Genetic structure and characteristics of Tibetan chickens
ABSTRACT: Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic d...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-08-01
|
| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579123002869 |
| _version_ | 1827891013012684800 |
|---|---|
| author | Shijun Li Xiaojian Zhang Xinyu Dong Ruiyang Guo Jiuhong Nan Jingwei Yuan Carina M. Schlebusch Zheya Sheng |
| author_facet | Shijun Li Xiaojian Zhang Xinyu Dong Ruiyang Guo Jiuhong Nan Jingwei Yuan Carina M. Schlebusch Zheya Sheng |
| author_sort | Shijun Li |
| collection | DOAJ |
| description | ABSTRACT: Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design. |
| first_indexed | 2024-03-12T21:17:46Z |
| format | Article |
| id | doaj.art-55d5c6e9c5b64deb835d4f7b90fd95f5 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-03-12T21:17:46Z |
| publishDate | 2023-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-55d5c6e9c5b64deb835d4f7b90fd95f52023-07-29T04:34:17ZengElsevierPoultry Science0032-57912023-08-011028102767Genetic structure and characteristics of Tibetan chickensShijun Li0Xiaojian Zhang1Xinyu Dong2Ruiyang Guo3Jiuhong Nan4Jingwei Yuan5Carina M. Schlebusch6Zheya Sheng7Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaDepartment of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, SwedenKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Corresponding author:ABSTRACT: Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.http://www.sciencedirect.com/science/article/pii/S0032579123002869Tibetan chickenpopulation structurecomplex demographygenetic analyses |
| spellingShingle | Shijun Li Xiaojian Zhang Xinyu Dong Ruiyang Guo Jiuhong Nan Jingwei Yuan Carina M. Schlebusch Zheya Sheng Genetic structure and characteristics of Tibetan chickens Poultry Science Tibetan chicken population structure complex demography genetic analyses |
| title | Genetic structure and characteristics of Tibetan chickens |
| title_full | Genetic structure and characteristics of Tibetan chickens |
| title_fullStr | Genetic structure and characteristics of Tibetan chickens |
| title_full_unstemmed | Genetic structure and characteristics of Tibetan chickens |
| title_short | Genetic structure and characteristics of Tibetan chickens |
| title_sort | genetic structure and characteristics of tibetan chickens |
| topic | Tibetan chicken population structure complex demography genetic analyses |
| url | http://www.sciencedirect.com/science/article/pii/S0032579123002869 |
| work_keys_str_mv | AT shijunli geneticstructureandcharacteristicsoftibetanchickens AT xiaojianzhang geneticstructureandcharacteristicsoftibetanchickens AT xinyudong geneticstructureandcharacteristicsoftibetanchickens AT ruiyangguo geneticstructureandcharacteristicsoftibetanchickens AT jiuhongnan geneticstructureandcharacteristicsoftibetanchickens AT jingweiyuan geneticstructureandcharacteristicsoftibetanchickens AT carinamschlebusch geneticstructureandcharacteristicsoftibetanchickens AT zheyasheng geneticstructureandcharacteristicsoftibetanchickens |