Molecular characterization and diversity analysis in chilli pepper using simple sequence repeats (SSR) markers

Abstract

India is considered to be the secondary center of diversity of chilli pepper, especially of Capsicum annuum. Simple sequence repeats (SSRs) are the most widely used marker system for plant variety characterization and diversity analysis especially in cultivated species which have low levels of polymorphism. The diversity analysis of 64 chilli pepper accessions, mostly of Indian origin, was performed using 50 SSR markers. Twenty seven (27) polymorphic primers amplified a total of 75 alleles with an average of 2.78 alleles per locus. Maximum of four alleles were amplified by the primer AVRDC PP 32. The polymorphic information content (PIC) values ranged from 0.39 (AVRDC PP 138) to 0.78 (AVRDC PP 18), with an average of 0.59. Based on the PIC values, primers AVRDC PP 18 was found to be the most informative (0.78), followed by the primers AVRDC PP 32 (0.69) and AVRDC PP 03 (0.66). Using the given set of primers, it was possible to characterize all but two pairs of accessions from each other. The analysis allowed grouping of the test germplasm into nine clusters. Based on diversity analysis, genotypes were identified for developing mapping populations, produce heterotic F₁ hybrids and attempt crosses for genetic improvement of the crop.

Keywords: Capsicum, genetic diversity, molecular characterization, simple sequence repeats (SSR) markers.

African Journal of Biotechnology, Vol 13(31), 3137-3143