Genomic insights into local adaptation of indigenous chickens
6 affiliations
- 1State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- 2Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu 225125, China
- 3Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- 4Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
- 5Nujiang Promotion Station of Livestock Technology, Nujiang, Yunnan 673199, China
- 6Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
Abstract
Indigenous chickens are an essential part of biodiversity and a vital protein resource to humans, yet global warming and environmental changes pose serious threats to their survival and productivity. Therefore, assessing population adaptive capacity under shifting environments is crucial for breeding resilient animals, and guiding conservation strategies. Here, we integrated ecological and whole-genome resequencing data from 1022 chickens from 44 Chinese indigenous populations to reveal genomic signatures of local adaptation. From 87 agroclimatic variables, we identified eight dominant environmental factors including solar radiation, precipitation, diurnal temperature range, and five landcover variables (cropland areas, water areas, trees coverage, bare ground and shrubs coverage) that shape ecological niches of indigenous chickens. Landscape and comparative genomics analyses revealed both known and novel candidate genes, such as UNC80, PTPRO, NCOR2, CSF2RB, NXT2 and PALLD for the solar radiation, precipitation, diurnal temperature range, cropland areas, trees coverage and bare ground, respectively. Particularly, adaptive non-coding variants harbored in these genes exhibited spatial allelic changes across populations and acted as regulatory elements via chromatin accessibility and DNA methylation, influencing adaptation in a tissue-specific manner. Our findings underscore the rich genetic diversity of Chinese indigenous chickens and provide new insights into genomic mechanisms of local adaptation, offering valuable references for domestic animal breeding, conservation, and climate resilience.
Related
- Integrative insights into physiology, nutrient dynamics and multi-omics reveal climate stress adaptation and genomic gaps in Rhododendron
- Osteomorphological Description and Osteometric Variation of Long Bones in Ethiopian Indigenous Naked Neck Chickens in Quara District, Northwest Ethiopia
- Genomic signals of local adaptation in UK black alder populations (Alnus glutinosa)
- Population Genomic Insights into Genetic Differentiation and Environmental Adaptation of the Asian Honey Bee (Apis cerana) in Sichuan, China.
- Climate-associated genomic variation across life stages reveals population-specific signals of local adaptation in European beech
BibTeX
@article{yuan2026genomic,
title = {{Genomic insights into local adaptation of indigenous chickens}},
author = {Jing-Wei Yuan and Xiao-Xu Jia and Xiao-Long Huang and Yun-Lei Li and Ai-Xin Ni and Guo-Hong Chen and Nen-Zhu Zheng and Sheng He and Yan-Yan Sun and Guo-Qiang Yi and Wei Han and Ji-Lan Chen},
journal = {Zoological Research},
year = {2026},
month = sep,
doi = {10.24272/j.issn.2095-8137.2025.592},
url = {https://doi.org/10.24272/j.issn.2095-8137.2025.592},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Genomic insights into local adaptation of indigenous chickens
AU - Jing-Wei Yuan
AU - Xiao-Xu Jia
AU - Xiao-Long Huang
AU - Yun-Lei Li
AU - Ai-Xin Ni
AU - Guo-Hong Chen
AU - Nen-Zhu Zheng
AU - Sheng He
AU - Yan-Yan Sun
AU - Guo-Qiang Yi
AU - Wei Han
AU - Ji-Lan Chen
PY - 2026
DA - 2026/09/18
JO - Zoological Research
DO - 10.24272/j.issn.2095-8137.2025.592
UR - https://doi.org/10.24272/j.issn.2095-8137.2025.592
AB - Indigenous chickens are an essential part of biodiversity and a vital protein resource to humans, yet global warming and environmental changes pose serious threats to their survival and productivity. Therefore, assessing population adaptive capacity under shifting environments is crucial for breeding resilient animals, and guiding conservation strategies. Here, we integrated ecological and whole-genome resequencing data from 1022 chickens from 44 Chinese indigenous populations to reveal genomic signatures of local adaptation. From 87 agroclimatic variables, we identified eight dominant environmental factors including solar radiation, precipitation, diurnal temperature range, and five landcover variables (cropland areas, water areas, trees coverage, bare ground and shrubs coverage) that shape ecological niches of indigenous chickens. Landscape and comparative genomics analyses revealed both known and novel candidate genes, such as UNC80, PTPRO, NCOR2, CSF2RB, NXT2 and PALLD for the solar radiation, precipitation, diurnal temperature range, cropland areas, trees coverage and bare ground, respectively. Particularly, adaptive non-coding variants harbored in these genes exhibited spatial allelic changes across populations and acted as regulatory elements via chromatin accessibility and DNA methylation, influencing adaptation in a tissue-specific manner. Our findings underscore the rich genetic diversity of Chinese indigenous chickens and provide new insights into genomic mechanisms of local adaptation, offering valuable references for domestic animal breeding, conservation, and climate resilience.
SN - 2095-8137
ER -