{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T09:54:22Z","timestamp":1791194062460,"version":"4.1.0"},"reference-count":95,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"DBT\u2013TWAS","award":["3240327686"],"award-info":[{"award-number":["3240327686"]}]},{"name":"Veterinary College and Research Institute, Namakkal, India"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The Salem Black goat is an indigenous Indian breed valued for its premium Black leather and high twinning rate, yet its genomic diversity and adaptive potential remain unexplored. We characterised genomic diversity, population structure, demographic history and selection signatures using whole-genome sequence data from 11 Salem Black goats (7 unrelated individuals retained after kinship filtering) analysed alongside 157 individuals from five global breeds (Red Sokoto\/Maradi, Tanzania Toggenburg, Omani Jabal Akhdar, Pakistani Kachan and Madagascar Diana), yielding a final dataset of 120 unrelated animals and 36,584 autosomal SNPs. Genomic inbreeding was estimated via runs of homozygosity; population structure was assessed using principal component analysis, ADMIXTURE, phylogenetic reconstruction, and genetic differentiation. Historical effective population size was inferred, and selection signatures were identified using the de-correlated composite of multiple signals (DCMS) approach. Salem Black goats showed the highest genomic inbreeding (FROH = 0.41), lowest observed heterozygosity (9.6%), and smallest recent effective population size (Ne\u224815), indicating severe recent inbreeding and genetic erosion. Population structure analyses identified Salem Black as a distinct lineage most closely related to Pakistani Kachan goats. Significant selection signals emerged only in Madagascar Diana, Omani Jabal Akhdar, and Tanzania Toggenburg goats, highlighting genes linked to heat tolerance, immunity, DNA repair, metabolism, and reproduction. These findings provide the first genomic characterization of Salem Black goats and identify their urgent conservation priority.<\/jats:p>","DOI":"10.3390\/ani16193123","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T08:57:18Z","timestamp":1791190638000},"page":"3123","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Insights into Inbreeding, Population Structure, and Selection Signatures in Salem Black and Global Goat Breeds"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3981-5672","authenticated-orcid":false,"given":"Oludayo Michael","family":"Akinsola","sequence":"first","affiliation":[{"name":"Department of Theriogenology and Production, Faculty of Veterinary Medicine, University of Jos, Jos 930103, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3279-3810","authenticated-orcid":false,"given":"Malarmathi","family":"Muthusamy","sequence":"additional","affiliation":[{"name":"Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, Tamil Nadu, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun Kumar","family":"Chinnasamy","sequence":"additional","affiliation":[{"name":"Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, Tamil Nadu, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7434-6205","authenticated-orcid":false,"given":"Chitra","family":"Ramasamy","sequence":"additional","affiliation":[{"name":"Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, Tamil Nadu, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7778-7815","authenticated-orcid":false,"given":"Pritam","family":"Pal","sequence":"additional","affiliation":[{"name":"Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal 132001, Haryana, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saravanan","family":"Ramasamy","sequence":"additional","affiliation":[{"name":"Department of AH Statistics and Computer Applications, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, Tamil Nadu, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mani","family":"Jeyakumar","sequence":"additional","affiliation":[{"name":"Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, Tamil Nadu, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5566-1370","authenticated-orcid":false,"given":"Imaben Grace","family":"Opaluwa-Kuzayed","sequence":"additional","affiliation":[{"name":"Department of Theriogenology and Production, Faculty of Veterinary Medicine, University of Jos, Jos 930103, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5849-2800","authenticated-orcid":false,"given":"Aranganoor Kannan","family":"Thiruvenkadan","sequence":"additional","affiliation":[{"name":"College of Poultry Production and Management, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Hosur 635110, Tamil Nadu, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0216-926X","authenticated-orcid":false,"given":"Sunday Olusola","family":"Peters","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Berry College, Mount Berry, GA 30149, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,10,5]]},"reference":[{"key":"ref_1","unstructured":"Department of Animal Husbandry and Dairying (DAHD), Government of India (2026, September 29). 20th Livestock Census: All India Report, Available online: https:\/\/dahd.gov.in\/."},{"key":"ref_2","first-page":"760","article-title":"Role of Goats in Livelihood Security of Rural Poor in the Less Favoured Environments","volume":"65","author":"Kumar","year":"2010","journal-title":"Indian J. 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