Abstract
Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken from China, which is characterized by its white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of these unique traits associated with WHYC is poorly understood. In this study, whole-genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 single nucleotide polymorphisms and 1,069,574 insertion/deletions were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. Comparative genomic analysis of WHYC and other yellow-feathered chicken breeds showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interactions. Several genes associated with disease resistance were also identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, our results suggest that PMEL and TYRP1 may contribute to the white feather coloring in WHYC. These findings can improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.
Highlights
Domestic chickens (Gallus gallus domesticus), the first domesticated bird, have gone through evolution by natural selection and artificial selection for more than 8,000 years [1,2]
Domestic chickens have many typical domestication characteristics compared with their wild ancestor, including body size, reproduction, growth rate, feather color, and behavior, the appearance of which may be closely related to human civilization [6]
The sequencing data of 12 Wuhua yellow chicken (WHYC) are available in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under accession number PRJNA624239
Summary
Domestic chickens (Gallus gallus domesticus), the first domesticated bird, have gone through evolution by natural selection and artificial selection (e.g., breeding for entertainment and consumption) for more than 8,000 years [1,2]. During the long history of domestication, several hundreds of distinct breeds have been reported worldwide [2,3]. Their meat and eggs are an important source of animal protein for humans. Domestic chickens have many typical domestication characteristics compared with their wild ancestor (the red jungle fowl), including body size, reproduction, growth rate, feather color, and behavior, the appearance of which may be closely related to human civilization [6]. Clarifying the genetic mechanisms underlying population differentiation and doi:10.20944/preprints202006.0089.v1 breeding history will improve our understanding of the evolution, domestication, and phenotypes of chickens and will provide new insights for future breeding programs [7]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
