analysis tools to discover that two such genes, NSP1 (Nodulation Signalling Pathway 1) and NSP2, remain conserved in erse members of the Brassicaceae despite the absence of these symbioses. We demonstrate the utility of SGS data for the discovery of putative gene homologs and their analysis in complex polyploid crop genomes with little prior sequence information. Furthermore, we show how this data can be applied to enhance downstream reverse genetics analyses. We hypothesize that Brassica NSP genes may function in the root in other plant-microbe interaction pathways that were recruited for mycorrhizal and rhizobial symbioses during evolution.
Publisher: International Society for Horticultural Science (ISHS)
Date: 11-2020
Publisher: Elsevier BV
Date: 05-2020
Publisher: Springer Science and Business Media LLC
Date: 08-03-2015
Publisher: Springer International Publishing
Date: 2018
Publisher: Oxford University Press (OUP)
Date: 29-07-2009
Publisher: Proceedings of the National Academy of Sciences
Date: 06-08-2019
Abstract: The avocado, Persea americana , is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently erged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia , and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor ersity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species.
Publisher: Elsevier BV
Date: 06-2016
Publisher: Burleigh Dodds Science Publishing
Date: 10-12-2019
Publisher: Springer Science and Business Media LLC
Date: 22-03-2014
Publisher: MDPI AG
Date: 13-06-2023
Abstract: Reproductively mature horticultural trees undergo an annual flowering cycle that repeats each year of their reproductive life. This annual flowering cycle is critical for horticultural tree productivity. However, the molecular events underlying the regulation of flowering in tropical tree crops such as avocado are not fully understood or documented. In this study, we investigated the potential molecular cues regulating the yearly flowering cycle in avocado for two consecutive crop cycles. Homologues of flowering-related genes were identified and assessed for their expression profiles in various tissues throughout the year. Avocado homologues of known floral genes FT, AP1, LFY, FUL, SPL9, CO and SEP2/AGL4 were upregulated at the typical time of floral induction for avocado trees growing in Queensland, Australia. We suggest these are potential candidate markers for floral initiation in these crops. In addition, DAM and DRM1, which are associated with endodormancy, were downregulated at the time of floral bud break. In this study, a positive correlation between CO activation and FT in avocado leaves to regulate flowering was not seen. Furthermore, the SOC1-SPL4 model described in annual plants appears to be conserved in avocado. Lastly, no correlation of juvenility-related miRNAs miR156, miR172 with any phenological event was observed.
Publisher: Oxford University Press (OUP)
Date: 13-02-2014
DOI: 10.1093/AOB/MCT301
Publisher: MDPI AG
Date: 03-02-2022
Abstract: Heat stress events during flowering in Brassica crops reduce grain yield and are expected to increase in frequency due to global climate change. We evaluated heat stress tolerance and molecular genetic ersity in a global collection of Brassica rapa accessions, including leafy, rooty and oilseed morphotypes with spring, winter and semi-winter flowering phenology. Tolerance to transient daily heat stress during the early reproductive stage was assessed on 142 lines in a controlled environment. Well-watered plants of each genotype were exposed to the control (25/15 °C day/night temperatures) or heat stress (35/25 °C) treatments for 7 d from the first open flower on the main stem. Bud and leaf temperature depression, leaf conductance and chlorophyll content index were recorded during the temperature treatments. A large genetic variation for heat tolerance and sensitivity was found for above-ground biomass, whole plant seed yield and harvest index and seed yield of five pods on the main stem at maturity. Genetic ersity was assessed on 212 lines with 1602 polymorphic SNP markers with a known location in the B. rapa physical map. Phylogenetic analyses confirmed two major genetic populations: one from East and South Asia and one from Europe. Heat stress-tolerant lines were distributed across erse geographic origins, morphotypes (leafy, rooty and oilseed) and flowering phenologies (spring, winter and semi-winter types). A genome-wide association analysis of heat stress-related yield traits revealed 57 SNPs distributed across all 10 B. rapa chromosomes, some of which were associated with potential candidate genes for heat stress tolerance.
Publisher: Springer Science and Business Media LLC
Date: 09-10-2019
DOI: 10.1007/S00705-018-4065-6
Abstract: Australian bean common mosaic virus (BCMV) isolates were sequenced, and the sequences were compared to global BCMV and bean common mosaic necrosis virus (BCMNV) sequences and analysed for conserved potyviral motifs to generate in planta RNA-interference (RNAi) resistance. Thirty-nine out of 40 previously reported potyvirus motifs were conserved among all 77 BCMV/BCMNV sequences. Two RNAi target regions were selected for dsRNA construct design, covering 920 bp of the nuclease inclusion b (NIb) protein and 461 bp of the coat protein (CP). In silico prediction of the effectiveness of these constructs for broad-spectrum defence against the 77 BCMV and BCMNV sequences was done via analysis of putative 21-nucleotide (nt) and 22-nt small-interfering RNAs (siRNAs) generated from the target regions. The effectiveness of both constructs for siRNA generation and BCMV RNAi-mediated resistance was validated in Nicotiana benthamiana transient assays.
Publisher: Cold Spring Harbor Laboratory
Date: 31-05-2019
DOI: 10.1101/654285
Abstract: The avocado, Persea americana , is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently- erged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia , and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced two lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor ersity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species. Avocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings, the admixed nature of Hass, and provide a look at how pathogen interactions have shaped avocado’s more recent genomic evolutionary history.
Publisher: Springer Science and Business Media LLC
Date: 16-07-2015
DOI: 10.1007/S13353-014-0231-Z
Abstract: Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically erse in iduals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the 'omics' of heterosis and the role of non-coding regions, particularly in relation to energy-use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive 'omics' networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.
Publisher: Springer Science and Business Media LLC
Date: 29-01-2010
DOI: 10.1007/S11103-010-9599-2
Abstract: Strigolactones have recently been identified as the long sought-after signal required to inhibit shoot branching (Gomez-Roldan et al. 2008 Umehara et al. 2008 reviewed in Dun et al. 2009). Here we briefly describe the evidence for strigolactone inhibition of shoot branching and, more extensively, the broader context of this action. We address the central question of why strigolactone mutants exhibit a varied branching phenotype across a wide range of experimental conditions. Where knowledge is available, we highlight the role of other hormones in dictating these phenotypes and describe those instances where our knowledge of known plant hormones and their interactions falls considerably short of explaining the phenotypes. This review will focus on bud outgrowth in herbaceous species because knowledge on the role of strigolactones in shoot branching to date barely extends beyond this group of plants.
Publisher: Springer Science and Business Media LLC
Date: 06-2021
Publisher: MDPI AG
Date: 18-01-2022
Abstract: High-quality DNA and RNA forms the basis of genomic and genetic investigations. The extraction of DNA and RNA from woody trees, like avocado (Persea americana Mill.), is challenging due to compounds which interact with nucleic acids and influence separation. Previously reported methods of DNA and RNA extraction from avocado have issues of low yield, quality and applicability across different cultivars and tissue types. In the current study, methods have been optimised for high-quality DNA extraction from 40 avocado cultivars and RNA extraction from multiple tissue types, including roots, stem, leaves, flowers and fruits. The method is based on the modification of the cetyltrimethylammonium bromide buffer, centred around the specific optimisation of chemicals, such as sodium dodecyl sulphate, polyvinylpyrrolidone, sodium sulphite, polyethylene glycol and β-mercaptoethanol. The DNA extraction method yielded high-molecular weight DNA from the leaf tissue of 40 avocado cultivars belonging to Mexican, Guatemalan and West Indian avocado horticultural groups. The method was further optimised for RNA extraction from different avocado plant parts, enabling extraction using amounts as low as ~10 mg of starting material. The DNA and RNA extracted was successfully used for long- and short-read sequencing and gene expression analysis. The methods developed may also be applicable to other recalcitrant plant species.
Publisher: International Society for Horticultural Science (ISHS)
Date: 07-2020
Publisher: Springer Science and Business Media LLC
Date: 05-06-2015
DOI: 10.1038/SREP11087
Abstract: Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was analyzed to provide a holistic overview of secondary metabolism and defense processes in the model medicinal fungus, Ganoderma sinense . We reported the 48.96 Mb genome sequence of G. sinense , consisting of 12 chromosomes and encoding 15,688 genes. More than thirty gene clusters involved in the biosynthesis of secondary metabolites, as well as a large array of genes responsible for their transport and regulation were highlighted. In addition, components of genome defense mechanisms, namely repeat-induced point mutation (RIP), DNA methylation and small RNA-mediated gene silencing, were revealed in G. sinense . Systematic bioinformatic investigation of the genome and methylome suggested that RIP and DNA methylation combinatorially maintain G. sinense genome stability by inactivating invasive genetic material and transposable elements. The elucidation of the G. sinense genome and epigenome provides an unparalleled opportunity to advance our understanding of secondary metabolism and fungal defense mechanisms.
Publisher: Elsevier BV
Date: 12-2018
Publisher: Wiley
Date: 25-05-2012
DOI: 10.1111/J.1438-8677.2011.00481.X
Abstract: The study of the relationship between plants and phytopathogenic fungi is one of the most rapidly moving fields in the plant sciences, the findings of which have contributed to the development of new strategies and technologies to protect crops. Plants employ sophisticated mechanisms to perceive and appropriately defend themselves against pathogens. A good ex le of plant and pathogen evolution is the gene-for-gene interaction between the fungal pathogen Leptosphaeria maculans, the causal agent of blackleg disease, and Brassica crops. This interaction has been studied at the genetic and physiological level due to its agro-economic importance. The newly available genome sequence for Brassica spp. and L. maculans will provide the resources to study the co-evolution of this plant and pathogen. Particularly, an understanding of the co-evolution of genes responsible for virulence and resistance will lead to improved plant protection strategies for Brassica canola and provide a model to understand plant-pathogen interactions in other major crops. This review summarises the research-to-date in the study of the Brassica-L. maculans gene-for-gene interaction, with a focus on the genetics of resistance in Brassica and the wealth of information to be gained from genome sequencing efforts.
Publisher: Springer Science and Business Media LLC
Date: 04-12-2015
DOI: 10.1007/S00425-014-2212-1
Abstract: Twenty-nine genes related to phenolic acid biosynthesis were identified in the Salvia miltiorrhiza genome. Nineteen of these are described for the first time, with ten genes experimentally correlating to phenolic acid biosynthesis. Vast stores of secondary metabolites exist in plants, many of which possess biological activities related to human health. Phenolic acid derivatives are a class of valuable bioactive pharmaceuticals abundant in the widely used Chinese medicinal herb, Salvia miltiorrhiza. The biosynthetic pathway for phenolic acids differs in this species from that of other investigated plants. However, the molecular basis for this is unknown, with systematic analysis of the genes involved not yet performed. As the first step towards unraveling this complex biosynthetic pathway in S. miltiorrhiza, the current genome assembly was searched for putatively involved genes. Twenty-nine genes were revealed, 19 of which are described here for the first time. These include 15 genes predicted in the phenylpropanoid pathway seven genes in the tyrosine-derived pathway six genes encoding putative hydroxycinnamoyltransferases, and one CYP98A, namely CYP98A78. The promoter regions, gene structures and expression patterns of these genes were examined. Furthermore, conserved domains and phylogenetic relationships with homologous proteins in other species were revealed. Most of the key enzymes, including 4-coumarate: CoA ligase, 4-hydroxyphenylpyruvate reductase and hydroxycinnamoyltransferase, were found in multiple copies, each exhibiting different characteristics. Ten genes putatively involved in rosmarinic acid biosynthesis are also described. These findings provide a foundation for further analysis of this complex and erse pathway, with potential to enhance the synthesis of water-soluble medicinal compounds in S. miltiorrhiza.
Publisher: Springer Science and Business Media LLC
Date: 21-06-2013
DOI: 10.1007/S10142-013-0324-5
Abstract: Next generation sequencing technology allows rapid re-sequencing of in iduals, as well as the discovery of single nucleotide polymorphisms (SNPs), for genomic ersity and evolutionary analyses. By sequencing two isolates of the fungal plant pathogen Leptosphaeria maculans, the causal agent of blackleg disease in Brassica crops, we have generated a resource of over 76 million sequence reads aligned to the reference genome. We identified over 21,000 SNPs with an overall SNP frequency of one SNP every 2,065 bp. Sequence validation of a selection of these SNPs in additional isolates collected throughout Australia indicates a high degree of polymorphism in the Australian population. In preliminary phylogenetic analysis, isolates from Western Australia clustered together and those collected from Brassica juncea stubble were identical. These SNPs provide a novel marker resource to study the genetic ersity of this pathogen. We demonstrate that re-sequencing provides a method of validating previously characterised SNPs and analysing differences in important genes, such as the disease related avirulence genes of L. maculans. Understanding the genetic characteristics of this devastating pathogen is vital in developing long-term solutions to managing blackleg disease in Brassica crops.
Publisher: Elsevier
Date: 2020
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.GENE.2013.09.033
Abstract: Helitrons are DNA transposable elements that are widely present in the genomes of erse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs.
Publisher: MDPI AG
Date: 13-10-2022
DOI: 10.3390/IJPB13040035
Abstract: Improving clonal rootstock propagation of avocado has been a major industry/research challenge globally for many decades. Tissue culture has been a focus for clonal propagation with substantial advancements in recent years. In the process of tissue culture, avocado rootstocks display differences in rooting and acclimation capacity. Such differences may relate to the specific structural characteristics of the rootstock. This study aimed to investigate the structural difference during tissue culture in two rootstocks ‘Reed’ and ‘Velvick’, with differing rooting and acclimation capacity. Histological investigations were carried out of stem vasculature, leaves and roots of tissue cultured plantlets. Quantitative parameters stomatal index, stomatal density, trichome density, vein-islet density and vein termination density were also analysed. Prominent fascicular cambium and fewer phloem fibres in stems positively correlated with rooting capacity. Acclimation success positively correlated to the presence of fully differentiated secondary xylem in root. Presence of smaller epidermal cells, high stomatal density and reduced vein termination density was associated with reduced acclimation success. These findings will support optimisation strategies for micropropagation of not only difficult-to-root and difficult-to-acclimate avocado rootstocks, but also, other woody perennials experiencing similar problems.
Publisher: Wiley
Date: 23-06-2012
DOI: 10.1111/J.1467-7652.2012.00716.X
Abstract: A thorough understanding of the relationships between plants and pathogens is essential if we are to continue to meet the agricultural needs of the world's growing population. The identification of genes underlying important quantitative trait loci is extremely challenging in complex genomes such as Brassica napus (canola, oilseed rape or rapeseed). However, recent advances in next-generation sequencing (NGS) enable much quicker identification of candidate genes for traits of interest. Here, we demonstrate this with the identification of candidate disease resistance genes from B. napus for its most devastating fungal pathogen, Leptosphaeria maculans (blackleg fungus). These two species are locked in an evolutionary arms race whereby a gene-for-gene interaction confers either resistance or susceptibility in the plant depending on the genotype of the plant and pathogen. Preliminary analysis of the complete genome sequence of Brassica rapa, the diploid progenitor of B. napus, identified numerous candidate genes with disease resistance characteristics, several of which were clustered around a region syntenic with a major locus (Rlm4) for blackleg resistance on A7 of B. napus. Molecular analyses of the candidate genes using B. napus NGS data are presented, and the difficulties associated with identifying functional gene copies within the highly duplicated Brassica genome are discussed.
Publisher: International Society for Horticultural Science (ISHS)
Date: 07-2020
Publisher: Elsevier BV
Date: 02-2015
DOI: 10.1016/J.GENE.2014.12.029
Abstract: Oilseed rape (Brassica napus) is one of the most important oilseed crops globally. To meet increasing demand for oil-based products, the ability to enhance desirable oil content in the seed is required. This study assessed the capability of five genes in the triacylglyceride (TAG) synthesis pathway to enhance oil content. The genes BnGPDH, BnGPAT, BnDGAT, ScGPDH and ScLPAAT were overexpressed separately in a tobacco (Nicotiana benthamiana) model system, and simultaneously by pyramiding in B. napus, under the control of a seed specific Napin promoter. ScLPAAT transgenic plants showed a significant increase of 6.84% to 8.55% in oil content in tobacco seeds, while a ~4% increase was noted for BnGPDH and BnGPAT transgenic seeds. Seed-specific overexpression of all four genes in B. napus resulted in as high a 12.57% to 14.46% increased in seed oil content when compared to WT, equaling close to the sum of the single-gene overexpression increases in tobacco. Taken together, our study demonstrates that BnGPDH, BnGPAT and ScLPAAT may effectively increase seed oil content, and that simultaneous overexpression of these in transgenic B. napus may further enhance the desirable oil content relative to single-gene overexpressors.
Publisher: Scientific Research Publishing, Inc.
Date: 2017
Publisher: Springer Science and Business Media LLC
Date: 20-08-2010
Abstract: The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR lification of the region in the target genome. The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.
Publisher: Oxford University Press (OUP)
Date: 08-05-2014
DOI: 10.1093/AOB/MCU061
Publisher: Springer Science and Business Media LLC
Date: 03-09-2019
Publisher: Wiley
Date: 28-01-2014
DOI: 10.1111/NPH.12706
Abstract: How do chromosomal regions with differing degrees of homology and homeology interact at meiosis? We provide a novel analytical method based on simple genetics principles which can help to answer this important question. This method interrogates high‐throughput molecular marker data in order to infer chromosome behavior at meiosis in interspecific hybrids. We validated this method using high‐resolution molecular marker karyotyping in two experimental Brassica populations derived from interspecific crosses among B. juncea , B. napus and B. carinata , using a single nucleotide polymorphism chip. This method of analysis successfully identified meiotic interactions between chromosomes sharing different degrees of similarity: full‐length homologs full‐length homeologs large sections of primary homeologs and small sections of secondary homeologs. This analytical method can be applied to any allopolyploid species or fertile interspecific hybrid in order to detect meiotic associations. This genetic information can then be used to identify which genomic regions share functional homeology (i.e., retain enough similarity to allow pairing and segregation at meiosis). When applied to interspecific hybrids for which reference genome sequences are available, the question of how differing degrees of homology and homeology affect meiotic interactions may finally be resolved.
Publisher: Springer Science and Business Media LLC
Date: 22-08-2014
DOI: 10.1007/S10142-014-0391-2
Abstract: Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic ersity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important hidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 s les screened. Although the assay was designed to B. napus, successful SNP lification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus in iduals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 s les.
Publisher: Springer Science and Business Media LLC
Date: 24-09-2013
DOI: 10.1007/S00425-013-1961-6
Abstract: Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.
Publisher: Elsevier BV
Date: 02-2021
Publisher: Springer New York
Date: 03-10-2015
DOI: 10.1007/978-1-4939-1966-6_2
Abstract: In iduals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.
Publisher: Elsevier BV
Date: 12-2022
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.
Publisher: International Society for Horticultural Science (ISHS)
Date: 06-2018
Publisher: International Society for Horticultural Science (ISHS)
Date: 09-2013
Publisher: MDPI AG
Date: 12-04-2019
Abstract: Recent development and implementation of crop cryopreservation protocols has increased the capacity to maintain recalcitrant seeded germplasm collections via cryopreserved in vitro material. To preserve the greatest possible plant genetic resources globally for future food security and breeding programs, it is essential to integrate in situ and ex situ conservation methods into a cohesive conservation plan. In vitro storage using tissue culture and cryopreservation techniques offers promising complementary tools that can be used to promote this approach. These techniques can be employed for crops difficult or impossible to maintain in seed banks for long-term conservation. This includes woody perennial plants, recalcitrant seed crops or crops with no seeds at all and vegetatively or clonally propagated crops where seeds are not true-to-type. Many of the world’s most important crops for food, nutrition and livelihoods, are vegetatively propagated or have recalcitrant seeds. This review will look at ex situ conservation, namely field repositories and in vitro storage for some of these economically important crops, focusing on conservation strategies for avocado. To date, cultivar-specific multiplication protocols have been established for maintaining multiple avocado cultivars in tissue culture. Cryopreservation of avocado somatic embryos and somatic embryogenesis have been successful. In addition, a shoot-tip cryopreservation protocol has been developed for cryo-storage and regeneration of true-to-type clonal avocado plants.
Publisher: Wiley
Date: 20-12-2014
DOI: 10.1111/PPL.12131
Abstract: Dietary consumption of functional foods enriched in anthocyanins benefit for human health by protection against far-ranging human diseases. Delphinidin-derived anthocyanins (valuable as blue pigments and antioxidants) are accumulated specifically in the fruits of Lycium ruthenicum but not in the fruits of Lycium barbarum, suggesting the differences of anthocyanin biosynthesis between the two species. In this study, anthocyanin profiling confirmed that anthocyanins were increasingly accumulated during fruit ripening in L. ruthenicum, and sharply increased at full expanded mature fruit, while no anthocyanin were detected at any stage of L. barbarum fruit development. Several genes involved in anthocyanin biosynthesis were characterized in L. ruthenicum and L. barbarum fruits. Expression profiling of these genes during fruit development showed a significant positive correlation between transcript abundance and anthocyanin accumulation in L. ruthenicum fruit. Meanwhile, transcripts in L. barbarum fruit were either undetectable or were downregulated during fruit ripening, before increasing slightly in the final stages of maturation. In addition, the ratio of LrF3'5H/LrF3'H transcription showed a gradual increase before 6 days after breaker (DAB) and a sharp enhancement at 10 DAB. Our results suggest that the expression patterns of both regulatory and structural genes and the transcriptional ratio of branch-node structural genes F3'5'H/F3'H may determine the phenotypic difference in anthocyanin biosynthesis between L. ruthenicum and L. barbarum fruits.
Start Date: 10-2021
End Date: 10-2025
Amount: $308,032.00
Summary: Novel Propagation and Conservation Technologies for Australian Macadamia. Australia’s $850M macadamia industry is a booming contributor to regional growth with a strong domestic market niche. However the industry is threatened by a severe plant supply bottleneck. Also wild germplasm for breeding is threatened with extinction. This project aims to innovate world-first tissue culture technologies for macadamia propagation and secure cryo-storage of germplasm, aided by cutting edge genomics. Expect .... Novel Propagation and Conservation Technologies for Australian Macadamia. Australia’s $850M macadamia industry is a booming contributor to regional growth with a strong domestic market niche. However the industry is threatened by a severe plant supply bottleneck. Also wild germplasm for breeding is threatened with extinction. This project aims to innovate world-first tissue culture technologies for macadamia propagation and secure cryo-storage of germplasm, aided by cutting edge genomics. Expected outcomes of these new, cross-disciplinary techniques are on-demand supply of superior trees to growers and the protection of invaluable germplasm. This should provide significant benefits for industry growth, food security and conservation de-risked from global change. Read more Read less
Funder: Australian Research Council
View Funded ActivityStart Date: 02-2023
End Date: 01-2027
Amount: $710,423.00
Summary: Cryobiotechnology innovations to help fight the Myrtle rust pandemic. This project aims to mitigate the impacts of Myrtle rust, a disease affecting >380 Australian taxa in the family Myrtaceae, by developing advanced techniques to conserve susceptible species. The project is expected to generate the biotechnology advances necessary to conserve multiple taxa on the brink of extinction, including species important to our emerging native botanicals industry. Expected outcomes for the project includ .... Cryobiotechnology innovations to help fight the Myrtle rust pandemic. This project aims to mitigate the impacts of Myrtle rust, a disease affecting >380 Australian taxa in the family Myrtaceae, by developing advanced techniques to conserve susceptible species. The project is expected to generate the biotechnology advances necessary to conserve multiple taxa on the brink of extinction, including species important to our emerging native botanicals industry. Expected outcomes for the project include novel protocols for initiating and maintaining sterile tissue cultures and advanced techniques for cryopreservation of susceptible species, providing insurance against extinction and sources of ex situ material for re-establishing the species in safe sites and for research into disease resistance. Read more Read less
Funder: Australian Research Council
View Funded Activity