Genomic Insights into Inbreeding, Population Structure, and Selection Signatures in Salem Black and Global Goat Breeds

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.