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  • 1
    Language: English
    In: Molecular breeding, 2019-07-20, Vol.39 (8), p.112-13
    Description: Clubroot is a destructive soil-borne pathogen of Brassicaceae that causes significant recurrent reductions in yield of cruciferous crops. Although there is some resistance in oilseed rape (a crop type of the species Brassica napus ), the genetic basis of that resistance is poorly understood. In this study, we used an associative transcriptomics approach to elucidate the genetic basis of resistance to clubroot pathotype ECD 17/31/31 across a genetic diversity panel of 245 accessions of B. napus . A single nucleotide polymorphism (SNP) association analysis was performed with 256,397 SNPs distributed across the genome of B. napus and combined with transcript abundance data of 53,889 coding DNA sequence (CDS) gene models. The SNP association analysis identified two major loci (on chromosomes A2 and A3) controlling resistance and seven minor loci. Within these were a total of 86 SNP markers. Altogether, 392 genes were found in these regions. Another 21 genes were implicated as potentially involved in resistance using gene expression marker (GEM) analysis. After GO enrichment analysis and InterPro functional analysis of the identified genes, 82 candidate genes were identified as having roles in clubroot resistance. These results provide useful information for marker-assisted breeding which could lead to acceleration of pyramiding of multiple clubroot resistance genes in new varieties.
    Subject(s): Acceleration ; Agriculture ; Agronomy ; Analysis ; Anopheles ; Article ; Association analysis ; Association genetics ; Biological diversity ; Biomedical and Life Sciences ; Biotechnology ; Brassica ; Brassica napus ; Breeding ; Chromosomes ; Clubroot ; Crop yield ; Crops ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Functional analysis ; Gene expression ; Genes ; Genetic analysis ; Genetic diversity ; Genetic research ; Genetics & Heredity ; Genomes ; Genomics ; Horticulture ; Life Sciences ; Life Sciences & Biomedicine ; Loci ; Nucleotide sequence ; Nucleotide sequencing ; Nucleotides ; Plant Genetics and Genomics ; Plant Pathology ; Plant Physiology ; Plant Sciences ; Polymorphism ; Rape plants ; Rapeseed ; Science & Technology ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Transcription ; Transcriptomics
    ISSN: 1380-3743
    E-ISSN: 1572-9788
    Source: Academic Search Ultimate
    Source: Web of Science - Science Citation Index Expanded - 2019〈img src="http://exlibris-pub.s3.amazonaws.com/fromwos-v2.jpg" /〉
    Source: Alma/SFX Local Collection
    Source: ProQuest Central
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  • 2
    Language: English
    In: The Plant journal : for cell and molecular biology, 2018-01, Vol.93 (1), p.181-192
    Description: Summary An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single‐nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high‐erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor‐effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take‐one‐out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ‐tocopherol methyl transferase converting γ‐tocopherol into α‐tocopherol) associated with the observed trait variation. The establishment of the first full‐scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops. Significance Statement The availability of a full‐scale association genetics platform for Brassica napus, based on functional genotypes, enables the genetic architecture of essentially any trait to be addressed in this important crop species.
    Subject(s): Acids ; Architecture ; association genetics ; Biological diversity ; Brass plating ; Brassica ; Brassica napus ; Crops ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; erucic acid ; Gene expression ; Gene polymorphism ; Genetic diversity ; Genetic research ; Genetics ; Genomics ; Genotype & phenotype ; Genotypes ; Loci ; Markers ; Nucleotide sequence ; Nucleotide sequencing ; Polymorphism ; Polyploidy ; Rape plants ; Rapeseed ; Rapeseed oil ; Resource ; Seeds ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Species ; Surgery ; Tocopherol ; Tocopherols ; Transcription ; transcriptomics ; Unsaturated fatty acids ; Variation ; Vitamin E
    ISSN: 0960-7412
    E-ISSN: 1365-313X
    Source: Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals
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  • 3
    Language: English
    In: Science (American Association for the Advancement of Science), 2018-10-19, Vol.362 (6412), p.343-347
    Description: Morphinan-based painkillers are derived from opium poppy ( L.). We report a draft of the opium poppy genome, with 2.72 gigabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 1.77 and 204 megabases, respectively. Synteny analysis suggests a whole-genome duplication at ~7.8 million years ago and ancient segmental or whole-genome duplication(s) that occurred before the Papaveraceae-Ranunculaceae divergence 110 million years ago. Syntenic blocks representative of phthalideisoquinoline and morphinan components of a benzylisoquinoline alkaloid cluster of 15 genes provide insight into how this cluster evolved. Paralog analysis identified P450 and oxidoreductase genes that combined to form the gene fusion essential for morphinan biosynthesis in opium poppy. Thus, gene duplication, rearrangement, and fusion events have led to evolution of specialized metabolic products in opium poppy.
    Subject(s): Addiction ; Analgesics ; Benzylisoquinolines - metabolism ; Biological evolution ; Biosynthesis ; Chemical properties ; Chromosomes ; Clusters ; Divergence ; Drug abuse ; Drug trafficking ; Evolution, Molecular ; Gene Duplication ; Gene Fusion ; Gene Order ; Gene rearrangement ; Genes ; Genetic aspects ; Genome, Plant ; Genomes ; Metabolism ; Morphinans - metabolism ; Multigene Family ; NADPH-Ferrihemoprotein Reductase - genetics ; Narcotics ; Opiates ; Opioids ; Opium poppy ; Oxidoreductase ; Papaver - genetics ; Papaver - metabolism ; Papaver somniferum ; Phthalideisoquinoline ; Plant Proteins - genetics ; Production processes ; Proteins ; Reproduction (copying) ; Synteny
    ISSN: 0036-8075
    E-ISSN: 1095-9203
    Source: Academic Search Ultimate
    Source: Alma/SFX Local Collection
    Source: Get It Now
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  • 4
    Language: English
    In: The Plant cell, 2011-02-01, Vol.23 (2), p.583-599
    Description: Arabidopsis thaliana COMATOSE (CTS) encodes an ABC transporter involved in peroxisomal import of substrates for β-oxidation. Various cts alleles and mutants disrupted in steps of peroxisomal β-oxidation have previously been reported to exhibit a severe block on seed germination. Oxylipin analysis on cts, acyl CoA oxidase1 acyl CoA oxidase2 (acx1 acx2), and keto acyl thiolase2 dry seeds revealed that they contain elevated levels of 12-oxo-phytodienoic acid (OPDA), jasmonic acid (JA), and JA-lle. Oxylipin and transcriptomic analysis showed that accumulation of these oxylipins occurs during late seed maturation in cts. Analysis of double mutants generated by crossing cts with mutants in the JA biosynthesis pathway indicate that OPDA, rather than JA or JA-lle, contributes to the block on germination in cts seeds. We found that OPDA was more effective at inhibiting wild-type germination than was JA and that this effect was independent of CORONATINE INSENSITIVE1 but was synergistic with abscisic acid (ABA). Consistent with this, OPDA treatment increased ABA INSENSITIVE5 protein abundance in a manner that parallels the inhibitory effect of OPDA and OPDA+ABA on seed germination. These results demonstrate that OPDA acts along with ABA to regulate seed germination in Arabidopsis.
    Subject(s): Abscisic Acid - metabolism ; Analysis ; Arabidopsis - drug effects ; Arabidopsis - genetics ; Arabidopsis - growth & development ; Arabidopsis thaliana ; Baker, Alison ; Biosynthesis ; Cyclopentanes - metabolism ; Endosperm ; Fatty acids ; Fatty Acids, Unsaturated - pharmacology ; Gene expression regulation ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Genes ; Germination ; Germination - drug effects ; Mutation ; Oxylipins - metabolism ; Phenotypes ; Plant cells ; Seed germination ; Seeds ; Seeds - drug effects ; Seeds - growth & development
    ISSN: 1040-4651
    E-ISSN: 1532-298X
    Source: JSTOR Life Sciences
    Source: JSTOR Ecology & Botany II
    Source: Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals
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  • 5
    Language: English
    In: BMC genomics, 2021-07-13, Vol.22 (1), p.539-539
    Description: Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood. Here, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC.C2 as a further candidate for vernalisation response. This study describes a new pipeline for performing associative transcriptomics studies in B. oleracea. Using flowering time as an example trait, it provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2. These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields.
    Subject(s): Analysis ; Associative Transcriptomics ; Brassica ; Brassica - genetics ; Brassica napus - genetics ; Brassica oleracea ; Breeding ; Cauliflower ; Environmental conditions ; Flowering ; Gene expression ; Genetic aspects ; Genetic engineering ; Genetic resources ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Growth ; GWAS ; Incompatibility ; Markers ; Phenotyping ; Physiological aspects ; Pipelines ; Plant Breeding ; Plants, Flowering of ; Population ; Population Structure ; Research ; RNA sequencing ; Self-incompatibility ; Synchronism ; Transcriptome ; Vegetables ; Vernalisation
    ISSN: 1471-2164
    E-ISSN: 1471-2164
    Source: BioMedCentral Open Access
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 6
    Language: English
    In: Plant biotechnology journal, 2019-10, Vol.17 (10), p.1998-2010
    Description: Summary Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large‐scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double‐low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double‐low and double‐high), accompanied by an increase in genetic load in the double‐low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra‐ and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.
    Subject(s): Adaptation ; allopolyploid ; Asia ; Asian rapeseed ; Biological evolution ; Biotechnology & Applied Microbiology ; Brassica ; Brassica napus ; Brassica napus - genetics ; Brassica rapa - genetics ; Chromosomes ; Crops ; Cultivars ; deleterious variations ; Domestication ; Europe ; Footprints ; Gene sequencing ; Genetic load ; Genome, Plant ; Genomes ; Genomics ; Hybridization ; Hybridization, Genetic ; introgression ; Life Sciences & Biomedicine ; Nucleotides ; Oilseeds ; Phenotype ; Plant Breeding ; Plant Sciences ; Polymorphism ; Population ; R&D ; Rapeseed ; Research & development ; Science & Technology ; selection footprints ; Selective breeding ; Single-nucleotide polymorphism ; Tetraploidy
    ISSN: 1467-7644
    E-ISSN: 1467-7652
    Source: Academic Search Ultimate
    Source: Web of Science - Science Citation Index Expanded - 2019〈img src="http://exlibris-pub.s3.amazonaws.com/fromwos-v2.jpg" /〉
    Source: ProQuest Central
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  • 7
    Language: English
    In: Plant biotechnology journal, 2017-05, Vol.15 (5), p.594-604
    Description: Summary Polyploidy, the possession of multiple sets of chromosomes, has been a predominant factor in the evolution and success of the angiosperms. Although artificially formed allopolyploids show a high rate of genome rearrangement, the genomes of cultivars and germplasm used for crop breeding were assumed stable and genome structural variation under the artificial selection process of commercial breeding has remained little studied. Here, we show, using a repurposed visualization method based on transcriptome sequence data, that genome structural rearrangement occurs frequently in varieties of three polyploid crops (oilseed rape, mustard rape and bread wheat), meaning that the extent of genome structural variation present in commercial crops is much higher than expected. Exchanges were found to occur most frequently where homoeologous chromosome segments are collinear to telomeres and in material produced as doubled haploids. The new insights into genome structural evolution enable us to reinterpret the results of recent studies and implicate homoeologous exchanges, not deletions, as being responsible for variation controlling important seed quality traits in rapeseed. Having begun to identify the extent of genome structural variation in polyploid crops, we can envisage new strategies for the global challenge of broadening crop genetic diversity and accelerating adaptation, such as the molecular identification and selection of genome deletions or duplications encompassing genes with trait‐controlling dosage effects.
    Subject(s): Brassica napus - genetics ; Brassica rapa - genetics ; Computational Biology - methods ; crop genomes ; Crops ; Crops, Agricultural - genetics ; genome structural evolution ; Genome, Plant ; Genomes ; mRNAseq ; Polyploidy ; RNA, Messenger ; Sequence Analysis, RNA - methods ; Triticum - genetics ; Triticum aestivum
    ISSN: 1467-7644
    E-ISSN: 1467-7652
    Source: Academic Search Ultimate
    Source: ProQuest Central
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  • 8
    Language: English
    In: Science (American Association for the Advancement of Science), 2012-06-29, Vol.336 (6089), p.1704-1708
    Description: Noscapine is an antitumor alkaloid from opium poppy that binds tubulin, arrests metaphase, and induces apoptosis in dividing human cells. Elucidation of the biosynthetic pathway will enable improvement in the commercial production of noscapine and related bioactive molecules. Transcriptomic analysis revealed the exclusive expression of 10 genes encoding five distinct enzyme classes in a high noscapine-producing poppy variety, HN1. Analysis of an F₂ mapping population indicated that these genes are tightly linked in HN1, and bacterial artificial chromosome sequencing confirmed that they exist as a complex gene cluster for plant alkaloids. Virus-induced gene silencing resulted in accumulation of pathway intermediates, allowing gene function to be linked to noscapine synthesis and a novel biosynthetic pathway to be proposed.
    Subject(s): Alkaloids ; Anticancer properties ; Antineoplastic Agents, Phytogenic - biosynthesis ; Biological and medical sciences ; Biosynthesis ; Capsules ; Classical genetics, quantitative genetics, hybrids ; Clusters ; Cough ; Enzymes ; Flowers & plants ; Fundamental and applied biological sciences. Psychology ; Gene silencing ; Genes ; Genes, Plant ; Genetic aspects ; Genetics of eukaryotes. Biological and molecular evolution ; Genomes ; Latex ; Libraries ; Low level ; Molecular Sequence Data ; Morphinans ; Multigene Family ; Narcotics ; Noscapine - metabolism ; Open reading frames ; Papaver - enzymology ; Papaver - genetics ; Papaver - metabolism ; Papaver somniferum ; Pharmaceutical sciences ; Physiological aspects ; Plant biology ; Poppies ; Pteridophyta, spermatophyta ; REPORTS ; Research ; Synthesis ; Vegetals
    ISSN: 0036-8075
    E-ISSN: 1095-9203
    Source: JSTOR Life Sciences
    Source: Academic Search Ultimate
    Source: Alma/SFX Local Collection
    Source: Get It Now
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  • 9
    Language: English
    In: Nature (London), 2017-01-12, Vol.541 (7636), p.212-216
    Description: Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we re-analyse association transcriptomic data, yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.
    Subject(s): Ascomycota - pathogenicity ; Biological diversity ; Conserved Sequence - genetics ; Denmark ; DNA sequencing ; Fraxinus - genetics ; Fraxinus - microbiology ; Genes, Plant - genetics ; Genetic Predisposition to Disease - genetics ; Genetic Variation ; Genome, Plant - genetics ; Genomics ; Iridoid Glycosides - metabolism ; Methods ; Nucleotide sequencing ; Observations ; Plant Diseases - genetics ; Plant Diseases - microbiology ; Plant Diseases - prevention & control ; Plant Proteins - genetics ; Population Density ; Sequence Analysis, DNA ; Species Specificity ; Transcriptome ; Trees - genetics ; Trees - microbiology ; United Kingdom
    ISSN: 0028-0836
    E-ISSN: 1476-4687
    Source: Get It Now
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  • 10
    Language: English
    In: Plant biotechnology journal, 2016-05, Vol.14 (5), p.1207-1214
    Description: Summary Using a combination of de novo transcriptome assembly, a newly developed 9495‐marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of nonredundant transcripts for each of the subgenomes of hexaploid wheat: A (47 160 unigenes), B (59 663 unigenes) and D (40 588 unigenes). We used these as reference sequences against which to map Illumina mRNA‐Seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a three‐way reciprocal BLAST approach, 15 527 triplet sets of homoeologues (one from each genome) were identified. Differential expression (P 〈 0.05) was identified for 5248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genomewide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome display tile plot, a visualization approach based on CMYK colour space, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).
    Subject(s): Abundance ; Analysis ; Barley ; Bread ; bread wheat ; Chromosomes ; differential expression ; Dominance ; Gene expression ; Gene Expression Regulation, Plant ; Gene mapping ; Gene Ontology ; Gene sequencing ; Genes ; Genetic engineering ; Genetic research ; genome dominance ; Genome, Plant - genetics ; Genomes ; Genomics ; Goat grass ; Hybridization ; Kinases ; Leaves ; Plant Leaves - genetics ; RNA ; Sequence Homology ; Single-nucleotide polymorphism ; Striations ; Transcription ; Transcriptome ; Triticum - genetics ; Triticum aestivum ; Wheat
    ISSN: 1467-7644
    E-ISSN: 1467-7652
    Source: Academic Search Ultimate
    Source: ProQuest Central
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