Guo Tingting, Zhao Hongchang, Yuan Chao, Huang Shuhong, Zhou Shiwei, Lu Zengkui, Niu Chun'e, Liu Jianbin, Zhu Shaohua, Yue Yaojing, Yang Yuxin, Wang Xiaolong, Chen Yulin, Yang Bohui
Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China.
Front Genet. 2021 Feb 23;12:604235. doi: 10.3389/fgene.2021.604235. eCollection 2021.
Long-term natural and artificial selection leads to change in certain regions of the genome, resulting in selection signatures that can reveal genes associated with selected traits, such as horns (i.e., polled/horned), high-quality wool traits, and high-altitude hypoxia adaptability. These are complex traits determined by multiple genes, regulatory pathways, and environmental factors. A list of genes with considerable effects on horn and adaptability traits has not been found, although multiple quantitative trait loci (QTL) have been identified. Selection signatures could be identified using genetic differentiation (F ), polymorphism levels θπ, and Tajima's D. This study aimed to identify selection signatures in fine-wool sheep and to investigate the genes annotated in these regions, as well as the biological pathways involved in horn and adaptability traits. For this purpose, the whole-genome sequence of 120 individuals from four breeds, which come from different elevations and habitats in China, was used to analyze selection signatures for horn and adaptability traits. Annotation of the consensus regions of F and θπ ratios revealed a list of identified genes associated with polled/horned and high-altitude hypoxia adaptability traits, such as , EE, , , , , , and . Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified genes related primarily to mismatch repair, metabolism, vascular smooth muscle contraction, and cardiac muscle contraction. This is the first study to demonstrate that selection signatures play an important role in the polled/horned and high-altitude hypoxia adaptability traits of fine-wool sheep breeds that have undergone high-intensity selection and adapted to different ecological environments in China. Changes observed in the genome of fine-wool sheep may have acted on genomic regions that affect performance traits and provide a reference for genome design and breeding.
长期的自然选择和人工选择导致基因组某些区域发生变化，从而产生选择印记，这些印记能够揭示与特定性状相关的基因，如角（即无角/有角）、优质羊毛性状以及高海拔低氧适应性。这些都是由多个基因、调控途径和环境因素决定的复杂性状。尽管已经鉴定出多个数量性状位点（QTL），但尚未发现对角和适应性性状有显著影响的基因列表。可以使用遗传分化（F ）、多态性水平θπ和 Tajima's D来识别选择印记。本研究旨在识别细毛羊中的选择印记，并研究这些区域注释的基因以及与角和适应性性状相关的生物学途径。为此，利用来自中国不同海拔和栖息地的四个品种的120个个体的全基因组序列，分析角和适应性性状的选择印记。对F 和θπ比率的共有区域进行注释，揭示了一系列与无角/有角和高海拔低氧适应性性状相关的已鉴定基因，如 、EE、 、 、 、 、 和 。基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析确定了主要与错配修复、代谢、血管平滑肌收缩和心肌收缩相关的基因。这是第一项证明选择印记在经过高强度选择并适应中国不同生态环境的细毛羊品种的无角/有角和高海拔低氧适应性性状中发挥重要作用的研究。在细毛羊基因组中观察到的变化可能作用于影响生产性能性状的基因组区域，并为基因组设计和育种提供参考。
