Analysis of SSRs Information in Capsicum spp. from EST Database

Abstract

SSR markers are useful in pepper linkage mapping and gene location. 446 SSR markers have been reported, but they are insufficient. It is costly to develop SSR markers from DNA library, whereas it seems much easy to find in EST sequences in the GenBank of pepper through internet. In this study, attempts have been made to develop SSR markers in the EST sequences by using bioinformatics. EST sequences were trimmed by ‘est-trimmer.pr software, while 116915EST sequences were obtained without poly ‘A’ or poly ‘T’, ranged between 100 and 700 bp. Using ‘e-PCR’ and ‘del.pl’ softwares, SSR sequences were identified. 2 508 micro satellite loci (larger than 20 repeats) were established and 755 SSR primers were designed using SSR finder software and Primer 3 software. There were 498 (0.43%) mono-, 1 026 (0.89%) di-, 518 (0.45%) tn-, 245 (0.21%) tetra-, 114 (0.10%) penta-, and 107 (0.09%) hexa-nucleotide SSRs. The estimated frequency of SSRs was approximately 1/25.12 kb. According to the distribution of SSRs in pepper, the mean length of pepper SSRs was 22.68 bp and the adenine rich repeats such as A/T, AG, AT, AAG, AAAT, and AAAC were predominant in each type of SSRs (mono-, di-, tri-, tetra-, penta-, and hexa-), whereas the C/G, CG, CCG repeats were less abundant. 210 primers were tested in 8 pepper cultivars and the PCR result revealed the existence of polymorphism among 127 (60.48%) SSR primers within 8 pepper cultivars. It is confirmed that pepper EST database could be efficiently exploited for availability of SSR markers.