Development and characterization of microsatellite markers from expressed sequence tags for analyzing genetic diversity among Phytophthora isolates from black pepper

Abstract

Bioinformatic mining of 56, 457 publicly available Expressed Sequence Tags of Phytophthora capsici in dbEST Genbank was performed to identify SSRs. A total of 223 SSRs was identified from 9831 UniGene sequences. The most and least frequent repeats were triniculeotides (69.505) and dinucleotides (1.3%) respectively. Thirty six SSR primers designed from ESTs were used to analyse the diversity of 114 Phytophthora isolates from black pepper and twenty nine could be successfully amplified and of these 3 were polymorphic among the Phytophthora isolates. A total of 48 alleles were detected of which only 33.3% were polymorphic. The similarity coefficient values of the dendrogram ranged from 0.79 to 1.00. The isolates were clustered into two major groups. Clustering did not follow the pattern of geographical origin of the isolates or plant part from where the isolates were obtained.