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, important economic 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 1747604 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 elimination 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.

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

“…We measured the relative copy numbers of one deletion and all duplications using qPCR on the QuantStudio TM 6 Flex Real-Time PCR System (Life Technologies, Carlsbad, CA, USA) using SYBR Green kit (Promega, Madison, WI, USA). Following a previous study on sheep 95 , DGAT2 gene was used as the internal reference gene. qPCR reaction was in 25 μL volume consisting of 12.5 μL 2× SYBR Green qPCR Mix (Life Technologies, Carlsbad, CA, USA), 1 μL (10 pmol/µL) each primer (forward and reverse), 2 μL template DNA (30 ng/μL), and 8.5 μL ddH 2 O.…”

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

“…Similar results were reported in other livestock species e.g., dairy cattle (182,823 CNVs) [ 70 ], yak (98,441 CNVs) [ 39 ], Nellore cattle (195,873 CNVs) [ 71 ], and goat (208,649 CNVs) [ 26 ]. Some other studies reported a wide range of CNVs from 12 CNVs in chicken [ 72 ] to 1,747,604 CNVs in sheep [ 23 ]. This discrepancy might be due to the differences in the sample size, algorithms used for CNV calling, and sequencing technology [ 73 ].…”

“…The maintenance of Wnt signaling pathway is a critical part to hair-inducing activity of dermal papilla through regulating the β-catenin pathway, and thereby required for follicle regeneration and growth of the hair shaft [ 94 , 95 ]. Interestingly, Yuan et al [ 23 ] demonstrated the contribution of Wnt signaling pathway to the hair follicle development process in Alpine Merino sheep by identifying Wnt-related signaling pathways associated with CNVR-harboring genes [ 23 ].…”

“…Genome-wide identification of CNVs can provide new insights into genomic variations, which can assist in developing genomic breeding strategies for American mink. Numerous studies have been performed to identify CNVR in other species e.g., cattle [20], pig [43], goat [26], sheep [23], chicken [17], and buffalo [37]. Several studies indicated that CNVs could be highly associated with economically important traits in these species [29,[67][68][69].…”

“…Characterisation of CNV has been widely studied in livestock species such as cattle [20][21][22], sheep [23][24][25], goat [26][27][28], pig [29][30][31], chicken [32][33][34], turkey [35,36], buffalo [37], yak [38,39], and rabbit [40], indicating that CNVs might have significant impacts on the economically important traits [41][42][43][44]. However, to our knowledge, there is no genome-wide CNV study in American mink.…”