Genome-environment association analysis reveals climate-driven adaptation of chickens
Abstract Background Domestic chickens are one of the most widely raised and distributed bird species, exhibiting remarkable environmental adaptability, which makes them valuable model organisms for investigating the genetic mechanisms underlying climate adaptation. This study aimed to enhance our un...
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| Format: | Article |
| Language: | deu |
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BMC
2025-07-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-025-00989-9 |
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| _version_ | 1849238093851262976 |
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| author | Xiurong Zhao Jinxin Zhang Junhui Wen Xinye Zhang Haiying Li Huie Wang Tao Zhu Changsheng Nie Xinghua Li Weifang Yang Guomin Cao Wenjie Xiong Xue Wang Zhonghua Ning Lujiang Qu |
| author_facet | Xiurong Zhao Jinxin Zhang Junhui Wen Xinye Zhang Haiying Li Huie Wang Tao Zhu Changsheng Nie Xinghua Li Weifang Yang Guomin Cao Wenjie Xiong Xue Wang Zhonghua Ning Lujiang Qu |
| author_sort | Xiurong Zhao |
| collection | DOAJ |
| description | Abstract Background Domestic chickens are one of the most widely raised and distributed bird species, exhibiting remarkable environmental adaptability, which makes them valuable model organisms for investigating the genetic mechanisms underlying climate adaptation. This study aimed to enhance our understanding of adaptive mechanisms in chickens by jointly analyzing genomic variations and climatic variables related to temperature and precipitation. To this end, whole-genome sequencing data were collected from 199 indigenous domestic chickens raised under diverse environmental conditions worldwide, and three genome-environment association analyses were performed. Results We identified 184 genes potentially associated with climate adaptation in chickens. Among these, the TSHR gene may play multiple roles in adaptation driven by different climatic factors. Immune-related genes also appear to contribute to climate adaptation in chickens. By calculating the allele frequencies of single nucleotide polymorphisms (SNPs) within candidate genes associated with temperature and precipitation adaptation, we identified five SNPs within four genes (ZNF536, ENSGALG00000049158, PAPPA, and EHMT1) that exhibited distinct geographic distribution patterns. Extended haplotype homozygosity (EHH) analysis of these SNPs revealed that haplotypes carrying the mutant allele exhibited slower decay in EHH compared to those carrying the wild-type allele. These results further indicate that the loci have experienced strong selective pressures, suggesting that the associated genes may play crucial roles in climate adaptation in chickens. Conclusions Overall, this study provides new insights into the genetic mechanisms underlying climate adaptation in domestic chickens. |
| format | Article |
| id | doaj-art-64f58140a0604dfb887db7b9293f92d9 |
| institution | Kabale University |
| issn | 1297-9686 |
| language | deu |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj-art-64f58140a0604dfb887db7b9293f92d92025-08-20T04:01:47ZdeuBMCGenetics Selection Evolution1297-96862025-07-0157111410.1186/s12711-025-00989-9Genome-environment association analysis reveals climate-driven adaptation of chickensXiurong Zhao0Jinxin Zhang1Junhui Wen2Xinye Zhang3Haiying Li4Huie Wang5Tao Zhu6Changsheng Nie7Xinghua Li8Weifang Yang9Guomin Cao10Wenjie Xiong11Xue Wang12Zhonghua Ning13Lujiang Qu14College of Grassland Science and Technology, China Agricultural UniversityFisheries Science Institute, Beijing Academy of Agriculture and Forestry SciencesInstitute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry SciencesNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityCollege of Animal Science, Xinjiang Agricultural UniversityKey Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Corps, Tarim UniversityNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityBeijing Municipal General Station of Animal ScienceAnimal Husbandry Station of FangchenggangAnimal Disease Prevention and Control Center of FangchenggangVVBK Animal Medical Diagnostic TechnologyNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityAbstract Background Domestic chickens are one of the most widely raised and distributed bird species, exhibiting remarkable environmental adaptability, which makes them valuable model organisms for investigating the genetic mechanisms underlying climate adaptation. This study aimed to enhance our understanding of adaptive mechanisms in chickens by jointly analyzing genomic variations and climatic variables related to temperature and precipitation. To this end, whole-genome sequencing data were collected from 199 indigenous domestic chickens raised under diverse environmental conditions worldwide, and three genome-environment association analyses were performed. Results We identified 184 genes potentially associated with climate adaptation in chickens. Among these, the TSHR gene may play multiple roles in adaptation driven by different climatic factors. Immune-related genes also appear to contribute to climate adaptation in chickens. By calculating the allele frequencies of single nucleotide polymorphisms (SNPs) within candidate genes associated with temperature and precipitation adaptation, we identified five SNPs within four genes (ZNF536, ENSGALG00000049158, PAPPA, and EHMT1) that exhibited distinct geographic distribution patterns. Extended haplotype homozygosity (EHH) analysis of these SNPs revealed that haplotypes carrying the mutant allele exhibited slower decay in EHH compared to those carrying the wild-type allele. These results further indicate that the loci have experienced strong selective pressures, suggesting that the associated genes may play crucial roles in climate adaptation in chickens. Conclusions Overall, this study provides new insights into the genetic mechanisms underlying climate adaptation in domestic chickens.https://doi.org/10.1186/s12711-025-00989-9 |
| spellingShingle | Xiurong Zhao Jinxin Zhang Junhui Wen Xinye Zhang Haiying Li Huie Wang Tao Zhu Changsheng Nie Xinghua Li Weifang Yang Guomin Cao Wenjie Xiong Xue Wang Zhonghua Ning Lujiang Qu Genome-environment association analysis reveals climate-driven adaptation of chickens Genetics Selection Evolution |
| title | Genome-environment association analysis reveals climate-driven adaptation of chickens |
| title_full | Genome-environment association analysis reveals climate-driven adaptation of chickens |
| title_fullStr | Genome-environment association analysis reveals climate-driven adaptation of chickens |
| title_full_unstemmed | Genome-environment association analysis reveals climate-driven adaptation of chickens |
| title_short | Genome-environment association analysis reveals climate-driven adaptation of chickens |
| title_sort | genome environment association analysis reveals climate driven adaptation of chickens |
| url | https://doi.org/10.1186/s12711-025-00989-9 |
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