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

Abstract

A comprehensive molecular analysis of 110 rice genotypes, comprising Oryza sativa, Oryza glaberrima, and the interspecific hybrid NERICA, was conducted using 34 microsatellite markers. This assessment revealed an extensive genetic diversity, with 3,866 polymorphic bands (95.1%) and 12 rare alleles (9.8%) identified across the polymorphic microsatellite loci. Notably, O. glaberrima and NERICA exhibited a significantly higher frequency of genotypes with rare alleles (12.5%) compared to O. sativa. A total of 123 alleles were detected, with an average of 3.62 alleles per locus, ranging from 2 to 7 alleles per locus. The allelic distribution varied among genotypes, with O. glaberrima displaying the lowest allelic number of 4 at locus RM182. The polymorphic information content (PIC) value averaged 0.56 per marker, with a range of 0.16 (RM182) to 0.78 (RM547), indicating a high level of genetic diversity among the rice genotypes. The PIC (Polymorphic Information Content) values for NERICA and O. glaberrima were calculated to be 0.51 and 0.37, respectively, indicating moderate to high genetic diversity. Cluster analysis revealed a clear grouping of rice genotypes into eight distinct clusters at a similarity coefficient of 68%, with genotypes sharing similar genetic backgrounds co-clustering. Notably, O. sativa exhibited significantly higher genetic diversity compared to O. glaberrima. These findings suggest that the genetic base of O. glaberrima can be expanded through the incorporation of novel alleles, which can be leveraged to introduce desirable traits in breeding programs, thereby enhancing the genetic potential of this species.