A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

• Published in: BMC genomics Vol. 22; no. 1; p. 78
• Main Authors: Yuan, Chao, Lu, Zengkui, Guo, Tingting, Yue, Yaojing, Wang, Xijun, Wang, Tianxiang, Zhang, Yajun, Hou, Fujun, Niu, Chune, Sun, Xiaopin, Zhao, Hongchang, Zhu, Shaohua, Liu, Jianbin, Yang, Bohui
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 23.01.2021; BioMed Central; BMC
• Subjects: Animal populations; Animals; Cattle; China; Chromosome Mapping; Chromosomes; Copy number; Copy number variation; Copy number variations; DNA Copy Number Variations; Fine-wool sheep; Gene mapping; Genes; Genetic aspects; Genetic diversity; Genetic research; Genomes; Genomics; Geographical distribution; Humans; Livestock; Metabolism; Physiological aspects; Polymorphism, Single Nucleotide; Population genetics; Quantitative Trait Loci; Relaxin; Sensory perception; Sheep; Sheep - genetics; Whole-genome resequencing; Wool; Zoological research; China; Whole-genome resequencing; Copy number variation; Fine-wool sheep
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-021-07387-7

Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing. A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. "Deletion" events took place more frequently than "duplication" or "both" events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39-55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection. In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.