{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:35:26Z","timestamp":1787567726778,"version":"build-2736575974"},"reference-count":42,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T00:00:00Z","timestamp":1787443200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"JSPS (Japan Society for the Promotion of Science) KAKENHI","doi-asserted-by":"publisher","award":["19K22367"],"award-info":[{"award-number":["19K22367"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"JSPS (Japan Society for the Promotion of Science) KAKENHI","doi-asserted-by":"publisher","award":["24K01906"],"award-info":[{"award-number":["24K01906"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002241","name":"JST SPRING","doi-asserted-by":"publisher","award":["JPMJSP2148"],"award-info":[{"award-number":["JPMJSP2148"]}],"id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Nepal is a small, landlocked country with marked elevational variation from the Terai plains to the Himalayas. Here, four indigenous goat populations (Chyangra, Sinhal, Khari, and Terai) are raised at different elevations. This study aimed to clarify the genetic structure of these populations and how they are formed and propagated across the Himalayan region. We analyzed 136 Nepalese goats using mitochondrial (mt) DNA D-loop and sex-determining region Y (SRY) 3\u2032-untranslated region (UTR) sequences, as well as 50 K SNP array data. The mtDNA haplogroups D (0.162) and G (0.03) were detected only in Chyangra, whereas haplogroup B was predominant in Sinhal (0.42), followed by Khari (0.260). Regarding SRY haplotypes, Y2B was detected in all populations, whereas Y1AB (0.42) was found only in Chyangra. Genome-wide SNP analysis showed that Chyangra was genetically related to Tibetan and Central Asian goats, while Terai resembled South Asian goats. Interestingly, Sinhal formed a distinct cluster, whereas Khari exhibited an admixed genetic structure. These findings suggest that Nepalese goats originate from at least three ancestral lineages and that an additional migration route may have existed through the southern Himalayas.<\/jats:p>","DOI":"10.3390\/ani16172641","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:20:02Z","timestamp":1787563202000},"page":"2641","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Inference of Genetic Structure and the Process of Population Formation in Nepalese Native Goats Using Uniparental and Genome-Wide Markers"],"prefix":"10.3390","volume":"16","author":[{"given":"Ryo","family":"Masuko","sequence":"first","affiliation":[{"name":"Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuka","family":"Katayama","sequence":"additional","affiliation":[{"name":"Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuto","family":"Nomura","sequence":"additional","affiliation":[{"name":"Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1339-8308","authenticated-orcid":false,"given":"Fuki","family":"Kawaguchi","sequence":"additional","affiliation":[{"name":"Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shinji","family":"Sasazaki","sequence":"additional","affiliation":[{"name":"Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4102-3869","authenticated-orcid":false,"given":"Manoj Kumar","family":"Shah","sequence":"additional","affiliation":[{"name":"National Swine Research Program, Nepal Agricultural Research Council, Pakhribas 56800, Nepal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9367-675X","authenticated-orcid":false,"given":"Jiaqi","family":"Wu","sequence":"additional","affiliation":[{"name":"Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 734-8551, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takahiro","family":"Yonezawa","sequence":"additional","affiliation":[{"name":"Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 734-8551, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5627-7082","authenticated-orcid":false,"given":"Hideyuki","family":"Mannen","sequence":"additional","affiliation":[{"name":"Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3406\/paleo.1999.4685","article-title":"Early Animal Husbandry in the Northern Levant","volume":"25","author":"Peters","year":"1999","journal-title":"Pal\u00e9orient"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2254","DOI":"10.1126\/science.287.5461.2254","article-title":"The Initial Domestication of Goats (Capra hircus) in the Zagros Mountains 10,000 Years Ago","volume":"287","author":"Zeder","year":"2000","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1006\/jasc.1999.0555","article-title":"A Metrical Analysis of a Collection of Modern Goats (Capra hircus aegargus and C. h. hircus) from Iran and Iraq: Implications for the Study of Caprine Domestication","volume":"28","author":"Zeder","year":"2001","journal-title":"J. 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