Table 1.
Summary of sequencing data quality of WHYCs.
Table 2.
Nucleotide diversity of 10 chicken breeds analyzed in this study.
Fig 1.
Identification of genomic regions with strong selective sweep signals in Wuhua yellow chicken.
Distribution of π radio and FST calculated for 100-kb windows sliding in 10-kb steps. (a) SG vs. WHYC, (b) CG vs. WHYC, and (c) NG vs. WHYC. Red points represent windows fulfilling the selected regions requirement. Genomic regions with both an extremely high π radio (top 5% level) and an extremely high FST value (top 5% level). (d) Venn diagram showing the shared genes between the three comparisons.
Fig 2.
Example of the (a) PMEL gene (green box), and (b) TYRP1 gene (yellow box) with selection signals in Wuhua yellow chicken. FST (blue) and π radio (red), the dotted lines show the threshold P-value (0.05).
Fig 3.
Top 20 of KEGG pathway enrichment analysis of candidate genes under selection in WHYC.
(a) SG vs. WHYC, and (b) NG vs. WHYC.
Table 3.
Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with candidate genes in WHYC.