Genetic Diversity of Tropical Hybrid Rice Germplasm Measured by Molecular Markers

Investigation of genetic diversity and relationships among breeding lines is of great importance to facilitate parent selection in hybrid rice breeding programs. In this study, we characterized 168 hybrid rice parents from International Rice Research Institute with 207 simple sequence repeat (SSR) and 353 single nucleotide polymorphism (SNP) markers. A total of 1 267 SSR and 706 SNP alleles were detected with the averages of 6.1 (SSR) and 2.0 (SNP) alleles per locus respectively across all lines. Based on the genetic distances estimated from the SSR and SNP markers separately and combined, the unrooted neighbor-joining cluster and STRUCTURE analyses consistently separated the 168 hybrid rice parents into two major groups: B-line and R-line, which is consistent with known parent pedigree information. The genetic distance matrices derived from the SSR and SNP genotyping were highly correlated (r = 0.81, P < 0.001), indicating that both of the SSR and SNP markers have distinguishable power to detect polymorphism and are appropriate for genetic diversity analysis among tropical hybrid rice parents. A subset of 60 SSR markers were also chosen by the Core Hunter with 368 alleles, and the cluster analysis based on the total and subset of SSR markers highly corresponded at r = 0.91 (P < 0.001), suggesting that fewer SSR markers can be used to classify and evaluate genetic diversity among parental lines.