Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Associative Transcriptomics in the polyploid crop species Brassica napus

ABSTRACT: Association Genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. The requirements for many markers and a genome sequence to order those markers have limited its exploitation in crops. To harness this approach for use in a broad range of crops, even those with complex genomes, we developed an approach based on transcriptome sequencing to exploit markers representing variation in both gene sequences and gene expression. We term this approach Associative Transcriptomics. Applying it successfully in Brassica napus, as an example, we identified that genomic deletions including orthologues of the transcription factor controlling aliphatic glucosinolate biosynthesis in Arabidopsis thaliana, HAG1 (At5g61420), underlie two QTL for glucosinolate content of seeds.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Brassica oleracea var. alboglabra

SUBMITTER: Robert Davey 

PROVIDER: E-MTAB-4309 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus.

Lu Guangyuan G   Harper Andrea L AL   Trick Martin M   Morgan Colin C   Fraser Fiona F   O'Neill Carmel C   Bancroft Ian I  

DNA research : an international journal for rapid publication of reports on genes and genomes 20140715 6

Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed 'associative transcriptomics' (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the iden  ...[more]

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