Abstract
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.
Highlights
Over the last 20 years, livestock geneticists have exploited the development of genomic tools and resources to identify regions of the genome showing evidence of selection
Sources of environmental selection Our analysis of genomic variation in Ethiopian sheep showed a stronger association with precipitation-related traits than for temperature- or altitude-related traits in the geographic distribution of genotypes, suggesting a possible role for precipitation-driven selection
This finding is consistent with a large-scale meta-analysis of many species that concluded that precipitation explained a greater proportion of variance in selection than did other climatic factors (Siepielski et al 2017)
Summary
Over the last 20 years, livestock geneticists have exploited the development of genomic tools and resources to identify regions of the genome showing evidence of selection. The design of these experiments and the choice of breeds has resulted in a focus on identification of signatures primarily related to artificial selection in commercial breeds (Gutierrez-Gil et al 2015; Randhawa et al 2016). Characterising environmental adaptation in plants and animals has traditionally been an expensive and time-consuming endeavour, requiring large-scale experiments carried out over a range of environmental conditions Such experiments are generally prohibitively expensive and challenging to carry out for non-model organisms with long generation times. This “landscape genomics” approach (Manel et al 2003) was initially mainly applied to wild species but can be applied to livestock (Bertolini et al 2018; Flori et al 2019; Joost et al 2008), with the additional complication that the location of particular livestock genotypes is influenced by both natural and human-directed forces
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