Ahmed R. Elbeltagy

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt’s Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

Genomic footprints of dryland stress adaptation in Egyptian fat-tail sheep and their divergence from East African and western Asia cohorts

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.

Initial genomic characterization of Italian, Egyptian and Pakistani goat breeds.

Selection and breeding practices in goats have differed greatly among countries and populations. These processes, together with natural selection and regional drift, have shaped the phenotypic variability of goat breeds (Kim et al., 2015). The availability of improved genomic analysis tools for this species may provide useful information on the history of selection, adaptation and differentiation of goats from different areas of the world, that can be evaluated by the study of gene frequencies and length of the Runs of Homozigosity (contiguous length of homozygous genotypes, ROH; Purfield et al., 2012). In current study, we examined using a goat medium density SNP chip animals from three different countries: Egypt (with lack of selection scheme), Italy (with several standardized breeds; Nicoloso et al., 2015) and Pakistan (with several breeds showing peculiar phenotypes) to produce a genomic landscape of goats breeds in these countries. A total of 1,123 animals of 39 different populations, and 48,895 SNP markers were analyzed. Genotypes were imputed on a country-based approach, and markers without known position in the genome were excluded from the analysis. MDS and ADMIXTURE plots confirmed the good differentiation among populations from the three countries. Runs of Homozygosity (ROH) were performed for each country and population allowed the detection of genomic regions with high homozygosity levels, common in at least two out of three sampling areas. These results provide new insights into goat genome structure within and among breeds and countries. The detection of conserved regions with different lengths may explain recent selection strategies or adaptation to different, extreme environmental conditions. The research was funded by INNOVAGEN project. Support by Iowa State University and the Ensminger funds for AE and AT as well as support by the Fulbright Foundation for AE are gratefully acknowledged. Sampling from Pakistan was funded by PAK-USAID project.