Molecular Characterization of Cowpea Genotypes for Genetic Diversity using RAPD and ISSR Techniques

Cowpea [Vigna unguiculata (L.) Walp] is an important pulse crop with wide nutritional and agronomic value. Genetic diversity is essential for its improvement and molecular markers such as RAPD and ISSR provide valuable information for assessing phylogenetic relationships and species distinctiveness.

In the present investigation, 78 cowpea germplasm lines, including three check varieties, were evaluated in a randomized complete block design with three replications. Out of these, 48 diverse genotypes were selected for molecular characterization using 22 primers (10 RAPD and 12 ISSR). DNA was extracted from young leaves and subjected to PCR amplification. Nine RAPD primers generated 1180 scoreable bands, while eight ISSR primers amplified 1215 bands across the 48 genotypes.

The polymorphic information content (PIC) values for RAPD primers ranged from 0.27 (RAPD-1) to 0.41 (RAPD-4), with a mean of 0.35. ISSR primers showed PIC values between 0.23 (UBC 815) and 0.42 (UBC 835), with a mean of 0.35. Similarity coefficients among genotypes based on RAPD markers ranged from 0.58 to 1.00, while ISSR-based similarity values ranged from 0.55 to 0.97 with a mean of 0.729. Dendrogram analysis grouped the genotypes into two major clusters. Combined RAPD and ISSR data produced similarity coefficients between 0.58 and 0.94 and the integrated dendrogram revealed 78–83% similarity with individual marker systems. The results indicate a high degree of genetic variation among the cowpea accessions, which can be effectively utilized in pre-breeding programs to broaden the genetic base and facilitate selection of superior lines.