Development of a set of SSR markers for characterization of Indian mustard germplasm and varieties

Simple sequence repeat (SSR) markers can serve as an important tool for characterization and genetic diversity evaluation in Indian mustard germplasm and varieties. For DNA fingerprinting of various Indian mustard varieties, it is necessary that a common set of SSRs be used by various laboratories so that the developed genetic profiles of various genotypes can be compared with one another. In this study, we evaluated the polymorphic potential of 350 SSR markers to derive a set of SSR markers for characterization of Indian mustard germplasm and varieties. Out of a total of 350 SSR markers evaluated, 310 (88.57%) SSRs produced polymorphic amplicons, while remaining 40 (11.43%) SSRs resulted into monomorphic products. The allele number varied from 2 to 7 with 3.22 average number of alleles per locus. Polymorphism information content (PIC) value ranged from 0.24 (Ol09A01) to 0.75 (nia-m141a) with an average PIC value of 0.40 per locus. A total of 95 (31%) SSR markers evaluated were having PIC values more than the average PIC value, which constitute the representative set of SSR markers. Unweighted pair group method with arithmetic averages (UPGMA)-dendrogram grouped all the 46 genotypes into two main clusters, while STRUCTURE analysis formed three subpopulations having admixture of alleles. This SSR marker set will facilitate systematic characterization and classification of various Indian mustard germplasm accessions and varieties.