Figure 4.

GWAS for Na Concentration and Identification of Os-HKT1;5, the Candidate Gene for the Repeatedly Scanned Locus on Chromosome 1.

(A) and (B) Manhattan (left) and Q-Q (right) plots for straw Na concentrations in the indica subpopulation in Wuhan ([A]; LP field) and Youxian ([B]; 2015), respectively. Red arrows point to the lead SNPs located close to Os-HKT1;5.

(C) Gene model of Os-HKT1;5. Filled black boxes represent the coding sequence. The gray vertical lines mark the polymorphic sites identified by high-throughput sequencing, and the asterisk represents the potentially functional site.

(D) Representation of pairwise r² values (a measure of LD) among all polymorphic sites in Os-HKT1;5, where the intensity of the color of each box corresponds to the r² value according to the legend.

(E) List for nine SNPs leading to nine amino acid changes in the coding sequence of Os-HKT1;5. Red text indicates the four variations identified by Ren et al. (2005). The two asterisks indicate the SNP showing strong linkage with the lead SNP of this locus.

(F) to (J) Box plots for Na concentrations in straws at SNP sf0111461701: NF in Wuhan (F); LN field in Wuhan (G); LP field in Wuhan (H); 2014 in Youxian (I); 2015 in Youxian (J). Box plots represent the interquartile range, the thick line in the middle of each box represents the median, the whiskers represent 1.5 times the interquartile range, and the dots represent outlier points. The data are based on two (for Wuhan) or three (for Youxian) biological replicates. DW, dry weight.