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.
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We thank The Genome Analysis Centre for generating Illumina sequence data. This work was supported by UK Biotechnology and Biological Sciences Research Council (BBSRC BB/H004351/1 (IBTI Club), BB/E017363/1, ERAPG08.008) and UK Department for Environment, Food and Rural Affairs (Defra IF0144). We would like to thank R. Snowdon, J. Barker and G. Teakle for providing germplasm. We would like to thank D. Manning and M. Turner of KWS-UK and P. Tillmann of Verband Deutscher Landwirtschaftlicher Untersuchungs und Forschungsanstalten (VDLUFA) Qualitatssicherung NIRS/NIT, Kassel, Germany, for their assistance with NIRS measurements.
The authors declare no competing financial interests.
Supplementary Figures 1–7 (PDF 11057 kb)
B. rapa and B. oleracea genome scaffolds forming the B. napus pseudomolecules (XLSX 93 kb)
Coordinates for splitting of Brassica rapa and Brassica oleracea genome assembly scaffolds (XLSX 14 kb)
Unigene-based map of the Brassica napus genome (XLSX 9050 kb)
Brassica napus accessions (XLSX 11 kb)
mRNAseq coverage data (XLSX 16 kb)
GWAS data matrix for 84 Brassica napus accessions (XLSX 22226 kb)
NIRS data for 53 accessions (XLSX 13 kb)
Structure Q matrix for K=2 populations (XLSX 12 kb)
WGCNA analysis (XLSX 39 kb)
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Harper, A., Trick, M., Higgins, J. et al. Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 30, 798–802 (2012) doi:10.1038/nbt.2302
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