Fig. 5: Colocalization of TRs affecting both grain width and gene expression.

a Manhattan plot showing associations between grain width and TR variations, PAVs, SNPs and Indels. Dashed lines of each color indicate the genome-wide threshold value for the corresponding variant type. Around the 1 Mbp region of the leading peak, 122 genes were expressed in the panicle tissue (Median of FPKM > 0 and Maximum of FPKM ≥ 1). Expression levels of the five indicated genes were significantly associated with grain width. b Manhattan plot showing associations between TRs and expression levels of the five genes in the panicle associated with grain width. The dashed line indicates the genome-wide threshold value. Posterior probability of causality for grain width (c) and expression levels of the three genes with significant eTRs (d). “#” indicates the value of the posterior probability. e Posterior probability of a TR being the causal variant for both grain width and LOC_Os06g03850 expression. The dashed line across c–e indicates the position of the same TR variant. f The candidate causal TR was in the promoter region of LOC_Os06g03850 and 7 alleles existed in the present dataset. g Associations between TR repeat numbers and grain width in the indica and japonica subpopulation of Oryza sativa. h Associations between TR repeat numbers and LOC_Os06g03850 expression in the panicle tissue among members of the indica and japonica subpopulation (green and red lines, respectively). In g and h, the error bands indicate 95% confidence intervals, p-values were calculated by two-sided t test. Source data are provided as a Source Data file.