Analysis of copy number variants in the cattle genome

Kijas, James W.; Barendse, W.; Barris, Wes; Harrison, B. E.; McCulloch, Russell; McWilliam, Sean; Whan, Vicki

doi:10.1016/j.gene.2011.04.011

Cited by 36 publications

(38 citation statements)

References 28 publications

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“…Array CGH and SNP arrays have been used to identify CNVs in cattle and dogs, and the average CNV size has ranged from 33 kb to 275 kb. However, close inspection of the probe spacing of the arrays used in these studies (200 bp to 50 kb) suggests that CNVs of the expected median size and smaller would be missed (Chen et al 2009;Nicholas et al 2009;Fadista et al 2010;Liu et al 2010;Hou et al 2011;Kijas et al 2011;Nicholas et al 2011). Although we failed to identify CNVs in intergenic regions because of the genecentric design of the array, we felt that the benefit of identifying smaller genic CNVs outweighed the identification of larger genic and intergenic CNVs.…”

Section: Discussionmentioning

confidence: 94%

Identification of copy number variants in horses

et al. 2012

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Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a wholeexome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein-and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.

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Section: Discussionmentioning

confidence: 94%

Identification of copy number variants in horses

et al. 2012

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“…In addition, the OvineSNP50 BeadChip has fewer probes than other mamalian BeadChips, such as those of humans [42], cattle [43]and pigs [44], and some…”

Section: Accepted Manuscriptmentioning

confidence: 99%

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

Zhang

et al. 2015

Genomics

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The sheep (Ovis aries) plays a major socio-economic role in the world. Copy number variations (CNVs) are increasingly recognized as a key and potent source of genetic variation and phenotypic diversity, but little is known about the extent to which CNVs contribute to genetic variation in Chinese sheep breeds. Analyses of CNVs in the genomes of eight sheep breeds were performed using the sheep SNP50 BeadChip genotyping array. A total of 111 CNV regions (CNVRs) were obtained from 160 Chinese sheep breeds. These CNVRs covered 13.75Mb of the sheep genome sequence. A total of 22 Go terms and 17 candidate genes were obtained from the functional analysis. Ten CNVRs were selected for validation, of which 7 CNVRs were further experimentally confirmed by quantitative PCR. Four candidate genes were selected to confirm the results of the functional analysis. These results provide a resource for furthering understanding of ruminant biology, and for further improving the genetic quality of sheep breeds.

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“…SNPs are also inefficient to capture some relevant genome polymorphisms, such as certain types of copy number variation (e.g. Kijas et al, 2011;Fontanesi et al, 2012). Nevertheless, they are quickly replacing microsatellites in paternity testing and genetic diversity studies, due to their robustness, low cost and automatic allele calling.…”

Section: Development Of High-throughput Snp Assays For the Analysis Omentioning

confidence: 99%

The characterization of goat genetic diversity: Towards a genomic approach

Ajmone‐Marsan

Colli

Han

et al. 2014

Small Ruminant Research

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a b s t r a c tThe investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers for each of the main livestock species, FAO has promoted the meta-analysis of local datasets, to achieve a global view of molecular genetic diversity. Analysis within the EU Globaldiv project of two large goat microsatellite datasets produced by the Econogene Consortium and the IAEA CRP-Asia Consortium, respectively, has generated a picture of goat diversity across continents. This indicates a gradient of decreasing diversity from the domestication centre towards Europe and Asia, a clear phylogeographic structure at the continental and regional levels, and in Asia a limited genetic differentiation among local breeds. The development of SNP panels that assay thousands of markers and the whole genome sequencing of livestock permit an affordable use of genomic technologies in all livestock species, goats included. Preliminary data from the Italian Goat Consortium indicate that the SNP panel developed for this species is highly informative. The existing panel can be improved by integrating additional SNPs identified from the whole genome sequence alignment of goats adapted to extreme climates. Part of this effort is being achieved

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Analysis of copy number variants in the cattle genome

Cited by 36 publications

References 28 publications

Identification of copy number variants in horses

Identification of copy number variants in horses

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

The characterization of goat genetic diversity: Towards a genomic approach

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