Characterization of genetic diversity in Cicer arietinum L. and Cajanus cajan L. Millspaugh using random amplified polymorphic DNA

Insufficient quality of molecular markers regarding their predictive and diagnostic values has delayed the benefits of estimating molecular diversity and marker-assisted selection in chickpeas and pigeonpeas. To evaluate the robustness of marker systems in detection of DNA polymorphism, 19 random amplified polymorphic DNA (RAPD) and 22 simple sequence repeats (SSR) were used to genetically differentiate eight genotypes of chickpeas and pigeonpeas showing resistance or susceptibility to Fusarium wilt. DNA polymorphism was quantified at 93 % and 87 % when using SSR and RAPD markers, respectively. The average number of amplicons obtained was 6.42 (RAPD) and 1.3 (SSR). DNA profiles revealed a high degree of polymorphism between genera while diversity level was low among the varieties. Significant polymorphism information content values of RAPD (0.49) and SSR (0.61) profiles were obtained. Unweighted pair group mean average cluster analysis of eight genotypes effectively placed the two genera in separate clusters with their respect to resistance or susceptibility to Fusarium wilt. There was a significant correlation between RAPD and SSR (r = 0.819) GS matrices. Pearson’s correlation (r) and Mantel statistic (t) were calculated to measure the degree of relationship between the similarity matrices obtained by RAPD and SSR (t = 4.006). These results illustrate the potential of both these marker systems to distinguish pulse crops at the genus, species, or variety level. The information will facilitate selection of genotypes to serve as parents for effective breeding programs in crop improvement and also in bridging the two important pulses crop for comparative genomics.