Abstract
BackgroundDomestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia.ResultsResults demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions.ConclusionsOur work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments.
Highlights
Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs
Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia
Three overlapping regions were detected on this chromosome: one near the UFM1 gene involved in brain development and abnormalities in humans [21]; the second, near neurobeachin (NBEA), a Candidate genes for adaptation of the Russian sheep breeds to environmental and climate challenges In the regions under putative selection we looked for genes that could be related to adaption of Russian sheep breeds to local environments (Table 2)
Summary
Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. After domestication about 9000–11,000 years ago on the territory of modern Iran [4], sheep have been spread worldwide, accompanying human migrations, e.g., the nomad’s expansion [2,3,4]. Both artificial selection and acclimatization to various environments have contributed to the diversity of local breeds, expressing distinct and sometimes contrasting phenotypes (e.g., polled and horned breeds, black and white fleece, breeds adapted to the hot temperatures in Africa and the cold climates of Siberia). Domestic sheep should be considered as a valuable model species to study genome reaction to both environmental adaptation and artificial selection
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