Development of chloroplast microsatellite markers in Capsicum: Insight into evolution of Bhut Jolokia - a clad of ghost chilli landraces

Abstract

In the present study, a total of 27 chloroplast specific SSRs (CpSSR) have been identified in the chloroplast genome of Capsicum annum L. The frequency of the SSRs was about one in 5.7 kb of the chloroplast genome. Out of 27 SSRs, 26 were mono-nucleotide repeats of A/T and one was a trinucleotide repeat (TTA). Further a set of seven markers were validated by genotyping 48 capsicum accessions comprising of cultivars from five different species and landraces of unknown identity. The seven SSR markers generated a total of 27 alleles among 48 samples used in this study. The size of the amplicons varied from 161 bp (CaCpM22 and 26) to 339 bp (CaCpM06). The polymorphic information content (PIC) value for the set of the primers used ranged from 0.11 to 0.48 with an average of 0.33. The number of alleles for markers ranged from three to six with an average of 3.28 alleles per marker. The phylogenetic analysis of the chilly accessions showed that the Bhut jolokia land race is clustered along with the C. frutescence indicating the it’s probable parentage. The chloroplast genome based SSR markers identified in the present study can be further used for the marker-assisted genomic studies