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

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.

Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds

“…Chromosome 26 had the smallest number of CNVRs. This observation was in agreement with Yuan et al 50 where they reported that the chromosome length had a significant positive linear relationship with the number of CNVRs (R 2 = 0.87) with the maximum found in chromosome 1 and the minimum found on 26. Conflicting results have also reported by Jenkins et al 43 in Texel, Coopworth, Perendale, Romania, and Merino sheep and Zhu et al 48 , in the study of CNVR-containing genomic regions in Tibetan sheep, stated that chromosome 3 had the highest number of CNVRs.…”

“…Therefore, the CNVRs detected in this study were compared with the QTLs reported in the sheep QTL database. The QTL categories found in this study were basically identical to those found in previously reported studies 50 , 52 , 71 . For example, the health-related QTLs found included fecal egg count QTLs, and worm count QTLs that previous studies have reported that worm disease infection rates in sheep can exceed 70% in many countries, causing huge losses to the livestock industry 72 .…”

“…However, the number of animals used in the current study may be one of the limitations affecting the number of CNVs identified in this study. Although, it should be considered that this is the only genomic information available from Afghan local sheep breeds and most of the similar published reports have been performed with almost the same or lower sample size in different indigenous sheep breeds 7 , 21 , 42 , 50 , 57 , 94 , 101 , however, there were validation or phenotypes in most of the previous studies. For example, quantitative PCR (qPCR) has been used to confirm subsets of CNVs identified in different studies 42 , 101 .…”

“…Many studies have shown that CNVRs contain QTLs associated with important economic traits in animals 50 , 70 . Therefore, the CNVRs detected in this study were compared with the QTLs reported in the sheep QTL database.…”

Prenatal diagnosis of a novel 7q31.31q31.33 microduplication with a favorable outcome

“…While many CNVs are known since almost 2 decades for European population, recent widespread application of chromosomal microarray analysis (CMA) in diagnosis in China revealed many new CNVs. Overall, clinical significance of these new CNVs needs to be still some considerations [ 2 , 3 ].…”