Fig. 3

Homoeologous gene expression trend regulation. a The proportion of regulation between eQTLs and genes between An and Cn subgenomes at 20 and 40 DAF. The individual layer of the bars represents the percentage of data for that category to the overall data for that subgroup. The regulatory eGenes-eQTLs between An and Cn subgenomes were defined as four types of regulation. An eQTL regulates the An gene; An eQTL regulates the Cn gene; Cn eQTL regulates the An gene; Cn eQTL regulates the Cn gene. b The module of aHGPs and sHGPs. Each row represents a homoeologous gene pair (HGP), and the inverted triangle represents a distant eQTL. c The propensity of genome-wide homoeologous gene expression on different chromosomes of An and Cn subgenomes at 20 DAF. d The expression propensity distribution of aHGPs and sHGPs at 20DAF and 40DAF. The aHGPs contain “An gene reg Cn gene” and “Cn gene reg An gene,” and the sHGPs contain “No relation” and “Mutual regulation.” “n” in each row represents the number of each modulation combination. The log₂foldchange represents the expression propensity. e Effect of local eQTLs on asymmetric regulation (An gene regulating Cn gene) of subgenomes. Horizontal coordinates indicate log₂foldchange of HGPs at 20 DAF and vertical coordinates indicate log₂foldchange of HGPs at 40 DAF. The left panel indicates affected by local eQTLs and the right panel represents unaffected by local eQTLs. f Comparison of gene correlations in different types of aHGPs at 20 DAF. “BG” represents all HGPs, “Local” represents aHGPs with local eQTLs, and “No Local” represents aHGPs without local eQTLs