Fig. 6: QTL and underlying candidate genes for coleoptile color (Rc).

a Image depicting the phenotypic variation for Rc (b) distribution of RILs for Rc (c) QTL peak obtained using IciMapping software (d) recombinants identified in the RILs for Rc along with the physical interval; the text on the left of the horizontal bar indicates RILs codes and the values on the right in orange shade indicate the trait values for Rc; L95 and L96 are the two parents used for generating the RILs. The horizontal bars indicate the genomic region covered by the QTL in the interval 808–810 Mb; each bar indicates each recombinant inbred line (RIL). The orange shaded regions in the horizontal bars represent the genomic region for the parent 1 (i.e., TA4342-L95) whereas the white shaded region in the horizontal bars indicate the genomic region for the parent 2 (i.e., TA4342-L96). e Annotated genes identified in the delimited physical interval of 124.3 to 125 Mb and (f) results from association mapping analysis using all 1.6 M imputed variants obtained for Rc where the x-axis shows physical position of each variant site on the reference genome and the vertical axis showing the -log10 of the p-value from association test. The lower blue horizontal line refers to the Bonferroni-corrected genome-wide significance threshold & the upper red line indicates a highly stringent genome-wide significance threshold of P-value ≤ 5 × 10⁻⁸. The location of a candidate orthologous gene identified at 124.5 Mb corresponding to the strongest associated variant site.