Genetic Variation and Population Structure of Asian Cultivated Rice

Abstract

Rice germplasms serve as repositories of genetic variation. Population structure analysis is crucial for the effective utilization of rice germplasm and provides an evolutionary framework for future biological research. In this study, we constructed a genetic variation map using a large population of 20 056 rice accessions. A total of 34 426 306 variants were identified, including 29 251 099 biallelic and 5 175 207 multiallelic variants. Population structure analysis of a subset of 5 668 accessions classified Asian cultivated rice into eight distinct groups: temperate japonica 1 (TEJ1), temperate japonica 2 (TEJ2), tropical japonica (TRJ), aromatic (ARO), aus (AUS), indica 1 (IND1), indica 2 (IND2), indica 3 (IND3). Comparative analysis revealed that japonica accessions from China were predominantly composed of TEJ1 and TEJ2, while indica varieties were mainly from IND1. In contrast, introduced japonica accessions were primarily TEJ1 and TRJ, with IND2 representing the major indica group. Foreign accessions represented all eight groups, whereas Chinese accessions lacked the ARO, AUS, and IND3 groups. Genetic diversity analysis revealed that IND3 and TEJ1 exhibited the highest and lowest nucleotide diversity, respectively. Geographically, TRJ was largely distributed in the Americas, ARO was concentrated in the Middle East, and notably, TEJ2 was identified as a group specific to China. Furthermore, we identified 52 regions with significant genetic differentiation. Two of these regions, harboring the cold-tolerant genes bZIP73 and COLD1, were selected for further analysis. Nucleotide diversity and haplotype network analyses indicated that both genes may have undergone positive selection and contribute to indica-japonica differentiation. Haplotype analysis also uncovered novel alleles, including a new mutation in COLD1 that may represent a favorable variant for enhancing cold tolerance in japonica accessions. Our study demonstrates that large-scale population analysis of genetic variation is a powerful method for dissecting population structure, elucidating the mechanisms of genetic differentiation, and identifying novel functional alleles.