Fig. 4

Regulatory evolution and homoeolog expression. a The extent of homoeolog expression bias (1st and 2nd columns) and expression changes under domestication (ratios, At/Dt, and total expression, At + Dt; 3rd and 4th columns, respectively) were measured for 22,394 homoeologous gene pairs. b Contingency tables between cis and trans regulatory divergence and homoeolog bias. A pair of homoeologous genes was considered to exhibit regulatory divergence (RD) if at least one homoeolog was found to be a RD gene (1st row). Homoeolog expression bias was characterized each within TX2094 and Maxxa (columns). Cells displaying significant over-representation (Fisher’s exact test; P < 0.05) are highlighted. c Cross-tabulation of regulatory evolution for 952 RD homoeolog pairs, indicating predominance of cis and trans effects. Cell color indicates the magnitude of significant over-representation based on −log₁₀(P-value) of Fisher’s exact test (i.e., P = 0.05 is converted to 1.3). d Boxplot of homoeolog expression ratio changes under domestication for RD homoeolog pairs. Black triangles indicate significant deviation from zero (Student’s t-test; P < 0.05), and the asterisk (*) denotes a significantly different ratio between At and Dt homoeologs. Boxplot elements: center line–median; box limits–upper (Q3) and lower (Q1) quartiles; whiskers–smallest and largest non-outlier; points–outliers. The source data underlying Fig. 4d are provided as a Source Data file.