Genetic diversity between two ecotypes of Egyptian clover varieties, namely Fahl (mono-cut) and Helaly (multi-cut) have been assessed based on forage yield and yield components as well as molecular marker systems. The two parental genotypes were crossed to produce seeds of F1 and F2 progenies. Analyses of variance indicated significant differences between four populations (P1 (Fahl), P2 (Helaly), F1 and F2) for fresh forage yield, number of florets/inflorescence, number of seeds/inflorescence and 1000 seed weight. The mean of F1 hybrid indicated over-dominance of the higher performance. The phenotypic and genotypic coefficients of variation were high for fresh forage yield, intermediate for 1000-seed weight and low for number of florets/inflorescence and number of seeds/inflorescence. Four molecular marker systems with 80 primers, 30 RAPD, 10 ISSR, 10 SRAP and 30 SSR were used for studying the genetic diversity between the two parents, out of which 64 primers (26 RAPD, 7 ISSR, 7 SRAP and 24 SSR) were polymorphic between the parents. The four molecular marker systems generated unique DNA bands for each parent. Twenty-one primers which produced higher unique bands in both parents were surveyed on bulked DNA from the extremes of four agro-morphological traits within and between the two ecotypes in F2 generations. Twenty-one primers produced bands distinguish between the bulked extremes for at least one trait within each ecotype or between the two ecotypes. All polymorphic primers were subjected to QTL analysis, out of them 23 only were mapped on three linkage groups with four agro-morphological traits and showed 24 putative QTLs.
Keywords: BSA; ISSR; RAPD; SRAP; Single marker.