Genetic structure and diversity of upland rice germplasm using diversity array technology (DArT)-based single nucleotide polymorphism (SNP) markers

Investigating genetic structure and diversity is crucial for rice improvement strategies, including mapping quantitative trait loci with the potential for improved productivity and adaptation to the upland ecology. The present study elucidated the population structure and genetic diversity of 176 rice germplasm adapted to the upland ecology using 7063 genome-wide single nucleotide polymorphism (SNP) markers from the Diversity Array Technology (DArT)-based sequencing platform (DArTseq). The SNPs were reasonably distributed across the rice genome, ranging from 432 SNPs on chromosome 9 to 989 SNPs on chromosome 1. The minimum minor allele frequency was 0.05, while the average polymorphism information content and heterozygosity were 0.25 and 0.03, respectively. The model-based (Bayesian) population structure analysis identified two major groups for the studied rice germplasm. Analysis of molecular variance revealed that all (100%) of the genetic variance was attributable to differences within the population, and none was attributable to the population structure. The estimates of genetic differentiation (PhiPT = 0.001; P = 0.197) further showed a negligible difference among the population structures. The results indicated a high genetic exchange or gene flow (number of migrants, Nm = 622.65) and a substantial level of diversity (number of private alleles, Pa = 1.52 number of different alleles, Na = 2.67; Shannon's information index, I = 0.084; and percentage of polymorphic loci, %PPL = 55.9%) within the population, representing a valuable resource for rice improvement. The findings in this study provide a critical analysis of the genetic diversity of upland rice germplasm that would be useful for rice yield improvement. We suggested further breeding and genetic analyses.