Fig. 4: Contributions of eTRs to gene expression variation in young leaf tissue.

a Comparison of gene expression models with or without eTR variant. R² indicated expression variations explained by the model. X-axis and Y-axis indicate R² of models including only the eBi-allelic variant and both eBi-allelic variant and eTR, respectively. Red dots indicate genes for which models including eTRs were significantly better than models including only eBi-allelic variants (Benjamini–Hochberg test, q value < 0.05); blue dots indicate those without significantly differences. b Original (unconditioned) eTR effect sizes (β) compared to conditioned eTR β. Red points indicate eTRs with consistent effect directions between conditioned and unconditioned analysis; the rest points indicate those with discordant effect directions. Not significant β are represented as 0. c Manhattan plot for OsPRR1. C_x represents eTR repeat number. Pie chart shows eTR and eSNP distribution. d Pearson correlation analysis between eTR repeat number and OsPRR1 leaf expression. Red and green regression lines indicate analyses including all accessions and only accessions with the major SNP type, respectively. e Plant height among accessions with different eTR repeat numbers. f Pearson correlation analysis between the eTR repeat number and plant height. Red and green regression lines indicate analyses including all accessions and only accessions with the major SNP type, respectively. g Schematic diagram indicating that mutated site of osprr1. h Morphologies of the osprr1 mutant and the wild type (Xiushui134). i Plant height of the osprr1 mutants (n = 36) and the wild type (n = 38) plants after heading stage. j Schematic diagram of the recombinant vectors containing OsPRR1 promoter for firefly luciferase complementation assay. REN Renilla luciferase, LUC firefly luciferase, pOsPRR1^C3(NH242) the vector containing the OsPRR1 promoter region with 3 TR copies, pOsPRR1^C4(NH027) the vector containing 4 TR copies. k Relative LUC/REN activity in tobacco protoplast transformed with pOsPRR1^C3 and pOsPRR1^C4 vector (n = 3). In d and f, the error bands indicate 95% confidence intervals (two-tailed t test). In i and k, data presented as mean ± SD, p-values were generated using two-tailed t test. Source data are provided as a Source Data file.