A large interactive visual database of copy number variants discovered in taurine cattle

Kommadath, Arun; Grant, Jason R.; Krivushin, Kirill; Butty, Adrien M.; Baes, C.F.; Carthy, Tara R.; Berry, D.P.; Stothard, Paul

doi:10.1093/gigascience/giz073

Cited by 28 publications

(25 citation statements)

References 67 publications

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“…This difference was not surprising, as the genomic coverage of SNP chips is poor, which results in the detection of longer CNVRs [17,18]. The CNVRs detected in this study accounted for 2.17% of the sheep reference genome, which falls within the range (0.8%-5.12%) reported for horses, pigs, cattle and chickens [19][20][21][22]. However, the CNVRs identi ed in individual species accounted for more than 10% of their reference genomes, which may be related to the different genetic backgrounds of the studied animals [23,24].…”

Section: Discussionsupporting

confidence: 55%

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

Yuan

Guo

et al. 2020

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 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.

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Section: Discussionsupporting

confidence: 55%

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

Yuan

Guo

et al. 2020

Preprint

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“…These CNVs were merged into 13,234 non-redundant CNV regions (CNVRs) with a total length of~40.5 Mb, corresponding to~1.5% of the autosomal genome sequence (Table S1). To validate CNVRs in this study, we collected cattle CNVRs in 12 published papers and converted them to ARS-UCD1.2 coordinate using UCSC liftover tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver) [15,16,[20][21][22][23][24][25][26][27][28][29]. We found 80.7% of CNVRs detected in our study were supported by the published cattle CNVRs in length.…”

Section: Genome-wide Cnv Detection For Ten Cattle Breedsmentioning

confidence: 72%

Comparative analyses of copy number variations between Bos taurus and Bos indicus

Xia

et al. 2020

BMC Genomics

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Background Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. Results Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. Conclusions This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.

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“…Previously known variants. Two sets of previously known variants were considered for comparison with the high confidence CNVR identified in this study: the CNV deposited on the Genomic Variant archive database of EMBL-EBI (DGVa; https://www.ebi.ac.uk/dgva, last accessed 2019-03-24) and the CNVR identified on the datasets A, B, and C described by Kommadath et al 31 .…”

Section: Effect Of the Genotype Array Density On The Identified Cnv mentioning

confidence: 99%

“…Variants detected with different methods, on different animals, and relying on different sources of information may overlap between 0 and 90 percent 12,26,[34][35][36][37] . Moreover, Kommadath et al 31 suggested the method used for CNV identification has the most impact on the overlap between studies. The advantages and disadvantages of the detection methods on GEN and WGS data were reviewed by Winchester et al 38 and Pirooznia et al 39 , respectively.…”

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confidence: 99%

High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data

Butty

Chud

Miglior

et al. 2020

Sci Rep

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Multiple methods to detect copy number variants (CNV) relying on different types of data have been developed and CNV have been shown to have an impact on phenotypes of numerous traits of economic importance in cattle, such as reproduction and immunity. Further improvements in CNV detection are still needed in regard to the trade-off between high-true and low-false positive variant identification rates. Instead of improving single CNV detection methods, variants can be identified in silico with high confidence when multiple methods and datasets are combined. Here, CNV were identified from whole-genome sequences (WGS) and genotype array (GEN) data on 96 Holstein animals. After CNV detection, two sets of high confidence CNV regions (CNVR) were created that contained variants found in both WGS and GEN data following an animal-based (n = 52) and a population-based (n = 36) pipeline. Furthermore, the change in false positive CNV identification rates using different GEN marker densities was evaluated. The population-based approach characterized CNVR, which were more often shared among animals (average 40% more samples per CNVR) and were more often linked to putative functions (48 vs 56% of CNVR) than CNV identified with the animal-based approach. Moreover, false positive identification rates up to 22% were estimated on GEN information. Further research using larger datasets should use a population-wide approach to identify high confidence CNVR. Dairy cattle genetics has made great advances since the effects of single nucleotide polymorphisms (SNP) have been recognized on a wide range of mono or polygenic traits economically important for the dairy industry 1-5. Genomic variation, however, is not only caused by SNP. Recent studies have shown that structural variants (SV) also have an important impact on phenotypes of a multitude of traits, such as milk production, reproduction, health, and feed efficiency 6-8. Types of SV include translocations, inversions and copy number variation 9. Copy number variants (CNV) form the most common class of SV in the human, plant and animal genome and can be identified as two types of event: copy number loss (CNL) or copy number gain (CNG). As the amount of DNA changes between samples with or without multiple copies of a segment, CNV are a type of the unbalanced structural variations 9. Although the number of bovine CNV described in the literature is lower than the number of SNP, the fact that they have multiple alleles makes them highly informative 10. The CNV can affect both monogenic traits, such as the coat color of cattle 11 , and polygenic traits such as feed efficiency, production traits, and reproduction traits of cattle 12,13. For instance, a study by Liu et al. 14 showed associations between CNV and production traits specifically in Holstein dairy cattle. Identifying CNV is challenging and no consensus on the best method of identification has been reached because multiple factors, starting with the source of information on which the CNV are identified, influence the results. Mo...

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A large interactive visual database of copy number variants discovered in taurine cattle

Cited by 28 publications

References 67 publications

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

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

Comparative analyses of copy number variations between Bos taurus and Bos indicus

High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data

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