Genetic diversity of a Capsicum germplasm collection from Nepal as determined by randomly amplified polymorphic DNA markers

Domesticated chile (Capsicum annuum L. var. annuum) is a widely cultivated spice and vegetable crop. It originated in the Western Hemisphere, but spread rapidly throughout the globe after the voyage of Columbus. However, very little is known about the genetic diversity of chile in Asia and especially in Nepal. Thus, research was conducted to document morphological as well as molecular characterization of C. annuum var. annuum landraces collected from Nepal. Genetic diversity in C. annuum var. annuum landraces from Nepal was investigated using randomly amplified polymorphic DNA (RAPD) markers and compared with that of C. annuum var. annuum landraces from the center of diversity, Mexico. RAPD marker based cluster analysis of C. annuum var. annuum clearly separated each accession. All accessions of C. annuum var. annuum from Nepal grouped into a single cluster at a similarity index value of 0.80, whereas, accessions from Mexico grouped into eight different clusters at the same similarity level indicating greater genetic diversity in Mexican accessions. RAPD analysis indicated that the Nepalese chile population went through an additional evolutionary bottleneck or founder effect probably due to intercontinental migrations. Some Nepalese accessions had unique RAPD markers suggesting that additional sources of genetic variation are available in Nepalese germplasm.