Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice varieties from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored.
The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on SNPs selected by QTL analysis also supported the inferred population structure.
The population structure, which was inferred in this study, contains ve subpopulations such that each subpopulation has a unique ecological system, genetic pattern, as well as agronomic traits. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.