Fig. 2.

Genome-wide selection in domestic chicken breeds. a Genomic regions with strong selective sweep signals among domestic chicken breeds. The length of the genomic region with strong selective sweep signals is shown for each breed. The numbers of shared genes and breed-specific genes in the region are also listed. “Shared selected gene number” is the number of genes selected in ≥2 chicken breeds. Violin plots show the zF_ST values and the θ_π ratio for the regions of the breeds that have undergone selection (grey) versus the whole genome (red) (bottom panels). The vertical black boxes denote the interquartile range (IQR) between the first and third quartiles (25th and 75th percentiles, respectively), and the white point inside denotes the median. b Genomic region with strong selective sweep signals on chromosome 6 in the domestic chicken breeds. The values of F_ST, log₂(θπ ratio) and absolute Tajima’s D difference are plotted. The region with zF_ST ≥ 5 is shaded. The genome annotations are shown at the bottom (black bar: coding sequences; blue bar: genes) and the boundaries of SLC16A12, LIPA, CH25H, PANK1 and IFIT5 are marked in red. c A heatmap shows the selected SNP sites and the region containing SLC16A12, LIPA, PDSS2, MC1R, TUBB3 and IFIT5 from RJFs, Tibetan chickens and other domestic chicken breeds. Mutations with amino acid changes are shown on the left