Development of EST-SSRs in watermelon (Citrullus lanatus var. lanatus) and their transferability to Cucumis spp.

Watermelon, an important fruit crop in the family Cucurbitaceae, currently has few available Simple Sequence Repeat (SSR) markers. This study developed Expressed Sequence Tag-Simple Sequence Repeat (EST-SSRs) markers from watermelon and examined their transferability to Cucumis spp. We mined and characterised EST-SSRs from 1,762 watermelon Expressed Sequence Tags (ESTs) retrieved from the National Centre for Biotechnology Information (NCBI) database. Two hundred and thirty-two SSRs were detected following an analysis of the EST sequences and primer pairs were designed for these sequences using the "SSR Primer" programme. A subset of 40 new primer pairs flanking di-, tri-, tetra-, and penta-nucleotide repeat sequences were synthesised. These primer pairs were evaluated for amplification and polymorphism using DNA from seven watermelon varieties from India. Clear amplification products were obtained for 31 primer pairs, of which seven were found to be polymorphic with a mean allele number of two per locus. In addition, 14 and 20 EST-SSR markers could also be transferred to muskmelon and cucumber, respectively. Thus, this study has provided a new set of EST-SSR markers for watermelon, muskmelon, and cucumber, which can be used for genetic diversity analysis, varietal identification, and genetic improvement of watermelon.