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. [10.1016/j.livsci.2016.08.006]
A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle
R.T.M.M. PrinsenPrimo
;M.G. StrillacciSecondo
;F. Schiavini;A. Rossoni;M. DolezalPenultimo
;A. BagnatoUltimo
2016
Abstract
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.
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