Skip to main content
. 2024 Sep 30;13(10):784. doi: 10.3390/biology13100784

Figure 4.

Figure 4

Candidate gene analysis of qSR12.1a and qSR3.1a for cold tolerance. Local Manhattan plot (top) of 150 kb upstream and downstream around the lead SNP rs12_5,753,724 (LOC_Os12g10710) (a) and rs3_25,249,852 (LOC_Os03g44760) (f). CDS-haplotypes of LOC_Os12g10710 (b) and LOC_Os03g44760 (g). The distribution of SR in the accessions for haplotypes (n > 40 accessions) of LOC_Os12g10710 (c) and LOC_Os03g44760 (h). Different letters above each boxplot indicate significant differences among haplotypes (p < 0.05, Duncan’s multiple range post-hoc test). Haplotype frequency distribution of LOC_Os12g10710 (d) and LOC_Os03g44760 (i) in different subpopulations. The type of each accession was from the metadata of the 3K-RGP [15]. Frequency of haplotypes of LOC_Os12g10710 (e) and LOC_Os03g44760 (j) in the landrace and modern variety populations. Letter n indicates the number of rice accessions belonging to the corresponding subpopulation in (c,d,h,i), or the variety type in (e,j), respectively. Horizontal lines indicate in the Manhattan plots indicate the genome-wide suggestive thresholds.