Genome-wide association mapping for key seed metabolites using a large panel of natural and derived forms of Brassica rapa L.

Abstract Brassica rapa L. (AA; 2n = 20) store considerable amounts of oil and protein reserves in the seeds. Genetic enhancement of these seed storage products is sought to meet specific requirements of the producers and consumers of edible oils, biofuels, animal feed and other industrial products. This necessitates the introduction of new genetic variation and a greater understanding of the trait genetics. We tested 195 germplasm lines of B. rapa for oil, protein and glucosinolates under the environment conditions differing for day length and ambient temperatures during development and maturation of the seeds. This helped to document phenotypic variations for these traits and also identify accessions with extreme phenotypes. DArT genotyping and genome wide association studies enabled detection of SNP markers within or near the genes that are associated directly or indirectly with the biosynthesis of oil (LTPG5, FRK7, SSE1, LACS8, LTPG33), protein (VTI1B, TSB2, SESA4, bZIP1, PPI1, K18J17.13) and glucosinolates (IMD1, MYB119, ILR3, IQD1, ADS2, SOT18). We also envisaged a gene, PLAT2. It is a member of PLAT-plant-stress subgroup of proteins. PLAT2 can be a target for breeding efforts aimed at improving abiotic stress tolerance. Introduction of novel allelic diversity may be more desirable for the development of designer genotypes rather than the simple repackaging of the genetic variation extant in the crop gene pools. It is for the first time that an attempt has been made to characterize allelic diversity extant in the ‘A’ sub genome of B. juncea for its deployment in B. rapa genepool.