Associative transcriptomics of traits in the polyploid crop species 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, John Innes Centre has developed associative transcriptomics, which uses transcriptome sequencing to identify and score molecular markers (SNPs) 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, the research team at JIC (Harper AL, Trick M, Higgins J, Fraser F, Clissold L, Wells R, Hattori C, Werner P, Bancroft I.) has 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.

See the abstract at Pubmed

Association Mapping in Plants

Association (linkage disequilibrium [LD]) studies represent a novel powerful approach to evaluate candidate genes regulating plant phenotype and identify alleles of key interest at these genes. It is based on correlation between gene sequence and plant performance for target traits, and represent a powerful approach to evaluate candidate genes regulating the plant phenotype.

This new technique takes into account the thousands of genes to evaluate for QTL effect and is a more efficient approach that does not require generation of segregating populations/large numbers of progeny. As it can utilize all of the historic recombination events in a diverse population of individuals it can generate higher resolution genetic maps and, is needed to complement current map based cloning methods.