Fig. 8

Gene haplotype distribution in 3,000 rice genome (3 K-RG) panel. (A) frequency of three haplotypes of GLT1 in different rice subgroups. (B) frequency of three haplotypes of PUP4 in different rice subgroups. (C) frequency of three haplotypes of SAC1 on Chromosome 7 in different rice subgroups. The frequency of each haplotype in 3 K-RG panel is mentioned within the parentheses. Haplotype analysis was performed using the non-synonymous SNPs within the genes using the Rice SNP-Seek Database (https://snp-seek.irri.org/_snp.zul). Grouping of rice germplasm into 12 subgroups was done following Wang et al. (2018). Admix, admixture; Aro, aromatic; Aus, aus; Ind1A, indica 1 A; Ind 1B, indica 1B, Ind2, indica 2; Ind3, indica 3; Indx, indica admixture; Japx, japonica admixture; Subtrop, subtropical japonica; Temp, temperate japonica; Trop, tropical japonica. Number of accessions in each subpopulation is mentioned on the top of each bar