Fig. 4

Gene expression characteristics of multiple tissues during duck domestication. A The differential test of genome-wide protein-coding genes from 16 important tissues between mallards and Pekin ducks. The differential expression test was done using t-test, and the level of significance is presented as ∗ (P < 0.05) and ∗  ∗ (P < 0.01). The comparison of body weight (B), liver weight (C), breast muscle weight (D), and muscle fiber area (E) between mallard and Pekin duck during dynamic development. The body weight and the breast muscle weight have increased significantly during duck domestication. F Principal variance component plots of the expression level of breast muscle, liver, and fat tissues in domesticated and wild duck samples. Each tissue contains six samples from three developmental stages (2 weeks, 4 weeks, and 6 weeks). The orange squares indicate wild-type ducks (mallard), and the purple squares indicate domesticated ducks (Pekin duck). PC, principal component. G The proportion of differentially expressed genes in genes with selected promoters (n = 304) and genes with nonselected promoter (n = 477) sets in different periods of breast muscle, the liver, and fat tissue. H The test of fold changes in whole differentially expressed genes in genes with selected promoters and genes with nonselected promoter sets. The up-regulated and down-regulated genes were tested by parameter test, and the P-value was corrected by Holm-Bonferroni method