Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain.
Genetics, Sequencing and Genotyping Unit, Advanced Research Facilities (SGIker), University of the Basque Country (UPV/EHU), Leioa, Spain.
Genet Sel Evol. 2018 Mar 22;50(1):9. doi: 10.1186/s12711-018-0378-x.
The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under selection: (1) regions underlying local adaptation of Sasi Ardi semi-feral sheep, (2) regions related to a long traditional dairy selection pressure in Latxa sheep, and (3) regions experiencing the specific effect of the modern genetic improvement program established for the Latxa breed during the last three decades.
Thirty-two selected candidate regions including 147 annotated genes were detected by using three statistical parameters: pooled heterozygosity H, Tajima's D, and Wright's fixation index F. For Sasi Ardi sheep, chromosomes Ovis aries (OAR)4, 6, and 22 showed the strongest signals and harbored several candidate genes related to energy metabolism and morphology (BBS9, ELOVL3 and LDB1), immunity (NFKB2), and reproduction (H2AFZ). The major genomic difference between Sasi Ardi and Latxa sheep was on OAR6, which is known to affect milk production, with highly selected regions around the ABCG2, SPP1, LAP3, NCAPG, LCORL, and MEPE genes in Latxa sheep. The effect of the modern genetic improvement program on Latxa sheep was also evident on OAR15, on which several olfactory genes are located. We also detected several genes involved in reproduction such as ESR1 and ZNF366 that were affected by this selection program.
Natural and artificial selection have shaped the genome of both Sasi Ardi and Latxa sheep. Our results suggest that Sasi Ardi traits related to energy metabolism, morphological, reproductive, and immunological features have been under positive selection to adapt this semi-feral sheep to its particular environment. The highly selected Latxa sheep for dairy production showed clear signatures of selection in genomic regions related to milk production. Furthermore, our data indicate that the selection criteria applied in the modern genetic improvement program affect immunity and reproduction traits.
当前绵羊表型多样性的广泛范围是绵羊为适应不同生产特性（如羊毛、牛奶和肉类）而进行选择以及对新环境进行自然适应的综合产物。在这项研究中，我们对来自比利牛斯山西部的 25 只 Sasi Ardi 和 75 只 Latxa 绵羊的基因组进行了扫描，以寻找三种受选择影响的区域：（1）Sasi Ardi 半野生绵羊的局部适应所涉及的区域；（2）Latxa 绵羊长期传统乳制品选择压力相关的区域；（3）在过去三十年中为 Latxa 品种建立的现代遗传改良计划所经历的特定影响的区域。
使用三个统计参数： pooled heterozygosity H、Tajima's D 和 Wright's fixation index F，共检测到 32 个候选选择区域，包括 147 个注释基因。对于 Sasi Ardi 绵羊，绵羊染色体 Ovis aries (OAR)4、6 和 22 显示出最强的信号，并包含与能量代谢和形态（BBS9、ELOVL3 和 LDB1）、免疫（NFKB2）和繁殖（H2AFZ）相关的几个候选基因。Sasi Ardi 和 Latxa 绵羊之间的主要基因组差异位于 OAR6 上，该区域已知会影响产奶量，Latxa 绵羊的 ABCG2、SPP1、LAP3、NCAPG、LCORL 和 MEPE 基因周围存在高度选择的区域。现代遗传改良计划对 Latxa 绵羊的影响也体现在 OAR15 上，该区域存在几个嗅觉基因。我们还检测到几个受该选择程序影响的与繁殖相关的基因，如 ESR1 和 ZNF366。
自然和人工选择塑造了 Sasi Ardi 和 Latxa 绵羊的基因组。我们的研究结果表明，与能量代谢、形态、生殖和免疫特征相关的 Sasi Ardi 特征受到了正选择的影响，以适应这种半野生绵羊的特殊环境。在乳制品生产中受到高度选择的 Latxa 绵羊在与产奶量相关的基因组区域显示出明显的选择迹象。此外，我们的数据表明，现代遗传改良计划中应用的选择标准会影响免疫和繁殖特征。
