Fig. 6

Polygenic interactions mediating floral transition inferred by conditional GWAS. a, b Manhattan plots for GWAS of PH (a) and DTT (b) run separately as two subgroups of 584 maternal lines (BRD1-CC, top panels) and 834 maternal lines (BRD1-TT, bottom panels), divided according to the genotype for the peak SNP of chr1.s_248796560 in the BRD1 QTL. The three dashed lines colored in red, green, and blue represent three significance thresholds with p-value = 2.2e− 07, 1e− 06, and 1e− 05, respectively. c Selection of the optimal genotypic combinations, namely Haplotype 1 (Hap1) and Haplotype 2 (Hap2) of the genes MADS69, ZCN8, and myb74 that favor early DTT and short PH without affecting EW. The 11 Hap2-bearing maternal lines exhibit early DTT, reduced PH and normal EW, and thus are determined to be the optimal haplotype combination. d Comparison of the DTT, PH, and EW phenotypes of the 11 maternal lines carrying the optimal haplotype (Hap2, blue) with the phenotypes of 48 Hap1 (red) and 280 Hap8 lines (green)