Evidence map›Paper›PMID 41443473›Full record

ArticleJournal of advanced research2026

Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens.

Semiu Folaniyi Bello, Endashaw Terefe, Haoqiang Ye, Adeniyi Charles Adeola, Zhen Zhou, Endashaw Jebessa, Lin Qi, Ridwan Olawale Ahmed, Kelvin Dodzi Aloryi, Obiajulu Emenike Ositanwosu and 12 more

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Article in Journal of advanced research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

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2citing papers in PubMed
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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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2 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

22 authors.

Semiu Folaniyi BelloState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China; Agriculture Research Group, Organization of African Academic Doctors (OAAD), Off Kamiti Road, P. O. Box 25305-00100, Nairobi, Kenya.
Endashaw TerefeArsi University, College of Agriculture and Environmental Science, Department of Animal Science, Asella, Ethiopia.
Haoqiang YeState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
Adeniyi Charles AdeolaState Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
Zhen ZhouState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
Endashaw JebessaState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Lin QiState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
Ridwan Olawale AhmedDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, United States.
Kelvin Dodzi AloryiDepartment of Horticultural Sciences, University of Florida, Gainesville, FL, United States.
Obiajulu Emenike OsitanwosuDepartment of Computer Science, Nnamdi Azikiwe University, P.M.B. 5025, Awka, Nigeria.
Sunday James EludodunDepartment of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria.
Zhaofeng ZhangState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
Bashir Bolaji TiamiyuDepartment of Plant Biology, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria; Department of Plant Science and Landscape Architecture, University of Connecticut, United States.
Afusat Kikelomo LadejobiAnimal Biotechnology Unit, Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, P.M.B 2240, Nigeria.
Abulgasim M AhbaraAnimal and Veterinary Sciences, SRUC, The Roslin Institute Building, Midlothian, Edinburgh, United Kingdom; Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya.
Bashir SalimCamel Research Center, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia.
Dylan O'Neill RothenbergCollege of Horticulture, South China Agricultural University, Guangzhou 510642 Guangdong, China.
Oludoyin Adeseun AdigunDepartment of Biology, University of Waterloo, Waterloo ON N2L 3G1, Canada; School of Science and the Environment/Boreal Ecosystems and Agricultural Sciences, Grenfell Campus, Memorial University of Newfoundland, Corner Brook, NL A2H 5G4, Canada.
Xiquan ZhangState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
Bolin CaiState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China. Electronic address: bolincai@scau.edu.cn.
Olivier HanotteLiveGene-Centre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia; School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom. Electronic address: olivier.hanotte@nottingham.ac.uk.
Qinghua NieState Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China. Electronic address: nqinghua@scau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

introductionDomestic chickens primarily descended from the wild red junglefowl, play a crucial role in global egg and meat production. China hosts diverse indigenous chicken populations that have adapted to various environmental conditions, including high-altitude with hypoxic and ultraviolet radiation stress.

methodWe analyzed whole-genome sequences of 118 birds from five Indigenous Chinese chicken populations and 295 chicken genomes from publicly available databases to identify genomic diversity, admixture, and selection signatures of chickens adapted to high-altitude environments. Selection signatures were identified using nucleotide diversity (π), Tajima's D, XPEHH, and XP-CLR, selection scan methods.

resultsWe observed a reduction in genetic diversity and historical declines in effective population size in high-altitude chicken, suggesting ongoing selection pressures shaping these populations. Selection scans identified nine genomic regions under strong positive selection, enriched for genes associated with hypoxia and ultraviolet radiation. Notably, five genes (TPK1, BAZ2B, MARCHF7, LLGL2, and RCAN3) were repeatedly detected across multiple selection signature analyses. RNA-seq analysis further confirmed the differential expression of these genes in the lung and heart tissues of chickens adapted to high and low altitudes, reinforcing their role in physiological adaptation to hypoxic environments. Altitude adaptation is driven by the selection of genes involved in oxygen metabolism, cellular stress response, and energy regulation.

conclusionOur study provides compelling genetic evidence for differentiation between high and low and high-altitude Chinese chicken populations. These findings also ensure our understanding of local adaptation in poultry and establish a genomic framework for breeding strategies to improve environmental resilience to altitude-related stressors.

Indexed as

Adaptation, PhysiologicalChickensGenetic VariationHypoxiaUltraviolet RaysWhole Genome SequencingAltitudeAnimalsChinaGenomeSelection, GeneticAltitude adaptationChickenGenetic diversityHypoxia adaptationSelection signatureWhole genome sequencing

Identifiers

PMID41443473
PMCPMC13539225

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