Molecular Diversity Analysis of Some Chilli (<i>Capsicum</i> spp.) Genotypes Using SSR Markers

Abstract

Chilli belongs to the genus Capsicum which possesses enormous wealth of genetic diversity. Extent of genetic diversity determines the success level of crop improvement programme. Simple sequence repeats (SSRs) are the most widely used marker system for molecular diversity analysis especially in cultivated species. The aim of our present study was to assess the molecular genetic diversity of 20 local chilli genotypes of Bangladesh using SSR markers. Genomic DNA was extracted from young leaves and PCR reactions were performed. Eleven SSR primers were used in PCR amplification. Total 10 alleles were detected for the five polymorphic SSR loci, with a mean of 2.00 alleles per primer. Gene diversity ranged from 0.333 to 1.00 with an average of 0.567. Polymorphic Information Content (PIC) values of the SSR primers ranged from 0.255 to 0.500 with an average value of 0.371. The similarity index matrix ranged from 0.00 to 1.000. It was highest in several germplasms viz . Pop-2 vs Pop-18; Pop-3 vs Pop-5 vs Pop-19 vs Pop-20 and the lowest in the germplasm Pop-8 vs Pop-18. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Means (UPGMA) indicated the segregation of 20 chilli genotypes into two main clusters. The SSR markers showed genetic variability in the studied pepper genotypes and they are powerful tools for estimating molecular diversity of chilli. The findings of the present study have potential applications in future breeding programme for the genetic improvement of chilli.