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

Abstract

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.

Figure 1

PCA plots showing the relationship between the breeds analyzed for each species. (a) Barki goats and exotic breeds. (b) Barki sheep and Exotic breeds.

Figure 2

Individual assignment probabilities generated with ADMIXTURE (1⩽K⩽12) in goats (a) and sheep (b). Each color represents a cluster, and the ratio of colored bars is proportional to the assignment probability of an individual to each cluster. MY and LM represent Myotonic and LaMancha goats, respectively.

Figure 3

Genome-wide differential selection (di) in goats (a) and sheep (b). The standardized F_ST value (di) calculated from pairwise breed comparisons are plotted for each SNP across the genome on the basis of an overlapping (5 SNP) window size of 20 SNPs for goats (a) and sheep (b).

Figure 4

Genome-wide |iHS| scores in Barki goats (a) and sheep (b). The standardized |iHS| scores generated using an overlapping (5 SNPs) sliding window of 10 SNPs are plotted across the genome. Details of |iHS| for each SNP on each chromosome is shown in Supplementary Figures S3 and S4 for goats and sheep, respectively.

Figure 5

Comparison of iHS scores between Barki sheep (OAR10) and Barki goat (CHI12). The absolute value of iHS (red circle) was plotted for each locus with the most frequent haplotype using 20-SNP window (black line) for each SNP position in Barki goats (a) or Barki sheep (b). The map position conserved in cattle is displayed with reference to the bovine genome assembly UMD3.1 in between (a) and (b). CHI, OAR and BTA represent notations for goat, sheep and cattle chromosomes, respectively.