Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World's Sheep
文献类型： 外文期刊
作者： Salehian-Dehkordi, Hosein 1 ; Xu, Ya-Xi 3 ; Xu, Song-Song 1 ; Li, Xin 1 ; Luo, Ling-Yun 3 ; Liu, Ya-Jing 3 ; Wang, Don 1 ;
作者机构： 1.Chinese Acad Sci, Inst Zool, CAS Key Lab Anim Ecol & Conservat Biol, Beijing, Peoples R China
2.Univ Chinese Acad Sci UCAS, Coll Life Sci, Beijing, Peoples R China
3.China Agr Univ, Coll Anim Sci & Technol, Beijing, Peoples R China
4.Xinjiang Acad Agr & Reclamat Sci, State Key Lab Sheep Genet Improvement & Hlth Bree, Shihezi, Peoples R China
5.Childrens Hosp Philadelphia, Ctr Appl Genom, Philadelphia, PA 19104 USA
6.Univ Utrecht, Fac Vet Med, Utrecht, Netherlands
7.Shahid Bahonar Univ Kerman, Dept Anim Sci, Kerman, Iran
关键词： sheep; GWAS; CNVs; selection; genetic adaptation
期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.599； 五年影响因子：4.888 ）
ISSN：
年卷期： 2021 年 12 卷
页码：
收录情况： SCI
摘要： Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (similar to 10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1, WNT7B, HMX1, and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3, KHDRBS2, and SDCCAG3 in Hu sheep; NOS3, BMP1, and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species.
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