Rice Science

Rice Science

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Genetic Variation and Population Structure of Asian Cultivated Rice (Oryza sativa L.)

  1. State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; Zhejiang Provincial Department of Agriculture Seed Management Station, Hangzhou 310000; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; #These authors contributed equally to this work
  • Contact: YANG Yaolong; WEI Xinghua
  • Supported by:

    This study was supported by the National Key Research and Development Program of China (Grant No. 2021YFD1200503), Rice Germplasm Identification Project of Zhejiang Province, China (Grant No. 2022JZJD001), and the Agricultural Science and Technology Innovation Program (Grant Nos. CAAS-CNRRI-2025-02, CAAS-ZDRW202503 and CAAS-ASTIP201X-CNRRI). We thanked the Public Laboratory of the China National Rice Research Institute for their technical support in high-performance computing cluster.

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Abstract: Rice germplasms serve as repositories of genetic variation. Population structure analysis is crucial for effective utilization of rice 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, comprising 29 251 099 biallelic and 5 175 207 multiallelic variants. A subset of 5 668 accessions was selected for population structure analysis, which classified Asian cultivated rice into eight distinct groups: TEJ1, TEJ2, TRJ, ARO, AUS, IND1, IND2, and IND3. Comparative analysis revealed that japonica accessions from China were predominantly composed of TEJ1 and TEJ2, while indica varieties were mainly IND1. In contrast, introduced japonica accessions were primarily TEJ1 and TRJ, with IND2 being the major indica group. Foreign accessions represented all eight groups, whereas Chinese accessions lacked the ARO, AUS, and IND3 groups. Genetic diversity analysis showed that IND3 and TEJ1 had the highest and lowest nucleotide diversity, respectively. Geographically, TRJ was largely distributed in America, while 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, containing 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 are responsible for 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 genetic variation analysis in large-scale populations is a powerful method for dissecting the population structure, elucidating the mechanisms of genetic differentiation and identifying novel functional alleles.

Key words: genetic variation map, population structure, genetic differentiation, Asian cultivated rice