Figure 2

Haplotype networks of OsCAX gene family and their associations with six traits in 3KRG. (a) OsCAX1a, (b) OsCAX1b, (c) OsCAX1c, (d) OsCAX2, (e) OsCAX3, (f) OsCAX4. Within each haplotype network, two adjacent gcHaps are separated by mutational changes with hatches indicating differences between the two most related haplotypes. The right side of each gene haplotype network corresponds to the phenotypic variation among the haplotypes. Boxplots are shown for the following traits: culm length (CL, cm); culm number (CN, count); grain length (GL, mm); 1000 grain weight (TGW, g); grain width (GW, mm); and days to heading (HD, day). The P values under trait names indicate differences between the haplotypes assessed by two-way ANOVA, with different letters on the boxplots indicating statistically significant differences at P < 0.05 based on Duncan’s multiple range test. The bar charts on the right show the differences in frequency of the predominant gcHaps between landraces (LANs) and modern varieties (MVs) in Xian and Geng. Chi-square tests were used to determine significant differences in the proportions of the same gcHap between the different populations with ****P < 0.0001, **P < 0.01, *P < 0.05, and n.s., not significant.