A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing
Chao Yuan,
Zengkui Lu,
Tingting Guo,
Yaojing Yue,
Xijun Wang,
Tianxiang Wang,
Yajun Zhang,
Fujun Hou,
Chune Niu,
Xiaopin Sun,
Hongchang Zhao,
Shaohua Zhu,
Jianbin Liu,
Bohui Yang
Affiliations
Chao Yuan
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Zengkui Lu
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Tingting Guo
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Yaojing Yue
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Xijun Wang
Gansu Provincial Sheep Breeding Technology Extension Station
Tianxiang Wang
Gansu Provincial Sheep Breeding Technology Extension Station
Yajun Zhang
Xinjiang Gongnaisi Breeding Sheep Farm
Fujun Hou
Aohan Banner Breeding Sheep Farm
Chune Niu
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Xiaopin Sun
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Hongchang Zhao
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Shaohua Zhu
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Jianbin Liu
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Bohui Yang
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center
Abstract Background 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. Results 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. Conclusions 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.
