Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds
BackgroundIndia’s indigenous sheep breeds have evolved under extreme and diverse agro‐ecological pressures, yet the genomic basis of their resilience and local adaptation remains poorly understood.MethodThis study combines genomic inbreeding estimates, runs of homozygosity (ROH), population structur...
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2025.1621960/full |
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| author | Malarmathi Muthusamy Oludayo Michael Akinsola Oludayo Michael Akinsola Pritam Pal Chitra Ramasamy Saravanan Ramasamy Abdulraheem Arome Musa Aranganoor Kannan Thiruvenkadan |
| author_facet | Malarmathi Muthusamy Oludayo Michael Akinsola Oludayo Michael Akinsola Pritam Pal Chitra Ramasamy Saravanan Ramasamy Abdulraheem Arome Musa Aranganoor Kannan Thiruvenkadan |
| author_sort | Malarmathi Muthusamy |
| collection | DOAJ |
| description | BackgroundIndia’s indigenous sheep breeds have evolved under extreme and diverse agro‐ecological pressures, yet the genomic basis of their resilience and local adaptation remains poorly understood.MethodThis study combines genomic inbreeding estimates, runs of homozygosity (ROH), population structure analyses, and composite selection scans to investigate three native Indian breeds—Changthangi, Deccani, and Garole—within a panel of nine breeds that also includes populations from Africa (Ethiopian Menz), East and South Asia (Tibetan, Chinese Merino, Bangladesh Garole, Bangladesh East), and Europe (Suffolk).ResultsROH and heterozygosity estimates revealed strong contrasts: Bangladesh East sheep exhibited high genomic inbreeding (FROH≈14.4%) and low observed heterozygosity (∼30.6%), whereas Deccani sheep showed low inbreeding (FROH≈1.1%) and high observed heterozygosity (∼35.6%), consistent with broader gene flow and larger flock sizes. Changthangi and Garole showed moderate inbreeding and distinct ROH length profiles. Population structure analyses confirmed ecological clustering and gene flow shaped by geography and husbandry practices: high‐altitude breeds clustered together, while directional migration edges traced admixture from European Suffolk into Changthangi and from Chinese Merino into Ethiopian Menz. Historical effective population sizes showed sharp declines in most breeds, especially those under recent selection. Selection scans identified 118 significant genomic regions across breeds. In Changthangi, key pathways included purinergic signaling, thyrotropin-releasing hormone, and autophagy—consistent with cold and hypoxia adaptation. Deccani showed enrichment for immune adhesion and epidermal regeneration, reflecting parasite resistance and heat stress. Garole displayed signals for gap-junction communication and skeletal development, aligned with high fertility and compact stature.ConclusionThese findings reveal ecotype‐pecific adaptive nature shaped by polygenic selection, gene flow, and demography, offering actionable insights for sustainable smallholder breeding strategies. |
| format | Article |
| id | doaj-art-3b88a068a1374bb1b9ad5cad5bec62f5 |
| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-08-01 |
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| series | Frontiers in Genetics |
| spelling | doaj-art-3b88a068a1374bb1b9ad5cad5bec62f52025-08-21T04:10:24ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-08-011610.3389/fgene.2025.16219601621960Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breedsMalarmathi Muthusamy0Oludayo Michael Akinsola1Oludayo Michael Akinsola2Pritam Pal3Chitra Ramasamy4Saravanan Ramasamy5Abdulraheem Arome Musa6Aranganoor Kannan Thiruvenkadan7Department of Animal Genetics and Breeding, Veterinary College and Research Institute, TANUVAS, Namakkal, IndiaDepartment of Animal Genetics and Breeding, Veterinary College and Research Institute, TANUVAS, Namakkal, IndiaDepartment of Theriogenology and Production, Faculty of Veterinary Medicine, University of Jos, Jos, NigeriaAnimal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, IndiaDepartment of Animal Genetics and Breeding, Veterinary College and Research Institute, TANUVAS, Namakkal, IndiaDepartment of Animal Genetics and Breeding, Veterinary College and Research Institute, TANUVAS, Namakkal, IndiaResearch Institute for Farm Animal Biology (FBN), Dummerstorf, GermanyCollege of Poultry Production and Management, TANUVAS, Hosur, IndiaBackgroundIndia’s indigenous sheep breeds have evolved under extreme and diverse agro‐ecological pressures, yet the genomic basis of their resilience and local adaptation remains poorly understood.MethodThis study combines genomic inbreeding estimates, runs of homozygosity (ROH), population structure analyses, and composite selection scans to investigate three native Indian breeds—Changthangi, Deccani, and Garole—within a panel of nine breeds that also includes populations from Africa (Ethiopian Menz), East and South Asia (Tibetan, Chinese Merino, Bangladesh Garole, Bangladesh East), and Europe (Suffolk).ResultsROH and heterozygosity estimates revealed strong contrasts: Bangladesh East sheep exhibited high genomic inbreeding (FROH≈14.4%) and low observed heterozygosity (∼30.6%), whereas Deccani sheep showed low inbreeding (FROH≈1.1%) and high observed heterozygosity (∼35.6%), consistent with broader gene flow and larger flock sizes. Changthangi and Garole showed moderate inbreeding and distinct ROH length profiles. Population structure analyses confirmed ecological clustering and gene flow shaped by geography and husbandry practices: high‐altitude breeds clustered together, while directional migration edges traced admixture from European Suffolk into Changthangi and from Chinese Merino into Ethiopian Menz. Historical effective population sizes showed sharp declines in most breeds, especially those under recent selection. Selection scans identified 118 significant genomic regions across breeds. In Changthangi, key pathways included purinergic signaling, thyrotropin-releasing hormone, and autophagy—consistent with cold and hypoxia adaptation. Deccani showed enrichment for immune adhesion and epidermal regeneration, reflecting parasite resistance and heat stress. Garole displayed signals for gap-junction communication and skeletal development, aligned with high fertility and compact stature.ConclusionThese findings reveal ecotype‐pecific adaptive nature shaped by polygenic selection, gene flow, and demography, offering actionable insights for sustainable smallholder breeding strategies.https://www.frontiersin.org/articles/10.3389/fgene.2025.1621960/fullindigenous sheepgenomic inbreedingruns of homozygosity (ROH)selection signaturespolygenic adaptationpopulation structure |
| spellingShingle | Malarmathi Muthusamy Oludayo Michael Akinsola Oludayo Michael Akinsola Pritam Pal Chitra Ramasamy Saravanan Ramasamy Abdulraheem Arome Musa Aranganoor Kannan Thiruvenkadan Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds Frontiers in Genetics indigenous sheep genomic inbreeding runs of homozygosity (ROH) selection signatures polygenic adaptation population structure |
| title | Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds |
| title_full | Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds |
| title_fullStr | Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds |
| title_full_unstemmed | Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds |
| title_short | Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds |
| title_sort | comparative genomic insights into adaptation selection signatures and population dynamics in indigenous indian sheep and foreign breeds |
| topic | indigenous sheep genomic inbreeding runs of homozygosity (ROH) selection signatures polygenic adaptation population structure |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1621960/full |
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