Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations

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.

Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity

“…Wiener et al. (2021) in an analysis carried out on Ethiopian sheep populations highlighted a stronger effect of precipitation‐related traits on genome features compared to other climate and environmental variables. Signatures of selection harbouring genes involved in the adaptation to temperature and altitude have been detected in cattle and other Bos species using a ROH based approach (Freitas et al., 2021).…”

Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds

“…Conserving these diversity is important for raising the efficiency of production and imporoving adaptation to environments. Until now, different studies have been done to identify genes related to production and daptation traits in sheep using methods such as methylated DNA immunoprecipitation sequencing [ 19 – 21 ], RNA-Seq analyses [ 22 – 27 ], whole genome sequencing nalyses [ 28 , 29 ] and genome-wide association studies [ 30 – 33 ]. Although Iranian indigenous sheep breeds display high genetic potential for production, researches to increase their productivity is less carried out compared to other sheep breeds.…”

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

“…PLCB1 (Phospholipase C Beta 1) encoded by the protein plays an important role in the intracellular transduction of many extracellular signals. PLCB1 has been associated with environmental factors and tissue-specific expression patterns in sheep and has been identified as a potential selection target in several studies ( Li et al, 2020 ; Wiener et al, 2021 ). STEAP3 (STEAP3 Metalloreductase) encodes a multipass membrane protein that functions as an iron transporter.…”