猪部分内脏器官性状和乳头数的QTL检测

猪部分内脏器官性状和乳头数的QTL检测 JournalofGeneticsandGenomics (FormerlyActaGeneticaSinica) April2007,34(4):307—314 Availableonlineat,^n^,,IIf.sciencedirect.com 一, 蟹ScienceDirect DetectionofQuantitativeTraitLociAssociatedwithSeveral InternalOrganTraitsandTeatNumberTraitinaPigPopu- … lation JinghuZhang一,YuanzhuXiong一,BoZuo,MinggangLei,SiwenJiang,Feng'eLi, RongZheng,JialianLi,DequanXu . KeyLaboratoryofSwineGeneticsandBreeding,MinistryofAgriculture,CollegeofAnimalScienceandVeterinaryMedicine,HuazhongAgri- culturalUniversity,Wuhan430070,China; 2.DepartmentofBiologyScience&Technolog~ZhangzhouNormalCollege,Zhangzhou363000.China Abstract:Quantitativetraitloci(QTL)weredetectedfor8internalorgantraits,3carcasslengthtraits,andteatnumbertraitin214 pigsinaresourcepopulationthatincluded180F2individuals.Atotalof39microsatellitemarkerswereexaminedonSSC4,SSC6, SSC7,SSC8,andSSC13.Thegenetictraitsincludedheartweight ?,lungweight(LW),liverandgallbladderweight(LGW), spleenweight(SPW),stomachweight(STW),smallintestineweight(srw),largeintestineweight(LrW),kidneyweight(KW), carcasslengthtothefirstcervicalvertebra(CL1),carcasslengthtothefirstthoracicvertebra( CL2),ribnumbers(RNS),andteat numbersfiNS).Resultsindicatedthat,3highlysignificantQTL(P?0.01atchromosome— wiseleve1)forHW(at30cMonSSC6), RNS(at115cMonSSC7),TNS(at110cMonSSC7),and6significantQTL(尸? 0.05atchromosome—wiseleve1)forLW(at119 cMonSSC13),LGW(at94cMonSSC6),SPW(at106cMonSSC8),SIW(0cMonSSC4),LI W(170cMonSSC4),andTNS (at95cMonSSC6)weredetected.ThephenotypicvariancesforwhichtheseQTLwereaccou ntedrangedfrom0.04%to14.06%. MostoftheseQTLhadnotbeenpreviouslyreported. Keywords:pig;quantitativetraitloci(QTL);internalorganweighttraits;carcasslengthtraits ;teatnumbertrait SinceAnderssonPt口f.f1】issuedthefirstartic1eOf QTLresearchinpigs;manystudieswereconducted inswineonQTLmapping,leadingtosignificantpro- gressinthisfield[261. Thedevelopmentofinternalorgansisexpected tocoordinatewiththedevelopmentoftheentirebody. Thedevelopmentofintemalorgansreflectsbody constitutionwhichcouldimpactontheproductive potentia1.Therefore,theinvestigationonQTLmap- pingofinternalorganweighttraitswouldhelpin understandingthegeneticbasisofinternalorgan developmentinpigs.However,suchstudieshave beenrare. Thecarcasslengthandribnumbersareimpor- tanttraitsrelatedtothecarcassconstitutionandpro- ductiontraitsinpigs,whicharedifferentbetween nativeandforeignpigbreeds.Theteatnumbertraitis animportantexternaltraitrelatedtothereproductive potentialinpigs.InformationaboutQTLmappingof these仃aitshasalsobeenscarce. Received:2006——05——08;Accepted:2006——05——19 ThisworkwassupportedbytheStateKeyBasicResearchandDevelopmentPlanofChina(No NaturalScienceFoundationofChina(No.30500358). ?Correspondingauthor.E-mail:xiongyzh@public.wh.hb.cn;Tel:+86—27— 87287390,Fax www.jgenetgenomics.org 2006CB102102),andtheNational +86.27—87394184 JournalofGeneticsandGenomics遗传Vo1.34No.42007 Inthisstudy,aresourcefamilypopulationis used,andQTLdetectionandgeneticanalysisfor theseinternalandexternaltraitsismade. 1MaterialsandMethods 1.1Populationandtraits Thepigresourcefamilypopulationwasestab. 1ishedbyrandomlymating3Yorkshireboarsto8 MeishanSOWS(fromJiadingCounty,Shanghai, China).Fivemalesand21femalesfromF1generation wereselectedandrandomlymatedtogive180indi— vidualscomposingFzpopulations,andtheprogeny wasraisedinaherdwiththesameequipmentand withordinaryfoodstandards,duringsummerandau— tumnOf2003. Eightinternalorgantraitswererecordedaccord. ingtothemethodofXiongandDeng[71atthetimeof slaughtering(Table1).Alltheintestinalgutswere freeofvisceralmaterialsandwaterwhentheywere weighed.Thecarcasslengthtraitsweremeasured fromtheendofcarcasstothefirstcervicalvertebra (CL1)ortothefirstthoracicvertebra(CL2).Therib numbersandtheteatnumbersweretakenbydirectly countingonthecarcass. Table1Descriptivestatisticsfortraitsdatainthisresearch 1?2Microsatellites,PCRamplification,andge. notypescoring AtOtaloI39microsatellitemarkersonSSC4.6. 7,8,and13wereselectedbasedontheUSDA— MARCGenomeDatabasemap,onwhichtheloci intervalswereabout20—30cM(Table21.Allthemi. crosatelliteDNAprimerswereprovidedbyU.S.Pig GenomeCoordinator(MaxERothschild).PCRand genotypingwereaccordingtothemethodofZhanget 口f【8]. 1.3Methodofstatisticalanalysis LinkageanalysiswasperformedusingtheCRI. MAPsoftware(version2.4)【9J.Onlinesoftware[1~】 ()wasusedtocarryoutQTL analysis.Thefollowingstatisticalmodelwasfitted basedonalinearmodelintermsofadditiveand dominancecontributionsforaQTL[,11,. y=+sex+family+covariate+Coa+Cdd+e where,Ydenotestheobservations;denotesthemean; sexandfamilydenotethefixedeffectoftraits;the covariatedenotesthecarcassweightfortheinterna1 orgaJlweighttraitsandthecarcasstraits.anddefault fortheteatnumbertrait.ThecoefficientCadenotes theprobabilityoftheadditiveeffect(口),andcdde. 1^n^n^,.jgenetgenomics.org IM=InformativeMeioses notesthatofthedominanceeffect(,atthechromo somepositionoftheQTLthathadbeenidentified. Theadditiveeffect()anddominanceeffect(de— notetheparameterstobeestimatedfortheQTL.In thisstudy,theadditiveeffects()wereestimatedas [P(QQ)一P(qq)]/2,inwhichadenotestheQTL allelefromYorkshire,andqdenotestheQTLallele fromMeishan.Thedominanceeffect(iSestimated asP(aq)一[P(QQ)+P(qq)]/2,fortheQTLthathad ,^n^n^f.jgenetgenomics.org beenidentified.Thus,positivevaluesoftheadditive effectsdenotedincreasingeffectsoftheQTLbythe allelefromYorkshire,andtheoppositewastruefor thenegativevalues().There— sidualsarerepresentedbye. TheadditivefractionofFzphenotypicvariance ()explainedbyaQTLwascomputedassuming thatalternativealleleswerefixedineachbreed;that is,hzoaZ/2n. Chromosome—wisesignificance 310JournalofGeneticsandGenomics遗传Vo1.34No.42007 thresholdswerecalculatedempiricallybypermutation testll3J . ofwhichthenumberwas1,000. 2Results Thestatisticalparametersofthe12lntemalor' gantraits,carcasslengthtraits,andteatnumbertraits areshowninTable1.Theresultsshowedthatthe varianceoftheobservedvaluewasbroad,andmaybe theresultofgeneticdifferencesamongtheindividu— als. Thelinkagemapconstruction(Table2)shows thattheordersofthemicrosatellitemarkerswere identicaltothatreportedbyUSDA?MARS (),butthe averagelengthsofthetwosexeswerelongerthan thoseintheUSDAmap.Theseweresimilartothe previousresearchbvSuet?[14andZuoet?Z【l5J. ResultsfromtheQTLanalysisareshowninTa? ble3andFig.1.Atotalof9QTLforthesetraitswere detected. QTLforHW,LW,LGW,andSPW:Therewasa QTLwithaverysignificanteffectonHWatposition of30cM.betweenthemarkersw1841andswl3O2on SSC6rP<0.O1).TheQTLcouldaccountforabout 9.52%ofthephenotypicvariationinthepopulation, withanegativeadditiveeffectofO.022kg.which suggestedthattheQTLalleleeffectfromYorkshire decreasedheartweight,andheterozygouspigshada Table3EstimatesofQTLpositionsforcertaincarcasstraits positivedominanteffectonincreasingheartweight by0.026kg.TherewasanotherQTLwithasignifi— canteffectonLWatpositionof120cM.atthe markersw520onSSC13<0.05),andtheQTL couldaccountforabout7.75%ofthephenotypic variation,withnegativeadditiveeffectanddominant effectonLW. QTLmappingresultsindicatedthat,aQTLwith asignificanteffectonLGWwaslocatedatpositionof 95cM,betweenthemarkersswl129andsw1473on SSC6(P<0.05),whichcouldaccountforabout7.64 %ofthephenotypicvariationinFzpopulation.with positiveadditiveeffectonLGW.TI1eQTLwitha significanteffectonSPWwaslocatedatsw1037on SSC8,withpositiveadditiveeffectanddominantef- fect. QTLforSIWandLIW:TwoQTLwithsignifi— canteffectsonSIWandLIWwerelocatedatposi? tions0cM(sw489)and170cM(s0161),respectively, onSSC4.TheQTLforSIWcouldaccountforabout 13.47%ofthephenotypicvariationinthepopulation, withpositiveadditiveeffectanddominanteffectof increasingthesmallintestineweight.TI1eQTLfor LIWcouldaccountforaboutjust0.o4%ofthephe? notypicvariationinthepopulation,withnegativead— ditiveeffectanddominanteffectofdecreasingthe largeintestineweight,ofwhichthedominanteffect wasthemainfactorforthephenotypebytheQTL allelefromYorkshireinFzpopulation. ' significantatchromosome-wiselevel(尸<0.05);verysignificantatchromosome— wiselevel(尸<0.01) WWW.jgenetgenomics.org JinghuZhangela1.:DetectionofQuantitativeTraitLociAssociatedwithSeveralInternalOr ganTraitsandTeatNumberTrait311 Var ratio 60 5O 40 rat Wair . 3.0 war ratio 20 l0 OO Position(cM) Position(cM) 7.0 60 50 Vat4.0 ratio3 .0 2.0 1.O 0.0 25 20 Var15 ratio 10 5 0 Position(cM) Position(cM) 1^n^n^,.jgenetgenomics.org Position(cM) war rat10 war ratio Position(cM) SPWSSC8(D) Position(cM1 LIWSSC4(F) 8.O 6.0 40 2.0 00 Position(cM) Position(cM) Fig.1QTLmappingresultsofinternalorganweight traitsandreproductivetraits A:HWonSSC6;B:LWonSSC13;C:LGWonSSC6;D: SPWonSSC8;E:SIWonSSC4;F:LIWonSSC4;G:TNS onSSC6:H:TNSonandSSC7:I:RNSonSSC7.Theab— scissaindicatestherelativepositiononthelinkagemap. TheordinaterepresentstheF-ratio. 3l2JournalofGeneticsandGenomics遗传Vo1.34No.42007 QTLforRNSandTNS:AsignificantQTLfor CLwasnotdetected,butahighlysignificantQTL(P ?0.01atthec~omosomeleve1)forRNSwas mappedtoposition115cM,betweenmarkerssw352 andsw252,onSSC7.Itcouldaccountforabout 4.80%ofthephenotypicvariationinthepopulation. withpositiveadditiveeffectanddominanteffectof increasingtheribnumber. TwoQTLwithsignificanteffectsonTNSwere locatedatpositionsof95cMonSSC6(between swl129andsw1473,significantatc~omosome—wise leve1)and110cMonSSC7(atsw352,highlysignifi— cantatc~omosome—wiseleve1).Theadditiveeffects oftheQTLcouldaccountforabout14.06%and 11.30%ofthephenotypicvariationinthepopulation, respectively,butonehadpositiveadditiveeffect(on SSC7)andanotherhadnegativeadditiveeffect(on SSC6). 3Discussion Thefindingsofthepresentstudygivemore knowledgeabouttheinheritanceofinternalorgan weighttraitsinpigs.AverysignificantQTLforHW and5significantQTLforLW,LGW,SPW,SIW,and LIWweremapped.Mostofthemwerereportedfor thefirsttime. ReportsofQTLmappingforinternalorgan weighttraitsinrecentyearsarelistedbelow.The QTLforHWareat2cMonSSC2[刚.at33.1cMon SSC8t. at66cMonSSC4t引.at55.1cMon SSC1491. andsoon;andQTLforliverweightareat 118.8cMonSSC4t州. at43.4cMonSSC7[?.at29.6 cMonSSC8t?1,andat73.7cM(62.8—112cM)on SSC6.ThelastQTLnearthemarkers0087accounted forabout3.2%ofphenotypicvariance.ThisQTL wasnearthemappingresultsinthisresearch,butthe QTLeffectswerereversed.Thismaybeduetothe differentresourcefamilypopulationusedinthere— spectivestudies. QTLmappingresultsforCLandRNSinthisre— search8resimilartotheresultsbyZuot以【61.in whichtheRNSQTLwaslocatedbetween sw252一sw581onSSC7,withonlyabout12cMdif- ferencebetweenthem.Bothdetectedapositiveeffect onincreasingtheribnumberbytheQTLallelefrom YorkshireandbothcouldnotdetectQTLassociated CLinYorkshirexMeishanresourcepopulationtoo. SeveralstudieshavereportedthatQTLassoci— atedwithTNSweremappedto171cMonSSC6,62 cMonSSC7.and19cMonSSC8t,矧. TheQTLat 171cMonSSC6hadsimilarmagnitudeanddirection ofgeneticeffectswiththeresultobservedinthis study,butthelocationwasdifferent.Anotherreport locatedtheTNSQTLat85.6cMonSSC7[25]withthe samedirectionofadditiveanddoITlinanteffecton TNSastheresultsofthisresearch.Itispossiblethat thesarueQTLwasmapped. Fromtheresultsofthisresearchandthereports, itcanbeconcludedthatasignificantnumberofQTL forinternalo唱antraits,carcasslength,ribnumber, andteatnumberexistinabroadregionofpiggenome. TheidentificationofDNAvariantsingenesresponsi— blefortheQTLeffectsrequiresfurtherfinemapping ofQTLandpositionalcloningbasedonthemapping inthenextinvestigation.Forthesesubsequentsteps, QTLmappinginsuitableresourcepopulationasthis researchhasdonerepresentsanessentialstarting pointandisthereforesignificantforanimalbreeding. Acknowledgements:Tlleauthorsarethankfultothe USDA--MARCforprovidingthemicrosatelliteprim-- ersandareespeciallygratefultoDr.TaraMatiseand Dr.ChunshengHefromRutgersfortheirhelpinus— ingtheCrimapsoftware.Tlleauthorsalsogratefully extendtheacknowledgementstotheteachersand postgraduatestudentsoftheKeyLaboratoryofSwine GeneticsandBreeding,MinistryofAgriculture,and theSwineBreedingCenterofChinafortheircoop— eration. 1^n『I,,^f.jgenetgenomics.org JinghuZhangeta1.:DetectionofQuantitativeTraitLociAssociatedwithSeveraln【en瑚 OrganTraitsandTeatNumberTrait313 References 1AnderssonL,HaleyCS,EilegrenH,KnottSA,JohanssonM, AnderssonK,Andersson-EklundL,Edfors—LiljaI,Fredholm M,HanssonI,H~tkanssonJ,Lundstr6mK.Geneticmapping ofquantitativetraitlociforgrowthandfatnessinpigs.Sci— ence,1994,263(5154):1771—1774. 2Andersson—EklundL,MarklundL,LundstromK,HaleyCS, AnderssonK,HanssonI,MoilerM,AnderssonL.M印ping quantitativetraitlociforcarcassandmeattraitsinaWildboar xLargeWhiteintercross.JournalofAnimalScience,1998,76: 700. 694— 3BidanelJP,RothschildM.Currentstatusofquantitativetrait locusmappinginpigs.PigNewsandInformation,2002, 23(2):39N一54N. 4SuYH,XiongYZ,ZhangQ,Jiangsw,YuL,LeiMG, ZhengR,DengCY.Detectionofquantitativetraitlocifor growthinLargeWhitexMeishanintercross.ActaGenetica Sinica.2002,29:607—611(inChinese?lanEnglishab— stract). 5SuYH,XiongYZ,ZhangQ,JiangSw,LeiMG,YuL, ZhengR,DengCY.M印pingquantitativetraitlociforfat depositionincarcassinpigs.ActaGeneticaSinica,2002,29: 681—684(inChinesewithanEnglishabstract). 6ZuoB,XiongYZ,SuYH,DengCY,ZhengR,LeiMG,YuL. M印pingandgeneticeffectanalysisofswinequantitativetrait lociusing24microsateilites.ActaVeterinariaetZootechnica Sinica(China),2003,34:139—146(inChinesewithanEng— lishabstract). 7XiongYZ,DengCY.Principleandmethodofswinetesting. ChineseAgriculturalPress,Beijing,1999(inChinese). 8ZhangJH,XiongYZ,ZuoB,LeiMGJiangSW,LiFE, ZhengR.LiJL.Geneticanalysisandlinkagemappingina resourcepigpopulationbymicmsatellitemarkers.ActaGe- neticaSinica,2007,34(1):10—16. 9GreenFallsK,CrooksS.DocumentationforCRIMAP, Version2.4.WashingtonUniversity,schoolofMedicine,St. Louis,Mo,1990. 10SeatonG,HaleyCS,KnottSA,KearseyM,VisscherPM. QTLexpress:mappingquantitativetraitlociinsimpleand complexpedigrees.BioinformaticsApplicationsNote,2002, 18(2):339—340. 11HaleyCS,KnottSA,ElsenJM.M印pingquantitativetrait lociincrossesbetweenoutbredfinesusingleastsquares.Ge- netics,1994,136:1195—1207 12OviloC,Perez-EncisoM,BarraganC,ClopA,RodriguezC, \^n^n^f.jgenetgenomics.org OliverMA.TomMA,Noguera几.AQTLforintramuscular fatandbackfatthicknessislocatedonporcinechromosome6. MammalianGenome.2O00.11:344—346. 13ChurchillGA,DoergeRW.Empiricalthresholdvaluesfor quantitativetraitmapping.Genetics,1994,138:963—971. 14SuYH,XiongYZ,ZhangQ,XiaXJiangSW,DengCY, ZhengR,LeiMG,YangZM.Constructionoflinkagemapof chromosomes1and3inLargeWhitexMeishanreference family.ActaGeneticaSinica,2002,29(1):16—20(inChinese wi?lanEnglishabstract). 15ZuoB,XiongYZ,SuYH,DengCYuL,ZhengR.Genetic linkagemapconstructionofsomemicrosateilitesonpig chromosomes4and7.JournalofAgriculturalBiotechnology, 2003,l1(1):70—74(inChinesewithanEnglishabstract). 16LeeSS,ChenMoranC,CepicaS,ReinerGBar