Fig. 5
Selective sweep analysis between the upland and lowland ecotype populations and GWAS analysis of overwintering rate. a Top: Selective sweep detection between two ecotypes on chromosome 3 K using SNPs and SVs (Fst method). The black dashed line indicates the top 5% sweep regions. Middle: GWAS of overwintering rate on chromosome 3 K. The black dashed line shows the significance threshold (− log10(P) > 6.69). Gray bars mark overlapping regions between selective sweeps and GWAS. Bottom: Schematic of PVB_3 K03611.1 and its upstream 61-bp deletion. b The expression levels (TPM) of PVB_3 K03611.1 under control and cold stress. *** indicates adjusted P-value < 0.001. The suffixes “L” and “R” represent leaves and roots, respectively. c Left: Luciferase (LUC) reporter gene expression observed by soaking in substrate solution; Right: Quantitative detection of the firefly luciferase and renilla luciferase in leaves inoculated with different recombinant vectors using a microplate plate-based fluorescence assay. The error bars indicate the mean ± s.d.; n = 3 biological replicates. * indicates P < 0.05 and **** indicates P < 0.0001. d The distribution proportions of three genotypes with a 61-bp deletion across different ecotypes of germplasm. 0/0 means consistent with the reference genome, 0/1 means heterozygous, and 1/1 means homozygous. e Overwintering survival rate of lowland accessions with three genotypes in BRKG (the name of the common garden) area. f Phenotypic changes of rice wild type and overexpression lines on days 0, 3, and 6 under 4 °C cold stress, scale bar represents 7 cm. The number in the suffix represents the overexpression line number. g Physiological parameters of PVB_3 K03611.1 overexpression lines and WT under cold stress. Top left: Relative expression levels of PVB_3 K03611.1 (N.D. indicates not detected). Remaining panels: SOD and POD activities, and MDA content in WT and overexpression lines after 24 h of cold stress at 4 °C. * indicates P < 0.05, ** indicates P < 0.01, and *** indicates P < 0.005