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

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      Author
      Bickhart, D.M.
      Hou, Y.
      Schroeder, S.G.
      Alkan C.
      Cardone, M.F.
      Matukumalli L.K.
      Song J.
      Schnabel, R.D.
      Ventura M.
      Taylor J.F.
      Garcia J.F.
      Van Tassell, C.P.
      Sonstegard, T.S.
      Eichler, E. E.
      Liu G.E.
      Date
      2012
      Source Title
      Genome Research
      Print ISSN
      10889051
      Volume
      22
      Issue
      4
      Pages
      778 - 790
      Language
      English
      Type
      Article
      Item Usage Stats
      149
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      100
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      Abstract
      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%, χ 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 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. © 2012 by Cold Spring Harbor Laboratory Press.
      Keywords
      apolipoprotein
      fatty acid binding protein 2
      taurine
      adaptation
      article
      beef cattle
      breeding
      cattle
      chromosome map
      comparative genomic hybridization
      copy number variation
      fluorescence in situ hybridization
      gene duplication
      gene sequence
      genome analysis
      lipid metabolism
      lipid transport
      molecular genetics
      nonhuman
      nucleotide sequence
      pedigree analysis
      polymerase chain reaction
      priority journal
      promoter region
      quantitative analysis
      quantitative trait locus
      sequence analysis
      Animals
      Cattle
      Chromosome Mapping
      Chromosomes, Mammalian
      Comparative Genomic Hybridization
      DNA Copy Number Variations
      Fatty Acid-Binding Proteins
      Female
      Gene Dosage
      Gene Duplication
      Genome
      Genomics
      In Situ Hybridization, Fluorescence
      Male
      Polymerase Chain Reaction
      Sequence Analysis, DNA
      Species Specificity
      Bos
      Permalink
      http://hdl.handle.net/11693/21516
      Published Version (Please cite this version)
      http://dx.doi.org/10.1101/gr.133967.111
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      • Department of Computer Engineering 1368
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