{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T02:03:59Z","timestamp":1783994639856,"version":"3.55.0"},"reference-count":100,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T00:00:00Z","timestamp":1783900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFE0113300"],"award-info":[{"award-number":["2022YFE0113300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation of Inner Mongolia Autonomous Region of China","award":["2025JQ022"],"award-info":[{"award-number":["2025JQ022"]}]},{"DOI":"10.13039\/501100011811","name":"Outstanding Youth Science Fund Cultivation Project of Inner Mongolia Agricultural University","doi-asserted-by":"publisher","award":["BR230304"],"award-info":[{"award-number":["BR230304"]}],"id":[{"id":"10.13039\/501100011811","id-type":"DOI","asserted-by":"publisher"}]},{"name":"China Agriculture Research System of MOF and MARA","award":["CARS-39"],"award-info":[{"award-number":["CARS-39"]}]},{"name":"Inner Mongolia Education Department Special Research Project For First Class Disciplines","award":["YLXKZX-NND-007"],"award-info":[{"award-number":["YLXKZX-NND-007"]}]},{"name":"Special A-class Team Project for Research and Innovation Team Construction of Inner Mongolia Agricultural University","award":["BR251201"],"award-info":[{"award-number":["BR251201"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>High-altitude environments, characterized by hypoxia, intense ultraviolet radiation, and low temperatures, pose major challenges to livestock survival. In recent years, researchers have gradually uncovered adaptive mechanisms in livestock across different altitudes using whole-genome resequencing. Previous studies of goat altitude adaptation have been limited by small breed numbers and low sequencing depth, hindering comprehensive exploration of adaptive mechanisms across different altitudes. This study analyzed whole-genome resequencing data from 151 individuals across 17 goat breeds representing three distinct altitude gradients (high, middle, and low). Using both SNPs and structural variations (SVs), we characterized population relationships, gene flow, and the SV landscape, including QTL\u2013SV associations and transposable element interactions. Selective sweep analyses using FST, \u03b8\u03c0 ratio, XP-CLR, XP-EHH, and LFMM identified several candidate genes associated with altitude adaptation, including ABCC4, RPS6, DSG4, and LY9, which were significantly enriched in pathways related to hypoxia response, oxidative stress, energy metabolism, angiogenesis, and nervous system regulation. Notably, ABCC4 showed ABCC4 showed recurrent candidate selection signals in both SNP and SV analyses, suggesting its potential involvement in altitude adaptation. These findings provide multi-level genomic evidence for goat adaptation to high-altitude stress and provide important insights into the adaptive evolution of goats.<\/jats:p>","DOI":"10.3390\/ani16142177","type":"journal-article","created":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T00:55:21Z","timestamp":1783990521000},"page":"2177","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated SNP and SV Analyses Reveal Genetic Mechanisms Underlying High-Altitude Adaptation in Goats"],"prefix":"10.3390","volume":"16","author":[{"given":"Wenze","family":"Li","sequence":"first","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yixin","family":"Su","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Can","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaokun","family":"Lin","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanhui","family":"Xue","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6808-1765","authenticated-orcid":false,"given":"Bouabid","family":"Badaoui","sequence":"additional","affiliation":[{"name":"Laboratory of Biodiversity, Ecology and Genome, Department of Biology, Faculty of Sciences Rabat, Mohammed V University, Rabat 10106, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaochun","family":"Yan","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1513-8921","authenticated-orcid":false,"given":"Qi","family":"Lv","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8386-7408","authenticated-orcid":false,"given":"Rui","family":"Su","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"11597","DOI":"10.1073\/pnas.0801317105","article-title":"Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact","volume":"105","author":"Zeder","year":"2008","journal-title":"Proc. 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