Microsatellites mining in Capsicum genomes and development of SSR markers in Capsicum baccatum

Abstract

Capsicum species is versatile vegetable cum spice crop, which have high commercial value because of its appealing color and pungency. Crop breeding and improvement of chilli requires genomic resources. Computational mining of chromosome wise microsatellites was carried out using search criteria of minimum repeats of 12 for mono, 6 for di and 5 for tri, penta &hexa nucleotides and identified 130942, 271650 and 2,78,143 perfect SSRs in C. baccatum cv. PBC81, C. annuum cv. Zunala and in C. chinense cv PI159236 genomes, respectively. Of these perfect SSRs; 8999, 18060 and 18019 were in compound form in the three species genomes respectively. Overall density of SSRs/Mbp observed was 173.66, 149.39 and 137.55 in C. baccatum, C. chinense and C. annuum. From 130942 perfect SSRs, total 59510 primer pairs were designed in C. baccatum and 16 SSR markers were primarily selected to test the usability and validated in a set of eight genotypes consisting of four accessions of C. annuum, one accession each of C. chinense and C. frutescens and two accessions of C. baccatum. All the 16 SSR markers exhibited expected size of amplification product. This C. baccatum based SSRs will be useful in characterization of germplasm and marker assisted breeding.