Associative transcriptomics of traits in the polyploid crop species Brassica napus

Sequencing a genome and identifying genetic markers lays the groundwork for genome-wide association studies, but can be difficult to achieve for polyploid species. Harper et al. present an approach for performing association studies using genetic maps and markers generated from transcriptome sequenc...

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Published in	Nature biotechnology Vol. 30; no. 8; pp. 798 - 802
Main Authors	HARPER, Andrea L, TRICK, Martin, HIGGINS, Janet, FRASER, Fiona, CLISSOLD, Leah, WELLS, Rachel, HATTORI, Chie, WERNER, Peter, BANCROFT, Ian
Format	Journal Article
Language	English
Published	New York, NY Nature Publishing Group 01.08.2012
Subjects	Agronomy. Soil science and plant productions Arabidopsis Arabidopsis thaliana Biological and medical sciences Biomarkers Biotechnology Brassica napus Brassica napus - genetics Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling - methods Genes Genetic aspects Genetic markers Genetic Markers - genetics Genetic research Genetics Genome-Wide Association Study - methods Genomes Genomics Genomics - methods Physiological aspects Plant Proteins - genetics Polyploidy Quantitative genetics Quantitative Trait Loci Rape (Plant) RNA Seeds Single nucleotide polymorphisms Transcription Factors - genetics Transcriptome United Kingdom Polyploidy Cruciferae Transcriptomics Dicotyledones Angiospermae Marker assisted selection Transcriptome Brassica napus Spermatophyta Molecular marker Cultivated plant
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Abstract	Sequencing a genome and identifying genetic markers lays the groundwork for genome-wide association studies, but can be difficult to achieve for polyploid species. Harper et al. present an approach for performing association studies using genetic maps and markers generated from transcriptome sequencing data alone and apply it to the polyploid crop Brassica napus.
AbstractList	Sequencing a genome and identifying genetic markers lays the groundwork for genome-wide association studies, but can be difficult to achieve for polyploid species. Harper et al. present an approach for performing association studies using genetic maps and markers generated from transcriptome sequencing data alone and apply it to the polyploid crop Brassica napus. Association genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. But most crops are polyploid, making it difficult to identify the required markers and to assemble a genome sequence to order those markers. To circumvent this difficulty, we developed associative transcriptomics, which uses transcriptome sequencing to identify and score molecular markers representing variation in both gene sequences and gene expression, and correlate this with trait variation. Applying the method in the recently formed tetraploid crop Brassica napus, we identified genomic deletions that underlie two quantitative trait loci for glucosinolate content of seeds. The deleted regions contained orthologs of the transcription factor HAG1 (At5g61420), which controls aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. This approach facilitates the application of association genetics in a broad range of crops, even those with complex genomes.
Audience	Academic
Author	CLISSOLD, Leah WERNER, Peter HATTORI, Chie HARPER, Andrea L FRASER, Fiona BANCROFT, Ian WELLS, Rachel TRICK, Martin HIGGINS, Janet
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Keywords	Polyploidy Cruciferae Transcriptomics Dicotyledones Angiospermae Marker assisted selection Transcriptome Brassica napus Spermatophyta Molecular marker Cultivated plant
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Snippet	Sequencing a genome and identifying genetic markers lays the groundwork for genome-wide association studies, but can be difficult to achieve for polyploid... Association genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by...
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SubjectTerms	Agronomy. Soil science and plant productions Arabidopsis Arabidopsis thaliana Biological and medical sciences Biomarkers Biotechnology Brassica napus Brassica napus - genetics Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling - methods Genes Genetic aspects Genetic markers Genetic Markers - genetics Genetic research Genetics Genome-Wide Association Study - methods Genomes Genomics Genomics - methods Physiological aspects Plant Proteins - genetics Polyploidy Quantitative genetics Quantitative Trait Loci Rape (Plant) RNA Seeds Single nucleotide polymorphisms Transcription Factors - genetics Transcriptome
Title	Associative transcriptomics of traits in the polyploid crop species Brassica napus
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