Fig. 4: GWAS analysis using the rice TIP map.

a Manhattan plot of GWAS for rice survival rates under cold stress using SVs based on the MH63 genome. The labeled quantitative trait locus (QTL) loci represent locations with high significance and continuous peaks. The genes in parentheses are previously reported cold-tolerance genes significantly associated with these loci. The two highlighted labels indicate loci strongly associated with OsCACT and OsPTR. b, c Manhattan plots of OsCACT (b) and OsPTR (c) associated loci. The dots represent the log-transformed P values of single-nucleotide polymorphism (SNP) and SV GWAS. The color of the dots reflects the linkage disequilibrium (LD) between the variant and the labeled lead SV. The bottom plots represent the gene structure at each respective locus. d, e ONT reads mapping based on MH63 (d) and T2T-NIP (e). The top plots display the gene structure diagrams. The four tracks labeled K, R, TB, and L represent haplotype A (HapA) for japonica, while the six tracks labeled KO, M, N, NJ, T, and Y represent haplotype B (HapB) for indica. The numbers at the right end of each track indicate the reads coverage, and the area between the two dashed lines represents the insertion (d) and the deletion (e). f, g Comparison of survival rates for different haplotypes of OsCACT (f) and OsPTR (g) under cold stress. The donut plots illustrate the distribution in different subpopulations and quantity of the 165 accessions across hapA, hapB, and heterozygous (Hetero) categories. The box plots show the survival rates of accessions with different haplotypes. In the box plots, the center line represents the median, the box bounds indicate the 25th and 75th percentiles, and the whiskers extend to the minimum and maximum values. n indicates the number of rice accessions in each haplotype group. Statistical analysis of these data was performed using a two-tailed Wilcoxon test. Source data are provided as a Source Data file.