Transcriptome-based association genetics in hexaploid wheat

Many crop species have complex genomes, making the conventional pathway to associating molecular markers with trait variation, which includes genome sequencing, both expensive and time-consuming. We used a streamlined approach to rapidly develop a genomics platform for hexaploid wheat based on the inferred order of expressed sequences. This involved assembly of the transcriptomes for the progenitor genomes of bread wheat, the development of a genetic linkage map comprising 9495 mapped transcriptome-based SNP markers, use of this map to rearrange the genome sequence of Brachypodium distachyon into pseudomolecules representative of the genome organization of wheat and sequence similarity-based mapping onto this resource of the transcriptome assemblies. To demonstrate that this approximation of gene order in wheat is appropriate to underpin association genetics analysis, we undertook Associative Transcriptomics for straw biomass traits, identifying associations and even candidate genes for height, weight and width.