{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T16:38:34Z","timestamp":1792600714280,"version":"4.5.0"},"reference-count":138,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T00:00:00Z","timestamp":1791504000000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFD1301200"],"award-info":[{"award-number":["2021YFD1301200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shaanxi Provincial Key R&D Program on Agricultural Core Technology Tackling","award":["2025NYGG006"],"award-info":[{"award-number":["2025NYGG006"]}]},{"name":"Modern Agricultural Industry Technology System of Shaanxi Province"},{"name":"Innovation Capability Support Program of Shaanxi","award":["2025JC-GXPT-013"],"award-info":[{"award-number":["2025JC-GXPT-013"]}]},{"name":"National Foreign Expert Project","award":["110000207920258086"],"award-info":[{"award-number":["110000207920258086"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>As one of the earliest domesticated and most globally ubiquitous livestock, pigs (Sus scrofa) have undergone profound environmental adaptation while following human expansion across diverse bioclimatic zones. Despite their evolutionary significance, the genomic mechanisms enabling pigs to thrive in disparate ecological settings remain poorly understood. Here, we present a comprehensive global analysis using a dataset of 1,151 pig genome sequences representing 146 distinct populations. By integrating three complementary genotype\u2013environment association (GEA) frameworks including redundancy analysis (RDA), BayPass, and latent factor mixed models (LFMM), we identified genomic regions and candidate genes associated with environmental variation. Our analysis detected several candidate genes associated with high-altitude adaptation, particularly those involved in ultraviolet radiation response. By integrating lung single-cell RNA sequencing analysis (scRNA) from high-altitude and commercial breeds, we identified ASXL1 as a candidate gene potentially involved in high-altitude adaptation. Meanwhile, scRNA revealed candidate regulatory pathways, including the NOTCH signaling pathway, that were overlooked by traditional GEA methods, suggesting the complex regulatory landscape of physiological adaptation. Together, this study integrates large-scale population genomics and scRNA to provide insights into the genetic associations and regulatory landscapes potentially contributing to environmental adaptation in domestic pigs, advancing our understanding of livestock evolutionary responses to diverse ecological conditions.<\/jats:p>","DOI":"10.1093\/molbev\/msag260","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T11:55:24Z","timestamp":1791374124000},"source":"Crossref","is-referenced-by-count":0,"title":["Integrative genotype\u2013environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs"],"prefix":"10.1093","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7765-469X","authenticated-orcid":false,"given":"Dong","family":"Li","sequence":"first","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]},{"name":"Animal Breeding and Genomics, Wageningen University and Research , Wageningen 6700 AH ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3741-0006","authenticated-orcid":false,"given":"Tiantian","family":"Yuan","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6746-3580","authenticated-orcid":false,"given":"Xiang","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-5905-3632","authenticated-orcid":false,"given":"Yu","family":"Quan","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9222-7082","authenticated-orcid":false,"given":"Xuekai","family":"Tian","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6048-4254","authenticated-orcid":false,"given":"Ye","family":"Cheng","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0055-388X","authenticated-orcid":false,"given":"Yulong","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9141-2216","authenticated-orcid":false,"given":"Xinglong","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-9707-4020","authenticated-orcid":false,"given":"Boyuan","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1788-7093","authenticated-orcid":false,"given":"Wansheng","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University , University Park, PA 16802 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4821-3585","authenticated-orcid":false,"given":"Yu","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7583-1576","authenticated-orcid":false,"given":"Rongrong","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0484-4545","authenticated-orcid":false,"given":"Martien A M","family":"Groenen","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genomics, Wageningen University and Research , Wageningen 6700 AH ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1317-5654","authenticated-orcid":false,"given":"Martijn F L","family":"Derks","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genomics, Wageningen University and Research , Wageningen 6700 AH ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6951-9968","authenticated-orcid":false,"given":"Taiyong","family":"Yu","sequence":"additional","affiliation":[{"name":"College of 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