{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:54:52Z","timestamp":1792788892341,"version":"4.5.0"},"reference-count":57,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T00:00:00Z","timestamp":1755475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012453","name":"China Agriculture Research System","doi-asserted-by":"publisher","award":["CARS-35"],"award-info":[{"award-number":["CARS-35"]}],"id":[{"id":"10.13039\/501100012453","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012453","name":"China Agriculture Research System","doi-asserted-by":"publisher","award":["GuikeJB23023003"],"award-info":[{"award-number":["GuikeJB23023003"]}],"id":[{"id":"10.13039\/501100012453","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangxi Science and Technology Program Project","award":["CARS-35"],"award-info":[{"award-number":["CARS-35"]}]},{"name":"Guangxi Science and Technology Program Project","award":["GuikeJB23023003"],"award-info":[{"award-number":["GuikeJB23023003"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Local adaptation allows animal populations to persist in diverse and changing environments, yet its genomic underpinnings remain poorly characterized in livestock. Chinese indigenous pigs, renowned for their rich phenotypic and ecological diversity, offer a powerful model for investigating environmental adaptation. Here, we integrated whole-genome resequencing data, environmental variables, genotype\u2013environment association (GEA) analyses, and functional annotation to explore the adaptive genomic landscape of 46 native pig breeds across China. Based on 578 individuals and 17.7 million SNPs, we performed genome-wide GEA using latent factor mixed models (LFMMs), identifying 8644 SNPs significantly associated with environmental factors, including 310 linked to precipitation in the wettest quarter (BIO16). Redundancy analysis (RDA) and gradient forest modeling identified BIO16 as a major environmental driver of genomic variation. Functional annotation of BIO16-associated SNPs revealed significant enrichment in regulatory elements and genes highly expressed in the lung, spleen, hypothalamus, and intestine, implicating immune and metabolic pathways in local adaptation. Among the candidate loci, MS4A7 exhibited strong association signals, population differentiation, and tissue-specific regulation, suggesting a role in precipitation-mediated adaptation. This work enhances our understanding of livestock adaptation and informs climate-resilient conservation and breeding strategies.<\/jats:p>","DOI":"10.3390\/ani15162412","type":"journal-article","created":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T07:53:12Z","timestamp":1755503592000},"page":"2412","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Local Climate Adaptation in Chinese Indigenous Pig Genomes"],"prefix":"10.3390","volume":"15","author":[{"given":"Yuqiang","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8812-5558","authenticated-orcid":false,"given":"Guangzhen","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6673-3691","authenticated-orcid":false,"given":"Wondossen","family":"Ayalew","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhanming","family":"Zhong","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7338-7718","authenticated-orcid":false,"given":"Zhe","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"dmm030783","DOI":"10.1242\/dmm.030783","article-title":"Genetically engineered pigs as models for human disease","volume":"11","author":"Perleberg","year":"2018","journal-title":"Dis. 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