第17章-分子标记辅助选择

第十七章分子标记辅助选择第一节分子标记辅助选择的基本原理第二节质量性状的标记辅助选择第三节数量性状的标记辅助选择第四节分子标记辅助选择的挑战与发展策略传统的育种主要是根据植株的表现型进行选择，而环境条件、基因间互作、基因型与环境互作等多种因素都会影响表型选择效率。育种者在长期的实践中不断探索运用遗传标记来提高育种的选择效率与育种预见性。遗传标记包括形态学标记、细胞学标记、生化标记与分子标记。以DNA多态性为基础的分子标记，目前已在作物遗传图谱构建、重要农艺性状基因的标记定位、种质资源的遗传多样性分析与品种指纹图谱及纯度鉴定等方面得到广泛应用，尤其是分子标记辅助选择（molecularmarker-assistedselection，MAS）育种更受到人们的重视。1、概念：通过基因定位找到与目标基因紧密连锁的分子标记后，可通过该分子标记间接地对目标性状进行选择。此法称分子标记辅助选择(MolecularAssistantSelection,MAS)。MAS是育种中的一个诱人领域,将给传统的育种研究带来革命性的变化。MAS主要应用在有利基因的转移和基因的累加等方面。第一节分子标记辅助选择的基本原理TesterM&LangridgeBreedingtechnologiestoincreasecropproductioninachangingworld.Science,2010,V327:818-822RR(1-r)20.9025抗性供体受体×RS2r(1-r)0.095SSr20.0025目的基因与标记连锁（交换值为r）亲本中的标记带型F1中的标记带型F2群体中3种标记带型当r=0.05时，根据标记基因型mm选择目的基因型RR，选错的概率约为0.10共显性DNA标记的辅助选择原理×mRMSmRMS×Definitions1)Phenotypicselection(PS)–basedonphenotypicvalue2)Marker-basedselection(MBS)–frommarkersthatrepresentQTLorarelinkedtoQTL3)Marker-assistedselection(MAS)–fromacombinationofphenotypicvalueandmarkerinformation4)Marker-assistedbackcrossing(MABC)5)Marker-assistedrecurrentselection(MARS)6)GenomicSelectionorGenome-wideSelection(GSorGWS)–SelectforbreedingvaluessummedacrossmanymarkerswithoutestimationofQTL(1)selectionwithouttestcrossingoraprogenytest;(2)selectionindependentofenvironments;(3)selectionwithoutlaboriousfieldworkorintensivelaboratorywork;(4)selectionatanearlierbreedingstage;(5)selectionformultiplegenesand/ormultipletraits;(6)wholegenomeselection.Usefulifconventionalscreeningmethodsarelaborious,costly,orenvironmentallydependent–Selectionsfordiseaseandinsectresistancecanbemadeintheabsenceofthepathogenorpest–GreatestpotentialadvantageoverphenotypicselectionfortraitswithlowpenetranceorlowheritabilityMayreducepopulationsizesneededforphenotypicselection–MaypermitselectionofindividualplantsMayspeedupthebreedingprocess–Maybeeffectiveforearlygenerationtesting–Selectionsattheseedlingstagecanbeagreatadvantageincropswithalonggenerationtime–Reducenumberofgenerationsinabackcrossingprogrambyselectingforrecoveryoftherecurrentparentgenomeaswellasgenesofinterestfromthedonorparent2、MostsuitableforMASPyramidgenesforasingletraitthatcouldnototherwisebedistinguishedatthephenotypiclevel–Accumulatingmultiplequantitativetraitloci(QTL)fordiseaseresistancemayprovideahigherlevelofresistanceand/ormoredurableresistancetochangesinthepathogenpopulation–MASmaypromotedeploymentoffewerresistancegenesGenesformultipletraitsofinterestmayalsobecombinedinonecultivarwithrelativeefficiencyMarkertechnologiesprovidethepotentialtounderstandtheunderlyingcausesofepistasisandGXE,whichcouldgreatlyimproveselectionefficiencyQualitativetraitsandquantitativetraitswithhighheritabilityaremoreamenabletoMASthanquantitativetraitswithlowheritability,whichisgenerallythecaseforphenotypicselectionaswell.Epistasis(oreffectofgeneticbackground)andgenotypebyenvironmentinteractions(GXE)canconfoundprogressfromMASjustastheydoinconventionalselectionschemes.EffortstoimprovetheprecisionofQTLestimationthroughincreasedreplicationandmultilocationaltestingwillalsoincreasetheefficiencyofphenotypicselection,therebyreducingthegainsthatmaybeattainedthroughMAS.Catch22:–Ifphenotypesarepoorindicatorsofgenotypes,youcannotmapQTLforuseinMAS–Ifphenotypicdataaregood,youdon’tneedMASParadoxofMAS1)Howtightlyitislinkedtogenescontrollingimportanttraits.2)Therelativeimportanceofthosegenesindeterminingthephenotype.3)TheconsistencyoflinkagedisequilibriumbetweenthemarkerandQTL4)ThefrequencyoftheQTL(MASwillbemorebeneficialwhentheQTLisinlowfrequency)3.TheutilityofamarkerdependsonRequirementsforwide-scaleapplicationofMASValidationofQTLinbreedingmaterials–MultiplemarkersinvicinityofQTLdesirableSimple,quick,inexpensiveprotocolsfortissuesampling,DNAextraction,genotyping,anddatacollectionEfficientdatatracking,management,andintegrationwithphenotypicdataDecisionsupporttoolsforbreeders–optimaldesignofselectionstrategies–accurateselectionofgenotypes大多数情况下，质量性状无需借助于分子标记，但采用分子标记辅助选择可提高选择效率：○表现型测定难度大或费用太高；○表现型只能在个体发育后期才能测量，而育种实践中希望在早期选择；○除目标性状外，还需对遗传背景进行选择；○质量-数量性状的选择。第二节质量性状的标记辅助选择1、标记辅助选择的基本方法1）前景选择（foregroundselection）——对目标基因的选择●单标记可靠性：取决于标记与目标基因间连锁的紧密程度。如，标记座位M/m与目标基因座位Q/q连锁，重组率为r，则在F2根据标记基因型M/M获得目标基因型Q/Q的概率为p=（1-r）2。选择正确率随重组率增加而迅速降低。★如要求正确率在90%以上，则标记与目标基因间的重组率必须＜5%。GenotypesofF2plantsforXa-21geneasdeterminedbyaPCRmarkerandprogenytestsPCRanalysisF3progencytestAccuracy（%）GenotypeNo.ofplantsGenotypeNo.ofplantsRR34RR3191.2Rr3Rr28RR485.7Rr24ThedistancebetweenmarkerpTA248andXa-21geneisabout1cM(RonldandTanksley,1991).The9%inaccuracymayreflecttheerrorinphenotypingorthevariationinrecombinationfrequencyfrommappingpopulationtobreedingpopulation.★如要求选到1株目标基因型的概率为P，则必须选择带有目标基因型M/M的植株的最少数目为：n=log（1-P）2/log（1-r）2即使重组率高达0.3，也只要选择7株具有基因型M/M的植株，就有99%的把握能保证其中有1株为目标基因型；而如果不用标记辅助选择（相当于标记与目标基因间无连锁，即r=0.5），则至少需要16株。●双边标记可靠性将大大提高。如标记M1/m1和M2/m2各位于目标基因座Q/q的一侧，与目标基因间的重组率分别为r1和r2，则：F1的基因型为M1QM2/m1qm2F1产生的标记基因型为M1M2的配子有两种类型，包含目标等位基因的M1QM2和包含非目标等位基因的双交换M1qM2，由于双交换发生频率很低，因此，在后代中通过同时跟踪M1和M2来选择目标等位基因Q，正确率必然很高。在无干扰时，F2代通过选择标记基因型M1M2/M1M2而获得目标基因型Q/Q的概率为：p=（1-r1）2（1-r2）2/[（1-