Fig. 4: Association results for 43 plant morphological, physiological, metabolic and disease resistance traits, and the contributions of the subgenome and HEB to complex trait variation.

a, Phenotypic diversity of plant architecture, leaf morphology and flowering morphology and color among five selected plants. The vertical dashed gray lines highlight the genomic positions of potential candidate genes. b, Manhattan plots of results from 43 GWAS scans. The red horizontal dashed lines indicate the Bonferroni-corrected genome-wide significance thresholds. The vertical dashed gray lines highlight the genomic positions of 16 SNPs associated with more than two traits. c, Heatmap illustrating the P values of 16 SNPs detected for more than two traits. Each cell represents −log₁₀(P) of a particular SNP (x axis) associated with a specific trait (y axis on the right). d, The reference genotype-to-phenotype map includes marker–trait associations detected in our study (orange), in previous reports (blue) and in both (green). Previously reported QTLs spanning more than 10 Mb and QTLs without probe sequences are not included here. e, Unequal contribution from two subgenomes to complex trait variation. f, The contribution of homoeologous genes whose expression bias (HEB) was either triggered or equalized by polyploidization to complex trait variation.