Abstract
African indigenous sheep are classified as fat-tail, thin-tail and fat-rump hair sheep. The fat-tail are well adapted to dryland environments, but little is known on their genome profiles. We analyzed patterns of genomic variation by genotyping, with the Ovine SNP50K microarray, 394 individuals from five populations of fat-tail sheep from a desert environment in Egypt. Comparative inferences with other East African and western Asia fat-tail and European sheep, reveal at least two phylogeographically distinct genepools of fat-tail sheep in Africa that differ from the European genepool, suggesting separate evolutionary and breeding history. We identified 24 candidate selection sweep regions, spanning 172 potentially novel and known genes, which are enriched with genes underpinning dryland adaptation physiology. In particular, we found selection sweeps spanning genes and/or pathways associated with metabolism; response to stress, ultraviolet radiation, oxidative stress and DNA damage repair; activation of immune response; regulation of reproduction, organ function and development, body size and morphology, skin and hair pigmentation, and keratinization. Our findings provide insights on the complexity of genome architecture regarding dryland stress adaptation in the fat-tail sheep and showcase the indigenous stocks as appropriate genotypes for adaptation planning to sustain livestock production and human livelihoods, under future climates.
Highlights
The development of high throughput genome-wide assays and associated computational tools, have made domestic livestock attractive for investigating how an organism’s genome is influenced by its production and natural environment
Population genetic relationships were assessed with principal component analysis (PCA) and discriminant analysis of principal components (DAPC) (Fig. 1)
The first two principal components of the DAPC and PCA accounted for 7.93% and 9.80% (PC1) and 4.58% and 6.74% (PC2), respectively of the total genetic variation
Summary
The development of high throughput genome-wide assays and associated computational tools, have made domestic livestock attractive for investigating how an organism’s genome is influenced by its production and natural environment. The genomes of African indigenous sheep have been subjected mainly to natural selection driven by tropical and sub-tropical climates, diseases and parasites Their productivity is much lower than that of commercial breeds under intensive production systems, indigenous sheep are often the only option available to millions of resource-poor farmers in agro-pastoral and pastoral production systems, where exotic improved genotypes under-perform under limited (quality and quantity) feed and water resources, and high ecto- and endo-parasite and disease challenges. This is evident in Egypt, a country within the Sahara desert, where sheep of the fat-tail type, are preferred by livestock keepers because of their excellent adaptation to desert-like conditions[8]. Comparative genome analysis with fat-tail sheep from East Africa and western Asia provided insights on the history of the genotype in northeastern and East Africa regions, and the subsequent inclusion of European commercial breeds in selection sweep analysis, allowed us to identify unique genome profiles of fat-tail hair sheep to dryland adaptation
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