In-silico detection of EST-SSR markers in three Brassica species and transferability in B. rapa

Species in the Brassica genus including B. rapa, B. oleracea, and B. napus are cultivated widely around the World as edible vegetables and for their oils. Although progress has been made in identifying molecular markers among Brassica species, expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers have not been applied in the analysis of Brassica species for gene or quantitative trait locus (QTL) mapping. In the present work, 25,631 EST-SSRs were identified among 1,017,392 Brassica ESTs. These SSR-motifs averaged 25 bp in length. Tri-nucleotide SSRs were the most abundant. Among these, AGG/CCT was the dominant motif, accounting for 25% of the total. A total of 20,683 primer pairs were designed successfully. Some of the primer pairs (3,262) from B. napus and B. oleracea were then transferred successfully to B. rapa for comparative sequence analysis and PCR amplification.