Identification and validation of in silico mined polymorphic EST-SSR for genetic diversity and cross-species transferability studies in Safflower

Safflower, an important oil seed and medicinal crop has rich genetic diversity but limited genetic resources, which could be utilized for its improvement. In a bid to enrich safflower’s genetic resources polymorphic genic SSRs were identified by in silico comparisons of the de novo assembled transcriptome sequences from two safflower genotypes. Of the 145 exon-derived primer pairs, 125 produced reproducible amplifications and 44 primer pairs yielded products that showed polymorphism even between the two closely related safflower accessions. Out of the 44 primer pairs, 10 primers that were utilized for assessing the genetic diversity and cross-species transferability on a diverse panel consisting of 24 accessions, revealed high genetic diversity in the panel and cross-species transferability of the markers. The UPGMA dendrogram clustered the wild types and safflower genotypes in three major groups, of which wild types clustered in a subgroup of major group II, whereas the remaining genotypes were scattered in all three clusters with the majority (73.68%) being clustered in group I. The in silico identified polymorphic exon derived genic SSRs are an important addition to the available genetic resources and can be deployed for marker assisted breeding programs for improvement of safflower.