Genetic Variation and Population Structure of Asian Cultivated Rice

doi:10.1016/j.rsci.2026.02.010

Abstract

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.

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

Li Wei, Zhang Mengchen, Chen Xiaoyang, Li Yan, Xu Qun, Wang Shan, Feng Yue, Wei Xinghua, Yang Yaolong. Genetic Variation and Population Structure of Asian Cultivated Rice[J]. Rice Science, 2026, 33(3): 367-380.

Figures/Tables 6

Fig. 1. Comprehensive characteristics of 11 366 (11.3-k) accessions in this study. A, Global geographical distribution of 11.3-k accessions. The size of the solid circles represents the number of varieties. B, Geographical distribution of 7 932 accessions from China. The size of the solid circles represents the number of varieties. C and D, Frequency distribution of 11.3-k accession heterozygosity (C) and missing data rate (D). E and F, Distribution of three rice types (L, IM, and IN) (E) and two rice subspecies (geng/japonica and xian/indica) (F) across 11.3-k and 5.6-k collections. UN, Uncertain type; L, Domestic landraces; IM, Improved domestic varieties; IN, Introduced varieties.

Fig. 2. Identification and evaluation of genomic variants. A, Proportion of single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in biallelic and multiallelic variants, respectively. B, Distribution of SNPs and InDels on different chromosomes in both biallelic and multiallelic variants. C-E, Heterozygous rate (C), missing data rate (D), and minor allele frequency (E) distribution of the biallelic variants.

Fig. 3. Population structure analysis based on 5.6-k rice accessions. A, Admixture plot of 5.6-k rice accessions. The columns in ADMIXTURE represent accessions. The accession groups are shown below the plot. B, A clear separation of two subspecies (xian and geng) and eight groups was achieved using the first and second principal components (PC1: 66.8%; PC2: 9.8%). C, Group TEJ2 was clearly distinguished using PC1 and PC4 (7.4%). MIX1 and MIX2 represent mixed groups from China and non-China, respectively. TEJ, Temperate japonica; TRJ, Tropical japonica; ARO, Aromatic; AUS, Aus; IND, Indica.

Fig. 4. Population diversity of 5.6 k rice accessions. A, Nucleotide diversity (π) and differentiation coefficient (FST) between introduced varieties (IN) and domestic landraces (L) accessions in different subspecies. G represent geng/japonica subspecies; X represent xian/indica subspecies. IN-G and IN-X represent geng/japonica and xian/indica subspecies in introduced varieties, respectively, and the same for L-G and L-X. The red numbers represent π values, while the black numbers represent the FST values between the two populations connected by the black lines. B, Nucleotide diversity and population divergence among eight major groups. Circles represent π values, and squares represent the heatmap of FST between all pairs of the eight groups. C, Decay of linkage disequilibrium in the whole genome of eight groups. TEJ, Temperate japonica; TRJ, Tropical japonica; ARO, Aromatic; AUS, Aus; IND, Indica.

Fig. 5. Global distribution patterns of eight major groups. A, Geographical distribution of eight major groups. B, Distribution frequency of eight major groups across different regions. TEJ, Temperate japonica; TRJ, Tropical japonica; ARO, Aromatic; AUS, Aus; IND, Indica.

Fig. 6. Genetic differentiation among eight groups in Asian cultivated rice. A, Genetic differentiation regions were obtained by calculating the FST value between each pair of the eight groups using a 100-kb sliding window with a 50-kb step. The regions with the top 1% differentiation coefficient (FST) value were determined as the significant genetic differentiation regions. The green arrows indicate the genetic differentiation regions. The red arrows indicate the regions where bZIP73 (Chr. 9) and COLD1 (Chr. 4) are located. B and C, Haplotype (Hap) network analysis of bZIP73 (B) and COLD1 (C). Different colors represent different groups of accessions. TEJ, Temperate japonica; TRJ, Tropical japonica; ARO, Aromatic; AUS, Aus; IND, Indica.

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