Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.
Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark.
J Anim Breed Genet. 2021 Sep;138(5):574-588. doi: 10.1111/jbg.12536. Epub 2021 Jan 16.
Selection, both natural and artificial, leaves patterns on the genome during domestication of animals and leads to changes in allele frequencies among populations. Detecting genomic regions influenced by selection in livestock may assist in understanding the processes involved in genome evolution and discovering genomic regions related to traits of economic and ecological interests. In the current study, genetic diversity analyses were conducted on 34,206 quality-filtered SNP positions from 450 individuals in 15 sheep breeds, including six indigenous breeds from the Middle East, namely Iranian Balouchi, Afshari, Moghani, Qezel, Karakas and Norduz, and nine breeds from Europe, namely East Friesian Sheep, Ile de France, Mourerous, Romane, Swiss Mirror, Spaelsau, Suffolk, Comisana and Engadine Red Sheep. The SNP genotype data generated by the Illumina OvineSNP50 Genotyping BeadChip array were used in this analysis. We applied two complementary statistical analyses, F (fixation index) and xp-EHH (cross-population extended haplotype homozygosity), to detect selection signatures in Middle Eastern and European sheep populations. F and xp-EHH detected 629 and 256 genes indicating signatures of selection, respectively. Genomic regions identified using F and xp-EHH contained the CIDEA, HHATL, MGST1, FADS1, RTL1 and DGKG genes, which were reported earlier to influence a number of economic traits. Both F and xp-EHH approaches identified 60 shared genes as the signatures of selection, including four candidate genes (NT5E, ADA2, C8A and C8B) that were enriched for two significant Gene Ontology (GO) terms associated with the adenosine metabolic procedure. Knowledge about the candidate genomic regions under selective pressure in sheep breeds may facilitate identification of the underlying genes and enhance our understanding on these genes role in local adaptation.
选择，无论是自然选择还是人工选择，都会在动物的驯化过程中在基因组上留下痕迹，并导致种群间等位基因频率的变化。检测家畜中受选择影响的基因组区域可能有助于理解参与基因组进化的过程，并发现与经济和生态利益相关的基因组区域。在本研究中，对来自 15 个绵羊品种的 450 个个体的 34206 个经过质量过滤的 SNP 位置进行了遗传多样性分析，这些品种包括来自中东的 6 个本土品种，即伊朗巴尔奇、阿夫沙里、莫加尼、卡拉克斯和努尔杜兹，以及来自欧洲的 9 个品种，即东弗里西亚羊、法兰西岛羊、莫雷鲁、罗曼、瑞士镜像、斯派尔斯羊、萨福克羊、科米萨纳和恩加丁红羊。本分析使用 Illumina OvineSNP50 Genotyping BeadChip 阵列生成的 SNP 基因型数据。我们应用了两种互补的统计分析方法，F（固定指数）和 xp-EHH（跨群体扩展单倍型纯合性），来检测中东和欧洲绵羊群体中的选择信号。F 和 xp-EHH 分别检测到 629 和 256 个基因，表明存在选择信号。使用 F 和 xp-EHH 鉴定的基因组区域包含 CIDEA、HHATL、MGST1、FADS1、RTL1 和 DGKG 基因，这些基因先前被报道影响许多经济性状。F 和 xp-EHH 方法都鉴定出 60 个共同的基因作为选择的标志，包括四个候选基因（NT5E、ADA2、C8A 和 C8B），这些基因富集了两个与腺苷代谢过程相关的显著基因本体论（GO）术语。了解绵羊品种中受选择压力影响的候选基因组区域，可能有助于鉴定潜在的基因，并增强我们对这些基因在局部适应中的作用的理解。
