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Genomic variations and signatures of selection in Wuhua yellow chicken

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 s...

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Autores principales: Weng, Zhuoxian, Xu, Yongjie, Li, Weina, Chen, Jiebo, Zhong, Ming, Zhong, Fusheng, Du, Bingwang, Zhang, Bin, Huang, Xunhe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584229/
https://www.ncbi.nlm.nih.gov/pubmed/33095808
http://dx.doi.org/10.1371/journal.pone.0241137
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author Weng, Zhuoxian
Xu, Yongjie
Li, Weina
Chen, Jiebo
Zhong, Ming
Zhong, Fusheng
Du, Bingwang
Zhang, Bin
Huang, Xunhe
author_facet Weng, Zhuoxian
Xu, Yongjie
Li, Weina
Chen, Jiebo
Zhong, Ming
Zhong, Fusheng
Du, Bingwang
Zhang, Bin
Huang, Xunhe
author_sort Weng, Zhuoxian
collection PubMed
description 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.
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spelling pubmed-75842292020-10-28 Genomic variations and signatures of selection in Wuhua yellow chicken Weng, Zhuoxian Xu, Yongjie Li, Weina Chen, Jiebo Zhong, Ming Zhong, Fusheng Du, Bingwang Zhang, Bin Huang, Xunhe PLoS One Research Article 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. Public Library of Science 2020-10-23 /pmc/articles/PMC7584229/ /pubmed/33095808 http://dx.doi.org/10.1371/journal.pone.0241137 Text en © 2020 Weng et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Weng, Zhuoxian
Xu, Yongjie
Li, Weina
Chen, Jiebo
Zhong, Ming
Zhong, Fusheng
Du, Bingwang
Zhang, Bin
Huang, Xunhe
Genomic variations and signatures of selection in Wuhua yellow chicken
title Genomic variations and signatures of selection in Wuhua yellow chicken
title_full Genomic variations and signatures of selection in Wuhua yellow chicken
title_fullStr Genomic variations and signatures of selection in Wuhua yellow chicken
title_full_unstemmed Genomic variations and signatures of selection in Wuhua yellow chicken
title_short Genomic variations and signatures of selection in Wuhua yellow chicken
title_sort genomic variations and signatures of selection in wuhua yellow chicken
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584229/
https://www.ncbi.nlm.nih.gov/pubmed/33095808
http://dx.doi.org/10.1371/journal.pone.0241137
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