{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T15:40:15Z","timestamp":1793720415990,"version":"4.6.1"},"reference-count":70,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2024,10,30]],"date-time":"2024-10-30T00:00:00Z","timestamp":1730246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Yunnan Swine Industry Technology System Program","award":["2023KJTX016"],"award-info":[{"award-number":["2023KJTX016"]}]},{"name":"Yunnan Swine Industry Technology System Program","award":["202102AE090039"],"award-info":[{"award-number":["202102AE090039"]}]},{"name":"Yunnan Swine Industry Technology System Program","award":["YNWR-CYJS-2018-056"],"award-info":[{"award-number":["YNWR-CYJS-2018-056"]}]},{"name":"Yunnan Swine Industry Technology System Program","award":["202301BD070001-075"],"award-info":[{"award-number":["202301BD070001-075"]}]},{"name":"Yunnan Province Important National Science &amp; Technology Specific Projects","award":["2023KJTX016"],"award-info":[{"award-number":["2023KJTX016"]}]},{"name":"Yunnan Province Important National Science &amp; Technology Specific Projects","award":["202102AE090039"],"award-info":[{"award-number":["202102AE090039"]}]},{"name":"Yunnan Province Important National Science &amp; Technology Specific Projects","award":["YNWR-CYJS-2018-056"],"award-info":[{"award-number":["YNWR-CYJS-2018-056"]}]},{"name":"Yunnan Province Important National Science &amp; Technology Specific Projects","award":["202301BD070001-075"],"award-info":[{"award-number":["202301BD070001-075"]}]},{"name":"Yunnan Province Agricultural Joint Specific Project","award":["2023KJTX016"],"award-info":[{"award-number":["2023KJTX016"]}]},{"name":"Yunnan Province Agricultural Joint Specific Project","award":["202102AE090039"],"award-info":[{"award-number":["202102AE090039"]}]},{"name":"Yunnan Province Agricultural Joint Specific Project","award":["YNWR-CYJS-2018-056"],"award-info":[{"award-number":["YNWR-CYJS-2018-056"]}]},{"name":"Yunnan Province Agricultural Joint Specific Project","award":["202301BD070001-075"],"award-info":[{"award-number":["202301BD070001-075"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Zhaotong pig (ZTP) is a Chinese indigenous pig breed in Yunnan Province, known for its unique body shape and appearance, good meat quality, strong foraging ability, and adaptability. However, there is still a lack of research on its genome. In order to investigate the genetic diversity, population structure, and selection signatures of the breed, we conducted a comprehensive analysis by resequencing on 30 ZTPs and comparing them with genomic data from 10 Asian wild boars (AWBs). A total of 45,514,452 autosomal SNPs were detected in the 40 pigs, and 23,649,650 SNPs were retained for further analysis after filtering. The HE, HO, PN, MAF, \u03c0, and Fis values were calculated to evaluate the genetic diversity, and the results showed that ZTPs had higher genetic diversity and lower inbreeding coefficient compared with AWBs. Population structure was analyzed using NJ tree, PCA, ADMIXTURE, and LD methods. It was found that ZTPs were population independent of AWBs and had a lower LD decay compared to AWBs. Moreover, the results of the IBS genetic distance and G matrix showed that most of the individuals had large genetic distances and distant genetic relationships in ZTPs. Selection signatures were detected between ZTPs and AWBs by using two methods, FST and \u03c0 ratio. Totals of 1104 selected regions and 275 candidate genes were identified. Finally, functional enrichment analysis identified some annotated genes that might affect fat deposition (NPY1R, NPY5R, and NMU), reproduction (COL3A1, COL5A2, GLRB, TAC3, and MAP3K12), growth (STAT6 and SQOR), tooth development (AMBN, ENAM, and ODAM), and immune response (MBL2, IL1A, and DNAJA3). Our results will provide a valuable basis for the future effective protection, breeding, and utilization of ZTPs.<\/jats:p>","DOI":"10.3390\/ani14213129","type":"journal-article","created":{"date-parts":[[2024,10,31]],"date-time":"2024-10-31T08:44:04Z","timestamp":1730364244000},"page":"3129","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Population Structure and Selection Signatures in Chinese Indigenous Zhaotong Pigs Revealed by Whole-Genome Resequencing"],"prefix":"10.3390","volume":"14","author":[{"given":"Yixuan","family":"Zhu","sequence":"first","affiliation":[{"name":"Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyi","family":"Wang","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongli","family":"Yang","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lixing","family":"Wang","sequence":"additional","affiliation":[{"name":"Yunnan Provincial Livestock Station, Kunming 650506, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0447-7727","authenticated-orcid":false,"given":"Chengliang","family":"Xu","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenkun","family":"Xu","sequence":"additional","affiliation":[{"name":"Yunnan Provincial Livestock Station, Kunming 650506, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4077-0216","authenticated-orcid":false,"given":"Qiang","family":"Chen","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingli","family":"Li","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoxiong","family":"Lu","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/ng.3199","article-title":"Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing","volume":"47","author":"Ai","year":"2015","journal-title":"Nat. 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