Efficiency of Three PCR based Marker Systems for Detecting DNA Polymorphism in Cicer arietinum L and Cajanus cajan L Millspaugh

Abstract

Insufficient quality of molecular markers regarding their predictive and diagnostic values has delayed the benefits of marker-assisted selection. To evaluate the robustness of marker systems in detection of DNA polymorphism, 19 RAPD, 22 SSR and 20 ISSR markers were used to genetically differentiate two major pulse crops possessing different important traits. Polymorphism was 95, 93 and 87 % by using ISSR, SSR and RAPD markers, respectively. The average number of amplicons/alleles obtained was 6.42 (RAPD), 1.3 (SSR) and 8.1 (ISSR). DNA profiles revealed high degree of intergeneric polymorphism, while the diversity level was considerably low among the varieties. Significant polymorphism information content (PIC) values of RAPD (0.49), SSR (0.61), ISSR (0.70) profiles were obtained. UPGMA cluster analysis of eight genotypes showed clear demarcation between the two genera falling in two separate clusters with their respective resistant and susceptible genotypes. There was a significant correlation between RAPD and SSR (r = 0.819), RAPD and ISSR (r = 0.997), SSR and ISSR (r = 0.843) GS matrices. The product moment 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), RAPD and ISSR (t = 4.473), SSR and ISSR (t = 4.120). These results illustrate the potential of all the three marker systems to distinguish pulses crop at genus leveL The information will facilitate selection of genotypes to serve as parents for effective breeding programs in crop improvement and in bridging the two important pulses crop for comparative genomics.