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

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dc.contributor.authorBickhart, Derek M.
dc.contributor.authorHou, Yali
dc.contributor.authorSchroeder, Steven G.
dc.contributor.authorAlkan, Can
dc.contributor.authorCardone, Maria Francesca
dc.contributor.authorMatukumalli, Lakshmi K.
dc.contributor.authorSong, Jiuzhou
dc.contributor.authorSchnabe, Robert D.
dc.contributor.authorVentura, Mario
dc.contributor.authorTaylor, Jeremy F.
dc.contributor.authorGarcia, José Fernando [UNESP]
dc.contributor.authorVan Tasse, Curtis P.
dc.contributor.authorSonstegard, Tad S.
dc.contributor.authorEichler, Evan E.
dc.contributor.authorLiu, George E.
dc.contributor.institutionARS
dc.contributor.institutionUniversity of Maryland
dc.contributor.institutionUniversity of Washington
dc.contributor.institutionUniv Bari
dc.contributor.institutionUniv Missouri
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.date.accessioned2014-05-20T15:34:44Z
dc.date.available2014-05-20T15:34:44Z
dc.date.issued2012-04-01
dc.description.abstractCopy 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 similar to 55.6-Mbp sequence-476 of which (similar to 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 (similar to 52%, chi(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.en
dc.description.affiliationARS, USDA, ANRI, Bovine Funct Genom Lab, Beltsville, MD 20705 USA
dc.description.affiliationUniv Maryland, Dept Anim & Avian Sci, College Pk, MD 20742 USA
dc.description.affiliationUniv Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA
dc.description.affiliationUniv Bari, Dept Genet & Microbiol, I-70126 Bari, Italy
dc.description.affiliationUniv Missouri, Div Anim Sci, Columbia, MO 65211 USA
dc.description.affiliationUNESP Univ Estadual Paulista, Aracatuba, SP, Brazil
dc.description.affiliationUniv Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA
dc.description.affiliationUnespUNESP Univ Estadual Paulista, Aracatuba, SP, Brazil
dc.description.sponsorshipNIH
dc.description.sponsorshipAgriculture and Food Research Initiative from USDA National Institute of Food and Agriculture
dc.description.sponsorshipNRI/AFRI from NIFA
dc.description.sponsorshipUSDA-ARS
dc.description.sponsorshipIdNIH: GM058815
dc.description.sponsorshipIdNIH: HG002385
dc.description.sponsorshipIdUSDA: 2009-65205-05635
dc.description.sponsorshipIdNRI/AFRI from NIFA: 2007-35205-17869
dc.description.sponsorshipIdNRI/AFRI from NIFA: 2011-67015-30183
dc.description.sponsorshipIdUSDA-ARS: 1265-31000-098-00
dc.format.extent778-790
dc.identifierhttp://dx.doi.org/10.1101/gr.133967.111
dc.identifier.citationGenome Research. Cold Spring Harbor: Cold Spring Harbor Lab Press, Publications Dept, v. 22, n. 4, p. 778-790, 2012.
dc.identifier.doi10.1101/gr.133967.111
dc.identifier.fileWOS000302203800018.pdf
dc.identifier.issn1088-9051
dc.identifier.lattes9991374083045897
dc.identifier.urihttp://hdl.handle.net/11449/42639
dc.identifier.wosWOS:000302203800018
dc.language.isoeng
dc.publisherCold Spring Harbor Lab Press, Publications Dept
dc.relation.ispartofGenome Research
dc.relation.ispartofjcr10.101
dc.relation.ispartofsjr12,367
dc.rights.accessRightsAcesso restrito
dc.sourceWeb of Science
dc.titleCopy number variation of individual cattle genomes using next-generation sequencingen
dc.typeArtigo
dcterms.licensehttp://genome.cshlp.org/site/misc/ifora.xhtml
dcterms.rightsHolderCold Spring Harbor Lab Press, Publications Dept
unesp.author.lattes9991374083045897
unesp.author.orcid0000-0002-7597-7313[5]
unesp.author.orcid0000-0002-5443-0706[4]
unesp.author.orcid0000-0001-9103-5150[3]
unesp.author.orcid0000-0001-7762-8777[9]
unesp.author.orcid0000-0001-5018-7641[8]
unesp.author.orcid0000-0002-8416-2087[12]
unesp.author.orcid0000-0003-2223-9285[1]
unesp.campusUniversidade Estadual Paulista (Unesp), Faculdade de Medicina Veterinária, Araçatubapt

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Artigos - Apoio, Produção e Saúde Animal - FMVA