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Intra- and inter-specific genetic variation analysis was conducted using amplified fragment length polymorphism (AFLP) profiling in Capsicum accessions in the germplasms collected from different geographical locations in India. A total of 24 accessions were investigated belonging to six species, namely C. annuum, C. baccatum, C. chinence, C. eximium, C. frutescens and C. luteum. Average similarity within the 15 accessions of C. annuum was highest (100%) between accessions CIMAP/CA45 and CIMAP/CA49 obtained from IISR, Kerala and 43% among the species CIMAP/CC1 and CIMAP/CB2. In this analysis, accessions were clustered more pronouncedly according to their geographical locations than to their taxonomic labels. A great degree of intermixing of present day domesticated chillies is evident from the present study.

AFLP Analysis for Genetic Diversity in Capsicum Annuum and Related Species