DetectinggeneticvariationsuchasCopyNumberVariants (CNVs)incattleprovidestheopportunitytostudy their associationwithquantitativetraits.CNVsareDNAsequencesof50bpuptoseveralMblong,whichcan varyincopynumberincomparisonwithareferencegenome.TheaimofthisstudywastoinvestigateCNVsin 1410samplesoftheBrownSwisscattlebreedusingIlluminaBovineHDSNPchipinformation,whichincludes 777,962SNPs.Afterstringentqualitycontrol,CNVswerecalledwiththeGoldenHelixSVS8.3.1(SVS)and PennCNV softwareandweresummarizedtoCNVregions(CNVRs)atapopulationlevel(i.e.overlapping CNVs), usingBEDTools.Additionally,commonCNVRs betweenthetwosoftwareweresetasconsensusre- gions. GeneswithinconsensusCNVRswereannotatedwithaGOanalysisusingtheDAVIDBioinformatics Resources6.7.Inordertovalidatetheseresults,quantitativePCRswereexecutedon15selectedCNVRs. The SVSsoftwareidentified25,030CNVssummarizedto398CNVRs,whichcomprised30gains,344 lossesand24complexCNVRs(i.e.containingbothlossesandgains),covering3.92%ofthebovinegenome. ThePennCNVsoftwareidentified 62,341CNVssummarizedto5578CNVRs,whichcomprised2638gains, 2404lossesand537complexCNVRs,covering7.68%ofthebovinegenome.ThelengthoftheseCNVRsranged from1244bpto1,381,355bp.Atotalof563consensusCNVRswerefoundcovering2.29%oftheUMD 3.1bovinegenomeassembly.Ofthese,24weregains,300werelossesand239werecomplexCNVRs.Atotal of 775official geneIDswereannotatedintheconsensusCNVRs.Amongthe537geneswithfunctionalin- formation, theGOandpathwayanalysiswasreported forthosewhoclusteredwithap-value o0.05. The quantitativePCRssuccessfullyvalidated14(93.33%)oftheselectedCNVRs. The resultofthisstudyisthe first comprehensivegenomicanalysisoftheBrownSwissbreedbasedonthe IlluminaBovineHDSNPchiponsuchalargenumberofanimalsthatenrichestheCNVmapinthebovine genome.These findingsalsoprovidevaluableinformationforfurtherCNVstudies.Finally,theresultsofthe CNVR mapdeliversnewinformationforfunctional,health andproductivetraitsconsideredinselection programsoftheBrownSwissbreed.
A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle / R.T.M.M. Prinsen, M.G. Strillacci, F. Schiavini, E. Santus, A. Rossoni, V. Maurer, A. Bieber, B. Gredler, M. Dolezal, A. Bagnato. - In: LIVESTOCK SCIENCE. - ISSN 1871-1413. - 191(2016 Sep), pp. 153-160.
Titolo: | A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle |
Autori: | STRILLACCI, MARIA GIUSEPPINA (Secondo) DOLEZAL, MARLIES ALEXANDRA (Penultimo) BAGNATO, ALESSANDRO (Ultimo) |
Parole Chiave: | CNV; Illumina Bovine HD BeadChip; Brown Swiss |
Settore Scientifico Disciplinare: | Settore AGR/17 - Zootecnica Generale e Miglioramento Genetico |
Data di pubblicazione: | set-2016 |
Rivista: | |
Tipologia: | Article (author) |
Digital Object Identifier (DOI): | http://dx.doi.org/10.1016/j.livsci.2016.08.006 |
Appare nelle tipologie: | 01 - Articolo su periodico |
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