Variation among and within Capsicum species revealed by RAPD markers

Germplasm characterization is an important link between the conservation and utilization of plant genetic resources. A total of 134 accessions from six Capsicum species maintained at the Asian Vegetable Research and Development Center were characterized using 110 randomly amplified polymorphic DNA (RAPD) markers. Ten pairs of potentially duplicated accessions were identified. Multidimensional scaling analysis of the genetic distances among accessions resulted in clustering corresponding to a previous species assignment except for six accessions. Diagnostic RAPDs were identified which discriminate among the Capsicum species. The diagnostic markers were employed for improved taxonomic identification of accessions since many morphological traits used in the identification of Capsicum are difficult to score. Three Capsicum accessions, misclassified based on morphological traits, were reassigned species status based on diagnostic RAPDs. Three accessions, not previously classified, were assigned to a species based on diagnostic RAPDs. Definitive conclusions about the species assignment of three other accessions were not possible. The level of diversity between Capsicum annuum accessions from the genebank and the breeding program were compared and no differences were observed either for RAPD variation or diversity. The utilization of genetic resources as a source of variance for useful traits in the breeding program may be the reason for the similarity of these two groups.