Development of novel EST-SSR markers for cucumber (Cucumis sativus) and their transferability to related species

We report on the development of novel simple sequence repeat (SSR) markers from publicly available Cucumis sativus expressed sequence tags (ESTs) and on their transferability among related species. In total, 533 di- to penta-type SSRs were identified from 6344 cucumber ESTs retrieved from GenBank. Identified SSRs mainly comprised of di- and tri-nucleotide repeats, of which AG and AAG motifs were much abundant. A total of 392 SSR-containing unigenes (non-redundant ESTs/consensus sequences) were suitable for primer design. From these, 35 primer pairs were designed as representative samples and 28 were usable markers. Twenty-six out of 28 usable markers revealed polymorphism among 21 cucumber accessions with 2–7 alleles detected (mean = 3.77) and their polymorphism information content (PIC) values ranged from 0.091 to 0.748 (mean = 0.388). The polymorphism observed herein partially arose from the null alleles which occurred at the multiple homoeoloci detected by the markers. Transferability of the 28 EST-SSR markers was investigated in four other cucurbits: melon, watermelon, pumpkin and gourd which showed frequency of 92.9%, 57.1%, 53.6% and 60.7%, respectively. The EST-SSR markers developed herein will complement the currently available genomic SSR markers and may be useful for genetic studies in cucumber and related species.