Genome-Wide Discovery of Candidate Genes Associated with Cold Tolerance in Rice at Various Growth Stages

doi:10.1016/j.rsci.2024.12.001

Abstract

Liu Jiajun, Wang Cuili, Sun Mingmao, Ma Xiaoding, Han Bing, Guo Xiaohong, Han Longzhi, Cui Di. Genome-Wide Discovery of Candidate Genes Associated with Cold Tolerance in Rice at Various Growth Stages[J]. Rice Science, 2025, 32(2): 137-142.

Figures/Tables 2

Fig. 1. Population structure and genetic diversity estimates for 166 mini-core Chinese rice germplasms. A, Geographic distribution of 166 rice mini-core germplasms in China. YN, Yunnan Province; HN, Hunan Province; SC, Sichuan Province; GD, Guangdong Province; GX, Guangxi Province; JX, Jiangxi Province; FJ, Fujian Province; GZ, Guizhou Province; JS, Jiangsu Province; AH, Anhui Province; HB, Hubei Province; HE, Hebei Province; LN, Liaoning Province. B, Estimated population structure for rice varieties (K = 6). C, Principal component analysis (PCA) plot of the first two principal components (PC1 and PC2) for rice varieties. D, Phylogenetic tree constructed based on inferred genetic distances. E, Genome-wide average linkage disequilibrium (LD) map for all germplasms (All) and the XI1, XI2, XI3, XI4, GJ1, and GJ2 subpopulations, respectively. The dotted line indicates that LD decrease to half of its maximum value, with the GJ subpopulation at 0.37 and the XI subpopulation at 0.25. F, Genetic diversity and subpopulation differentiation of 166 germplasms. The circle size and the number within each circle represent the genetic diversity (π) of each subpopulation; the number displayed on the horizontal line represents the calculated genetic differentiation coefficient (Fst) value between the two subpopulations. XI, Indica rice variety; GJ, Japonica rice variety.

Fig. 2. Localization of candidate gene OsOPR6 on chromosome 6. A, Partial Manhattan plot (upper panel) and linkage disequilibrium heatmap (lower panel) surrounding the peak on chromosome 6. The red dot indicates the position of a missense variant within the OsOPR6 gene. B, Gene structure and polymorphisms identified in OsOPR6. C‒E, Boxplots depicting the germination rate at low temperature at the germination stage (CGS, C), the grade of cold tolerance at the seedling stage (GCS, D), and the proportion of seed-setting rate per panicle under natural low temperature conditions at the booting and flowering stage (SStR-NL, E) for different haplotypes of OsOPR6. * and ** indicate significant differences between haplotypes at P < 0.05 and P < 0.01, respectively, as determined by a t-test. F, Expression analysis of OsOPR6 by qRT-PCR. UBI was used as an internal control. Data represent Mean ± SD (n = 3). RNA was extracted from rice young leaves under control and cold stress conditions for 8 h. CK, Control; CT, Cold stress for 8 h. B084, Bawangbian 1; B091, Xiaohonggu; B214, Xuanenchangtanqingzhan; B068, Gaoyangdiandao dahongmang; B148, Lengshuinuo; B245, Shanjiugu. * and ** indicate significant differences between the control and stress conditions at P < 0.05 and P < 0.01, respectively, as determined by a t-test. G, Frequency distribution of haplotypes Hap1 and Hap2 across different subpopulations.

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