The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.
L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
BMC Genomics. 2019 May 8;20(Suppl 3):294. doi: 10.1186/s12864-019-5537-0.
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 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.
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.
家化和数百年的选择性繁殖改变了绵羊品种的基因组，以应对环境挑战和人类需求。因此，地方品种的基因组是了解适应和人工选择反应机制的基因组变异的宝贵来源。为此，我们对在俄罗斯各地饲养的 15 个地方绵羊品种的基因组进行了高密度基因分型和全面的选择信号扫描。
结果表明，俄罗斯绵羊品种的基因组包含多个假定选择的区域。这些区域中有 50%以上与以前在绵羊基因组中选择性清除扫描中发现的区间相匹配。这些区域包含与形态、适应和驯化相关的知名候选基因（如 KITLG、KIT、MITF 和 MC1R）、羊毛质量和数量（如 DSG@、DSC@ 和 KRT@）、生长和饲料摄入（如 HOXA@、HOXC@、LCORL、NCAPG、LAP3 和 CCSER1）、繁殖（如 CMTM6、HTRA1、GNAQ、UBQLN1 和 IFT88）和与牛奶相关的性状（如 ABCG2、SPP1、ACSS1 和 ACSS2）。此外，多个假定与环境适应相关的基因在选定的区间中排名靠前（如 EGFR、HSPH1、NMUR1、EDNRB、PRL、TSHR 和 ADAMTS5）。此外，我们观察到，多个涉及人类遗传性感觉和自主神经病以及遗传疾病的关键基因，这些疾病伴随着无法感知疼痛和环境温度的能力，在俄罗斯的多个或单个绵羊品种中排名靠前，这表明了对恶劣气候条件的适应的可能机制。
我们的工作代表了对来自俄罗斯欧洲和亚洲血统的地方绵羊品种基因组进行选择信号全面扫描的首次尝试。我们证实，俄罗斯绵羊的基因组包含以前鉴定的选择信号，证明了我们综合方法的稳健性。在与俄罗斯恶劣环境适应相关的基因附近发现了多个新的选择信号。我们的研究为未来利用俄罗斯绵羊基因组发现特定遗传变异或单倍型以用于开发新一代高产品种奠定了基础，这些品种更适合欧亚大陆的各种环境。
