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Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds
BACKGROUND: Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and bioche...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171827/ https://www.ncbi.nlm.nih.gov/pubmed/32312230 http://dx.doi.org/10.1186/s12864-020-6736-4 |
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author | Huang, Xunhe Otecko, Newton O. Peng, Minsheng Weng, Zhuoxian Li, Weina Chen, Jiebo Zhong, Ming Zhong, Fusheng Jin, Sihua Geng, Zhaoyu Luo, Wei He, Danlin Ma, Cheng Han, Jianlin Ommeh, Sheila C. Zhang, Yaping Zhang, Xiquan Du, Bingwang |
author_facet | Huang, Xunhe Otecko, Newton O. Peng, Minsheng Weng, Zhuoxian Li, Weina Chen, Jiebo Zhong, Ming Zhong, Fusheng Jin, Sihua Geng, Zhaoyu Luo, Wei He, Danlin Ma, Cheng Han, Jianlin Ommeh, Sheila C. Zhang, Yaping Zhang, Xiquan Du, Bingwang |
author_sort | Huang, Xunhe |
collection | PubMed |
description | BACKGROUND: Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration. RESULTS: The whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein (RALY), leucine rich repeat containing G protein-coupled receptor 4 (LGR4), solute carrier family 23 member 2 (SLC23A2), and solute carrier family 2 member 14 (SLC2A14), besides the classical beta-carotene dioxygenase 2 (BCDO2), as major candidates pigment determining genes in the YFCs. CONCLUSION: We provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs. |
format | Online Article Text |
id | pubmed-7171827 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-71718272020-04-24 Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds Huang, Xunhe Otecko, Newton O. Peng, Minsheng Weng, Zhuoxian Li, Weina Chen, Jiebo Zhong, Ming Zhong, Fusheng Jin, Sihua Geng, Zhaoyu Luo, Wei He, Danlin Ma, Cheng Han, Jianlin Ommeh, Sheila C. Zhang, Yaping Zhang, Xiquan Du, Bingwang BMC Genomics Research Article BACKGROUND: Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration. RESULTS: The whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein (RALY), leucine rich repeat containing G protein-coupled receptor 4 (LGR4), solute carrier family 23 member 2 (SLC23A2), and solute carrier family 2 member 14 (SLC2A14), besides the classical beta-carotene dioxygenase 2 (BCDO2), as major candidates pigment determining genes in the YFCs. CONCLUSION: We provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs. BioMed Central 2020-04-20 /pmc/articles/PMC7171827/ /pubmed/32312230 http://dx.doi.org/10.1186/s12864-020-6736-4 Text en © The Author(s). 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Huang, Xunhe Otecko, Newton O. Peng, Minsheng Weng, Zhuoxian Li, Weina Chen, Jiebo Zhong, Ming Zhong, Fusheng Jin, Sihua Geng, Zhaoyu Luo, Wei He, Danlin Ma, Cheng Han, Jianlin Ommeh, Sheila C. Zhang, Yaping Zhang, Xiquan Du, Bingwang Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds |
title | Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds |
title_full | Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds |
title_fullStr | Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds |
title_full_unstemmed | Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds |
title_short | Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds |
title_sort | genome-wide genetic structure and selection signatures for color in 10 traditional chinese yellow-feathered chicken breeds |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171827/ https://www.ncbi.nlm.nih.gov/pubmed/32312230 http://dx.doi.org/10.1186/s12864-020-6736-4 |
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