Adaptations to Climate-Mediated Selective Pressures in Sheep

Abstract

Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic “footprints” in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.

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

“…This suggests that adaptation to hot arid environments may be mediated by a complex network of genes that act in tandem rather than the action of single candidate genes. This agrees with the findings of Lv et al (2014) and Kemper et al (2014). The former observed that adaptation results from the interaction of several complex traits that most often are controlled by several genes, while the latter noted that selection for complex traits leaves little or no classic signatures of selection owing to weak selection acting on several sites across the genome.…”

“…Apart from the candidate region that spanned BMP2 (OAR13) and SPP1 (CHI6), none of our candidate regions overlapped with those identified in previous studies in sheep (Kijas et al, 2012;Lv et al, 2014), cattle (Xu et al, 2015) and horses (Petersen et al, 2013), most likely owing to different study design, samples (breeds under different selection pressures) and statistical methods. Lv et al (2014) found TBC1D12 on OAR22 (15.3-15.4 Mb) and proposed it to be a strong candidate gene for selection in response to environmental stress. The authors found that the frequency of the causative SNP and its haplotype were higher in cold humid regions but low in hot dry regions.…”

“…The TRHDE (OAR3) gene encodes an extracellular peptidase that cleaves and inactivates thyrotropinreleasing hormone which is critical in regulating appetite and metabolism (Friedman et al, 1995). Apart from the candidate region that spanned BMP2 (OAR13) and SPP1 (CHI6), none of our candidate regions overlapped with those identified in previous studies in sheep (Kijas et al, 2012;Lv et al, 2014), cattle (Xu et al, 2015) and horses (Petersen et al, 2013), most likely owing to different study design, samples (breeds under different selection pressures) and statistical methods. Lv et al (2014) found TBC1D12 on OAR22 (15.3-15.4 Mb) and proposed it to be a strong candidate gene for selection in response to environmental stress.…”

“…The UGT8 (CHI6), GRIA1 (OAR5), PCDH9 (CHI12) and FGF11 (OAR11) genes are associated with the development and function of the nervous and endocrine systems (Monaghan et al, 1989;Barnard and Henley, 1990;Bosio et al, 1996;Smallwood et al, 1996;Halbleib and Nelson, 2006), while the BMP2 (OAR3), FGF2 (CHI17), FGF9 (CHI12, OAR10), GJB2 (CHI12), GJB6 (CHI12), GJA3 (CHI12, OAR12) and SPP1 (CHI6) genes encode proteins that influence body size, skeletal and embryonic development, and testicular embryogenesis (Abraham et al, 1986;Burgess and Maciag, 1989;Shimoyama et al, 1991;Ornitz et al, 1996;Ortega et al, 1998;Miyagi et al, 1999;Bandyopadyay et al, 2006). The BMP2 gene has also been reported to influence body size in cattle and sheep (Kijas et al, 2012;Xu et al, 2015) and the SPP1 gene was found to be located on a candidate region under selection in sheep (Lv et al, 2014), but the authors concluded that it had no role in the adaptation to climate-mediated selection pressure. The IL2, IL7, IL21 (all on CHI17) and IL1R1 (OAR3) genes encode cytokine receptors that participate in host defense mechanisms, including immune and inflammatory responses (Parrish-Novak et al, 2000).…”

“…The availability of genomic data that has been generated using genome-wide single nucleotide polymorphism (SNP) analyses and the comparison of genomic patterns of SNP variation between divergent breeds has successfully identified putative genomic regions and genes associated with differences in selection pressure in various livestock species including sheep (Kijas et al, 2012;Lv et al, 2014), Yak (Qiu et al, 2012), cattle (Xu et al, 2015) and chicken (Elferink et al, 2012).…”