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North-eastern Himalayan (NEH) region of India possesses numerous unique and traditionally important Capsicum landraces. The extent of phenotypic variation and phylogenetic relationship of the NEH Capsicum landraces is poorly understood. Therefore, Capsicum landraces consisting of 34  Capsicum annuum  L., 5  C. chinense  Jacq. and 57  C. frutescens  L, that were collected from different states NEH region of India, were studied for morpho-genetic diversity. Accessions were agro-morphologically characterised using the IPGRI minimal descriptors. Genetic diversity analysis was done using 20 microsatellite markers spanning all 13 linkage groups of Capsicum. Multivariate analyses indicated that  C. frutescens  accessions were agro-morphologically different from both  C. annuum  and  C. chinense . On an average, 3.6 alleles per locus were detected. Considerable genetic diversity (polymorphic information content, PIC = 0.46) was found within the accessions. The phylogenetic and model-based population structure analyses classified the landraces into two to three groups with varied species homogeneity with a majority of members in a cluster belonging to the same species. This study provides important information on the morpho-agronomic variability and genetic structure of chilli landraces of northeastern India which will be useful to identify groups with similar genetic backgrounds for conservation and effective selection of parents for future breeding programme.

Morpho-genetic screening and population structure analysis of Capsicum landraces of North-eastern Himalayan regions of India