Fig. 2

Mapping of OsC1 using GWAS and expression analysis of anthocyanidins biosynthesis relative genes. (A) Manhattan plots for GWAS of 3 anthocyanidins traits and leaf sheath color across 12 rice chromosomes. The strength of association is indicated as the negative logarithm of the P value for the linear mixed model. All metabolite-/phenotype-SNP associations with P value below 2.61E-07 (horizontal dashed line) are plotted against the genome location in intervals of 1 Mb. (B) Regional Manhattan plot for 3 anthocyanidins traits and leaf sheath color trait in 5.15 Mb − 5.50 Mb region on chromosome 6. (C) Heatmap of 10 wild and cultivated rice accessions by normalized log2 of relative content of the three anthocyanidins and FPKMs of 25 candidate genes in the region located commonly by mGWAS and pGWAS. Candidate gene OsC1 (LOC_Os06g10350) was noted by red font. (D) Expression analysis of OsC1 and anthocyanidin biosynthesis relative genes (OsF3H, OsDFR and OsANS) in Oryza rufipogon and Oryza sativa. ‘***’ and ‘*’ indicate p-value<0.001 and 0.05 for t-test, respectively