Comparative Genetic diversity between Oryza sativa, Oryza glabberima, and interspecific hybrid (NERICA) based on SSR markers

Abstract

Molecular profiling of the genetic diversity of 110 rice (Oryza sativa, Oryza glabberima, and interspecific hybrid (NERICA) genotypes based on 34 microsatellites revealed a total of 3866 (95.1%) polymorphic bands with 12 (9.8%) rare alleles across the polymorphic microsatellite loci. The number of genotypes with rare alleles were significantly higher (12.5%) in O. glaberrima = Nerica than O. sativa. A total of 123 alleles were detected with an average of 3.62 alleles ranging from 2 (RM17, RM216, RM480, RM495, RM514, RM518 and RM527) to 7 (RM481) across the genotypes with O. glaberrima having the least allelic number of 4 (RM182). The polymorphic information content (PIC) value was 0.56 per marker and ranged from 0.16 (RM182) to 0.78(RM 547). The PIC value in Nerica and O. glaberrima was 0.51 and 0.37 respectively. Cluster analysis grouped the rice genotypes into 8 groups at a similarity coefficient of 68% with genotypes of the same genetic similarities clustering together. Compared to O .glaberrima, O. sativa showed significantly higher genetic diversity. The genetic base in O. glaberrima can be widened and the rare alleles present therein exploited for desirable traits in breeding programmes.