Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) marker efficacy for maize hybrid identification

Knowledge as to genetic diversity and relationships among maize hybrids is important for breeding strategies. The main aims of this study were to (1) estimate molecular genetic diversity among 30 maize hybrids by random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers; and (2) compare the genetic relatedness values obtained from these marker types. A set of 30 maize hybrids was assessed. To compare these two methods, genetic parameters were computed such as the number of polymorphic bands, average number of alleles per locus, effective number of alleles per locus, expected heterozygosity, effectiveness index of analysis and polymorphism information content (PIC). Better results were provided by SSR. The discrimination ability of individual markers was also determined. The SSR system provided an average PIC of 0.71 (ranging from 0.47 to 0.91) and RAPD provided an average value of 0.61 (ranging from 0.44 to 0.82). Genetic similarities (GS) were estimated using Nei and Li's coefficients for SSR and Jaccard's coefficient for RAPD. For SSR, GS ranged from 26.3 to 88.5% (with average of 58.8%); for RAPD, GS ranged from 6.7 to 86.7% (with average of 49.5%). Hybrids were clustered using unweighted pair group method with arithmetic mean (UPGMA). The correlation between similarity matrices for RAPD and SSR was 0.11.