Genomic Insights into Inbreeding, Population Structure, and Selection Signatures in Salem Black and Global Goat Breeds.
6 affiliations
- 1Department of Theriogenology and Production, Faculty of Veterinary Medicine, University of Jos, Jos 930103, Nigeria.
- 2Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, Tamil Nadu, India.
- 3Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal 132001, Haryana, India.
- 4Department of AH Statistics and Computer Applications, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, Tamil Nadu, India.
- 5College of Poultry Production and Management, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Hosur 635110, Tamil Nadu, India.
- 6Department of Animal Science, Berry College, Mount Berry, GA 30149, USA.
Abstract
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≈15), 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.
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BibTeX
@article{akinsola2026genomic,
title = {{Genomic Insights into Inbreeding, Population Structure, and Selection Signatures in Salem Black and Global Goat Breeds.}},
author = {Oludayo Michael Akinsola and Malarmathi Muthusamy and Arun Kumar Chinnasamy and Chitra Ramasamy and Pritam Pal and Saravanan Ramasamy and Mani Jeyakumar and Imaben Grace Opaluwa-Kuzayed and Aranganoor Kannan Thiruvenkadan and Sunday Olusola Peters},
journal = {Animals : an open access journal from MDPI},
year = {2026},
month = oct,
doi = {10.3390/ani16193123},
url = {https://europepmc.org/article/MED/42883092},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genomic Insights into Inbreeding, Population Structure, and Selection Signatures in Salem Black and Global Goat Breeds.
AU - Oludayo Michael Akinsola
AU - Malarmathi Muthusamy
AU - Arun Kumar Chinnasamy
AU - Chitra Ramasamy
AU - Pritam Pal
AU - Saravanan Ramasamy
AU - Mani Jeyakumar
AU - Imaben Grace Opaluwa-Kuzayed
AU - Aranganoor Kannan Thiruvenkadan
AU - Sunday Olusola Peters
PY - 2026
DA - 2026/10/05
JO - Animals : an open access journal from MDPI
DO - 10.3390/ani16193123
UR - https://europepmc.org/article/MED/42883092
AB - 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≈15), 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.
SN - 2076-2615
ER -