Figure 4.

A, GWAS results through the CMLM and MLMM approaches (Manhattan and quantile-quantile plots) for RV, LWR, and SWR in water-deficit stress. Significant SNPs (colored red in the Manhattan plots) are distinguished by threshold P value lines (solid black = −log₁₀ P = 4 and dotted black = Bonferroni-corrected significance threshold). Significant SNPs on MLMM Manhattan plots are numbered in the order that they were included in the model as a cofactor. CLV1, CLAVATA1; Gβ, G-protein β-subunit; KT, potassium transporter; OXR, oxidoreductase; POX, peroxidase; PPR, pentatricopeptide. B, Identified LD blocks based on pairwise r² values between SNPs on chromosome 9 with a priori candidate genes in the table below (for details, see Supplemental Tables S8 and S10). The color intensity of the box corresponds with the r² value (multiplied by 100) according to the legend at right. A significant SNP (14829621) marked with the yellow rectangle was commonly associated with RV, LWR, and SWR.