Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits

The development of more productive crops will be key to addressing the challenges that climate change, population growth and diminishing resources pose to global food security. Advanced ‘omics techniques can help to accelerate breeding by facilitating the identification of genetic markers for use in marker‐assisted selection. Here, we present the validation of a new Associative Transcriptomics platform in the important oilseed crop Brassica juncea. To develop this platform, we established a pan‐transcriptome reference for B. juncea, to which we mapped transcriptome data from a diverse panel of B. juncea accessions. From this panel, we identified 355 050 single nucleotide polymorphism variants and quantified the abundance of 93 963 transcripts. Subsequent association analysis of functional genotypes against a number of important agronomic and quality traits revealed a promising candidate gene for seed weight, BjA.TTL, as well as additional markers linked to seed colour and vitamin E content. The establishment of the first full‐scale Associative Transcriptomics platform for B. juncea enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops. Significance Statement We present the development of a new pan‐transcriptome reference for Brassica juncea, and the establishment of an Associative Transcriptomics platform for dissecting the genetic architecture of complex traits in this crop, which provides a valuable resource for molecular breeding in B. juncea. We validate this platform by identifying and testing predictive marker associations for important quality traits; seed size, seed colour and γ‐tocopherol content.