High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia
Abstract Background Domestication 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 adapt...
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| Language: | English |
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BMC
2019-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5537-0 |
| _version_ | 1818385175671734272 |
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| author | Andrey A. Yurchenko Tatiana E. Deniskova Nikolay S. Yudin Arsen V. Dotsev Timur N. Khamiruev Marina I. Selionova Sergey V. Egorov Henry Reyer Klaus Wimmers Gottfried Brem Natalia A. Zinovieva Denis M. Larkin |
| author_facet | Andrey A. Yurchenko Tatiana E. Deniskova Nikolay S. Yudin Arsen V. Dotsev Timur N. Khamiruev Marina I. Selionova Sergey V. Egorov Henry Reyer Klaus Wimmers Gottfried Brem Natalia A. Zinovieva Denis M. Larkin |
| author_sort | Andrey A. Yurchenko |
| collection | DOAJ |
| description | Abstract Background Domestication 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. Results Results 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. Conclusions Our 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. |
| first_indexed | 2024-12-14T03:33:59Z |
| format | Article |
| id | doaj.art-62f19e55199d4ac3bf54d102b124af3d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T03:33:59Z |
| publishDate | 2019-05-01 |
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| series | BMC Genomics |
| spelling | doaj.art-62f19e55199d4ac3bf54d102b124af3d2022-12-21T23:18:40ZengBMCBMC Genomics1471-21642019-05-0120S311910.1186/s12864-019-5537-0High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from RussiaAndrey A. Yurchenko0Tatiana E. Deniskova1Nikolay S. Yudin2Arsen V. Dotsev3Timur N. Khamiruev4Marina I. Selionova5Sergey V. Egorov6Henry Reyer7Klaus Wimmers8Gottfried Brem9Natalia A. Zinovieva10Denis M. Larkin11The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS)L.K. Ernst Federal Science Center for Animal HusbandryThe Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS)L.K. Ernst Federal Science Center for Animal HusbandryResearch Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of SciencesAll-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian CenterSiberian Research Institute of Animal HusbandryInstitute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN)Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN)L.K. Ernst Federal Science Center for Animal HusbandryL.K. Ernst Federal Science Center for Animal HusbandryThe Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS)Abstract Background Domestication 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. Results Results 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. Conclusions Our 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.http://link.springer.com/article/10.1186/s12864-019-5537-0Local sheep breedsSelectionAdaptationGenotypingRussian Federation |
| spellingShingle | Andrey A. Yurchenko Tatiana E. Deniskova Nikolay S. Yudin Arsen V. Dotsev Timur N. Khamiruev Marina I. Selionova Sergey V. Egorov Henry Reyer Klaus Wimmers Gottfried Brem Natalia A. Zinovieva Denis M. Larkin High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia BMC Genomics Local sheep breeds Selection Adaptation Genotyping Russian Federation |
| title | High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia |
| title_full | High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia |
| title_fullStr | High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia |
| title_full_unstemmed | High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia |
| title_short | High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia |
| title_sort | high density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from russia |
| topic | Local sheep breeds Selection Adaptation Genotyping Russian Federation |
| url | http://link.springer.com/article/10.1186/s12864-019-5537-0 |
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