Fig. 6: Natural variation of hub genes in regulatory network contribute to grain traits in wheat.

a Ratio of SNPs from hub TFs, target genes identified in the network and 89 & 1649 randomly selected genes (replicated 100 times) that caused significant (P < 0.05, two-tailed Student’s t test) variation in wheat grain traits. TGW, GW, GL and GL/GW represent thousand grain weight, grain width, grain length and ratio of grain length to grain width, respectively. b Regulatory network of genes with SNPs that were significantly (P < 0.05, two-tailed Student’s t test) associated with variation in GW, GL, GL/GW or/and TGW in wheat. The octagon with brown, dark olive green and blue edges indicate that the genes were marked by H3K27me3, H3K4me3 and H3K9ac, respectively. Those genes with two modifications were in octagons with either purple or light blue edges. c Effects of different haplotypes of three function known hub genes on GL/GW, GL (mm), GW (mm) and TGW (g). For GW, GL and TGW, the sample sizes for the H1 and H2 haplotypes of TraesCS3B02G400200 were 218 and 107. For TraesCS4B02G173600, the sample sizes were 39 and 348 for GL, and 45 and 357 for both GW and TGW. For TraesCS7A02G272100, the H1 and H2 sample sizes were 218 and 49 across all three traits. The P value above the line is calculated using a two-tailed Student’s t test. The box plots display the median (horizontal line), second to third quartiles (box), with the maxima and minima as whiskers, and outliers as points beyond 1.5 times the interquartile range. Source data are provided as a Source Data file.