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Accession: PRJNA146323 ID: 146323

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

See Genome Information for Bos taurus
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 1,265 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 aCGH, qPCR and 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%, chi squared 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 WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome. Overall design: 5 NimbleGen Bos Taurus UMD3 custom 2.1M whole genome high density aCGH
AccessionPRJNA146323; GEO: GSE31018
Data TypeVariation
ScopeMultiisolate
OrganismBos taurus[Taxonomy ID: 9913]
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos; Bos taurus
PublicationsBickhart DM et al., "Copy number variation of individual cattle genomes using next-generation sequencing.", Genome Res, 2012 Feb 2;22(4):778-90
SubmissionRegistration date: 25-Jan-2012
Bovine Functional Genomics Lab., United States Department of Agriculture
RelevanceAgricultural
Project Data:
Resource NameNumber
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PubMed1
PMC1
Other datasets
GEO DataSets1
GEO Data Details
ParameterValue
Data volume, Spots10832320
Data volume, Processed Mbytes241
Data volume, Supplementary Mbytes538

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