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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doaj-52680e8f4b2a4c39a8087e0358de27e92021-03-04T12:24:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-011510e024113710.1371/journal.pone.0241137Genomic variations and signatures of selection in Wuhua yellow chicken.Zhuoxian WengYongjie XuWeina LiJiebo ChenMing ZhongFusheng ZhongBingwang DuBin ZhangXunhe HuangWuhua 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.https://doi.org/10.1371/journal.pone.0241137 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Zhuoxian Weng Yongjie Xu Weina Li Jiebo Chen Ming Zhong Fusheng Zhong Bingwang Du Bin Zhang Xunhe Huang |
spellingShingle |
Zhuoxian Weng Yongjie Xu Weina Li Jiebo Chen Ming Zhong Fusheng Zhong Bingwang Du Bin Zhang Xunhe Huang Genomic variations and signatures of selection in Wuhua yellow chicken. PLoS ONE |
author_facet |
Zhuoxian Weng Yongjie Xu Weina Li Jiebo Chen Ming Zhong Fusheng Zhong Bingwang Du Bin Zhang Xunhe Huang |
author_sort |
Zhuoxian Weng |
title |
Genomic variations and signatures of selection in Wuhua yellow chicken. |
title_short |
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_sort |
genomic variations and signatures of selection in wuhua yellow chicken. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2020-01-01 |
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. |
url |
https://doi.org/10.1371/journal.pone.0241137 |
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