Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds
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 proper...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2020
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110642 |
| _version_ | 1855539471831793664 |
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| author | Huang, X. Otecko, N.O. Peng, M. Weng, Z. Li, W. Chen, J. Zhong, M. Zhong, F. Jin, S. Geng, Z. Luo, W. He, D. Ma, C. Han Jianlin Ommeh, S.C. Zhang, Y. Zhang, X. Du, B. |
| author_browse | Chen, J. Du, B. Geng, Z. Han Jianlin He, D. Huang, X. Jin, S. Li, W. Luo, W. Ma, C. Ommeh, S.C. Otecko, N.O. Peng, M. Weng, Z. Zhang, X. Zhang, Y. Zhong, F. Zhong, M. |
| author_facet | Huang, X. Otecko, N.O. Peng, M. Weng, Z. Li, W. Chen, J. Zhong, M. Zhong, F. Jin, S. Geng, Z. Luo, W. He, D. Ma, C. Han Jianlin Ommeh, S.C. Zhang, Y. Zhang, X. Du, B. |
| author_sort | Huang, X. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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.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.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 | Journal Article |
| id | CGSpace110642 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1106422025-01-27T15:00:52Z Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds Huang, X. Otecko, N.O. Peng, M. Weng, Z. Li, W. Chen, J. Zhong, M. Zhong, F. Jin, S. Geng, Z. Luo, W. He, D. Ma, C. Han Jianlin Ommeh, S.C. Zhang, Y. Zhang, X. Du, B. animal breeding breeds chickens indigenous breeds poultry 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.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.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. 2020-12 2020-12-27T14:22:57Z 2020-12-27T14:22:57Z Journal Article https://hdl.handle.net/10568/110642 en Open Access Springer Huang, X., Otecko, N.O., Peng, M., Weng, Z., Li, W., Chen, J., Zhong, M., Zhong, F., Jin, S., Geng, Z., Luo, W., He, D., Ma, C., Han, J., Ommeh, S.C., Zhang, Y., Zhang, X. and Du, B. 2020. Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds. BMC Genomics 21(1):316. |
| spellingShingle | animal breeding breeds chickens indigenous breeds poultry Huang, X. Otecko, N.O. Peng, M. Weng, Z. Li, W. Chen, J. Zhong, M. Zhong, F. Jin, S. Geng, Z. Luo, W. He, D. Ma, C. Han Jianlin Ommeh, S.C. Zhang, Y. Zhang, X. Du, B. 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 | animal breeding breeds chickens indigenous breeds poultry |
| url | https://hdl.handle.net/10568/110642 |
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