Genomic characteristics of cattle copy number variations

Hou, Yali; Liu, George E.; Bickhart, Derek M.; Cardone, Maria Francesca; Wang, Kai; Kim, Euisoo; Matukumalli, Lakshmi K.; Ventura, Mario; Song, Jiuzhou; VanRaden, P.M.; Sonstegard, Tad S.; Tassell, Curtis P. Van

doi:10.1186/1471-2164-12-127

Cited by 188 publications

(282 citation statements)

References 48 publications

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“…Using the Btau_4.0 assembly, we previously applied an approach combining MegaBlast and WSSD to detect cattle SD and discovered 94.4 Mbp of duplicated sequence in the reference genome (Liu et al 2009). Our earlier array-based studies in cattle have also uncovered significant differences in CNV frequency among breeds, as well as several genes associated with CNVs like ULBP and PGR (Liu et al 2010;Hou et al 2011). These studies confirm that CNVs are common, associated with SDs, and often occur in gene-rich regions in cattle.…”

supporting

confidence: 63%

“…We chose to investigate 12 predicted CNVRs in different animals, using two distinct primer sets per locus (see Supplemental Table S4). Our qPCR analysis used a modified ddCT method to determine relative CN as described previously (Hou et al 2011). The only exception was that we used absolute CN estimates from the DTTRACE data set at each qPCR locus that was not diploid in Dominette (our control sample).…”

Section: Experimental Validationmentioning

confidence: 99%

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Copy number variation of individual cattle genomes using next-generation sequencing

Bickhart¹,

Hou²,

Schroeder³

et al. 2012

Genome Res.

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Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising~55.6-Mbp sequence-476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (~52%, x 2 test; P-value <0.05). In contrast, genes related to pathogen-and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and

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supporting

confidence: 63%

Section: Experimental Validationmentioning

confidence: 99%

Copy number variation of individual cattle genomes using next-generation sequencing

Bickhart¹,

Hou²,

Schroeder³

et al. 2012

Genome Res.

Self Cite

277

310

View full text Add to dashboard Cite

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“…There was high variability in the total number and length of the CNVRs identified in the different studies and only a small number of CNVRs identified in the present study were reported in other studies, which has also been reported by Bagnato et al (2015). The greatest coincidence of CNVRs was found with the studies of Hou et al (2011Hou et al ( , 2012a, with 31.1% and 29.9% common CNVRs respectively, and the total lengths of overlapping regions were 7.6 and 7.4 Mb respectively. Thirty-five CNVRs in our study coincided with CNVRs reported by Prinsen et al (2016) and the length of the overlapping regions was 6.6 Mb.…”

Section: Cnv and Cnvr Detectionmentioning

confidence: 37%

“…Copy-number variations have been shown to be associated with complex traits in several species, including chimpanzee (Perry et al 2008), rat (Guryev et al 2008) and mouse (Adams et al 2005), and in livestock species such as cattle (Liu et al 2010;Hou et al 2011), goat (Fontanesi et al 2010), sheep (Fontanesi et al 2011) and horse (Dupuis et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide detection of copy-number variations in local cattle breeds

et al. 2019

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Abstract. The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina's BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRs identified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total, 178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathway analyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases. Our results have provided significant information for the construction of more-complete CNV maps of the bovine genome and offer an important resource for the investigation of genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for future studies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.

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“…A closer look at the surrounding region revealed that the SNP resides within two partly overlapping copy number variation (CNV) regions which were previously associated with resistance to gastrointestinal nematodes in cattle (Ensembl, UMD 3.1; BTA6: 9 524 225–10 295 238 bp and 9 914 188–10 346 486 bp) (Hou et al . 2011, 2012). …”

Section: Resultsmentioning

confidence: 99%

An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance

et al. 2018

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SummaryGenetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non‐additive genetic variation, we present an approach using genome‐wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein–Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome‐wide markers were tested for associations between heterozygosity and bTB status using marker‐based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy‐Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome‐wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy‐number‐variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large‐scale data.

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Genomic characteristics of cattle copy number variations

Cited by 188 publications

References 48 publications

Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variation of individual cattle genomes using next-generation sequencing

Genome-wide detection of copy-number variations in local cattle breeds

An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance

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