Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

Ma, Youji; Zhang, Quanwei; Lu, Zengkui; Zhao, Xingxu; Zhang, Yong

doi:10.1016/j.ygeno.2015.08.001

Cited by 25 publications

(49 citation statements)

References 46 publications

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“…Liu 16 identified 238 CNVRs by assessing 329 individuals from 3 breeds using the Ovine SNP 50 BeadChip, but only 12 of these CNVRs on 10 chromosomes were also identified in our results ( Supplementary File 1: Table S8 ). The most recent study on CNV in sheep was carried out by Ma 17 , who identified 111 CNVRs by subjecting 160 individuals from 8 breeds to analysis using the Ovine SNP 50 BeadChip; only 8 of these CNVRs on 4 chromosomes were also identified in our results ( Supplementary File 1: Table S9 ).…”

Section: Resultsmentioning

confidence: 73%

Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays

Zhu

Fan

Yuan

et al. 2016

Sci Rep

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Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the genetic mechanisms underlying the phenotypic differences among Chinese indigenous sheep with tails of three different types, we used ovine high-density 600K SNP arrays to detect genome-wide copy number variation (CNV). In large-tailed Han sheep, Altay sheep, and Tibetan sheep, 371, 301, and 66 CNV regions (CNVRs) with lengths of 71.35 Mb, 51.65 Mb, and 10.56 Mb, respectively, were identified on autosomal chromosomes. Ten CNVRs were randomly chosen for confirmation, of which eight were successfully validated. The detected CNVRs harboured 3130 genes, including genes associated with fat deposition, such as PPARA, RXRA, KLF11, ADD1, FASN, PPP1CA, PDGFA, and PEX6. Moreover, multilevel bioinformatics analyses of the detected candidate genes were significantly enriched for involvement in fat deposition, GTPase regulator, and peptide receptor activities. This is the first high-resolution sheep CNV map for Chinese indigenous sheep breeds with three types of tails. Our results provide valuable information that will support investigations of genomic structural variation underlying traits of interest in sheep.

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Section: Resultsmentioning

confidence: 73%

Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays

Zhu

Fan

Yuan

et al. 2016

Sci Rep

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“…This difference is not surprising, as the current study used a high-density SNP array containing more than 600 K probes, whereas Ma et al . 11 and Liu et al . 10 used low-density SNP arrays with 50 K probes.…”

Section: Discussionmentioning

confidence: 94%

Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array

Liu

Pan

et al. 2017

Sci Rep

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Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.

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“…The CNVRs identified in these previous studies were different to some extent, which may have been related to the differences in sheep breeds, sample sizes, CNV detection platforms and CNV calling algorithms used. However, it is noteworthy that the CNVRs identified in this study had high overlapping ratios ( [7,11,13,15,16,28]. The four studies with which there were high overlapping ratios all used Chinese indigenous sheep breeds or Chinese cultivated sheep breeds as the study subjects, whereas the two studies with which there were low overlapping ratios used foreign sheep breeds.…”

Section: Discussionmentioning

confidence: 71%

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

Yuan

Guo

et al. 2019

Preprint

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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 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.

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Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

Cited by 25 publications

References 46 publications

Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays

Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays

Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array

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

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