Racial and Allelic DiversityEvolutionary Genetics of MaizeThe Bottom Line for DiversityPopulation Statistical AnalysisRelative Loss of Diversity (π)Slide 6Slide 7Slide 8Testing for Phenotypic EffectsSlide 10Slide 11Slide 12Slide 13Slide 14Slide 15NAM Population DevelopmentNested Association AnalysisSlide 18Linkage MappingQuantitative Trait Locus (QTL) Mapping of Stalk TraitsSlide 21Slide 22Linkage Disequilibrium (LD)Association Analysis MethodologyPopulation Structure and AssociationsRacial and Allelic DiversityS. Flint-Garcia, USDA-ARS, Columbia, MO- August 17, 2006 -Germplasm Enhancement of MaizeEvolutionary Genetics of Maize•Domesticated from Zea mays ssp. parviglumis•Single domestication event in Mexican highlands•6,000~9,000 years ago•Plant architecturee.g. tb1•Seed coat e.g. tga1Doebley et al. (1997) Nature 386: 485-488Matsuoka et al. (2002) PNAS 99: 6080-6084Wang et al. (2005) Nature 436: 714-719 SelectionTeosinteModern InbredsLandracesThe Bottom Line for DiversityTeosintesMaizeLandracesMaizeInbred Lines Unselected GeneDomestication Gene Improvement GenePlant BreedingDomesticationIn which category do the genes responsible for YOUR trait belong?2 - 4% (~1200) of maize genes have undergone selectionSelection ScreensVery low genetic diversityGenes that contribute to agronomic traits have been targets of selection.Teosinte (N=13) Inbreds (N=12)Population Statistical Analysis•Diversity Statistics–π = average number of pair-wise differences per nucleotide site 42 differences in 78 (13*12/2) comparisons0 differences in 66 (12*11/2) comparisonsAverage πinbreds = 0.0065Relative Loss of Diversity (π)•Average πteosinte = 0.0098 •Average πinbred = 0.0065~ 66% diversity retainedNeutral Gene -adh11 10000 0.01 0.03 0.02 0.042000(bp)InbredsTeosinteπAuxin response factor, ARF1 0 0.01 0.021000 2000 30001(bp)πInbredsTeosinteYamasaki et al. (2005) Plant Cell 17: 2859-2872Wright et al. (2005) Science 308: 1310-131400.020.040.060.080 200 400 600(bp)InbredsTeosinteProline Dehydrogenaseπ00.050.10.150.20.25% total AATeosintesLandracesInbred LinesAlanineArginineAspartic AcidCysteineGlutamic AcidGlycineHistidineIsoleucineLeucineLysineMethioninePhenylalanineProlineSerineThreonineTryptophanTyrosineValineT vs LRLR vs Inb** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** **T vs Inb** ** ** ** ** ** ** ** ** **** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** **05101520253035Total Amino Acid******% kernel wtTCA Cycleα-Keto-glutarateOxalo-acetateGlucose3-Phospho-glyceratePhosphoenolpyruvatePyruvateAcetyl-CoAO-AcetylserineSerineGlycineCysteineCysteine synthasePyruvateValineLeucine2-isopropyl-malatesynthase Lysine2,3-Dihydro-dipicolinateDHDP synthaseCystathionine γ-synthase CystathionineHomocysteine Methionine S-Adenosyl-methionineSAM synthetase II Cysteine Aspartate Amino-transferaseAspartateAspartate4-seminaldehydeAsparagineAsparagine synthetaseAspartate kinase Glutamate Isoleucine2-KetobutyrateHomoserine4-phosphateThreonineThreonine deaminase Acetohydroxyacid synthaseGlutamate dehydrogenaseGlutamateArginineProlineProlinedehydrogenaseGlutamineHistidineNitrateReductaseNH4NO3–NO2– NH4 Hexokinase(N:C sensing)Trans-cinnamic acidLigninPALTyrosinePhenylalanineChorismate mutasePrephenateAnthranilateSynthase βAnthranilateTryptophanIndole-3-glycerolphosphateTryptophanSynthase β1 ChorismateShikimateDAHPErythrose 4-PSAM synthetase IAlanineAdapted from Buchanan et al 200001020304050607080Ash Carbohydrate Crude Fat Crude Fiber Moisture Crude ProteinPercentLR vs InbT vs LR**T vs Inb**********ns*********ns**********TeosintesLandracesInbred LinesTesting for Phenotypic EffectsTeosintesInbred LinesUnselected (Neutral) GeneDomestication/Improvement Gene SelectionMu transposon insertion knockoutB73B73B73B73B73Teosinte-B73NILsB73Effect of teo background & teo alleleEffect of B73 allele if additive gene action8-7-06B73 x teosinte BC18-7-06Teosinte (ssp. parviglumis)7-24-06B73 x teosinte BC16’ tall7-24-063’ tall12’ tall9’ tall7-24-06Ames218147-24-06PI3840637-24-06PI3840657-24-06PI384066Teosinte BC27-24-06Ames218898-7-067-24-06PI3840718-7-067-24-06Ames217858-7-06Ames217868-7-06Ames217898-7-06LandracesGuirua Nal-tel Conico Costeno CristalinoNorteno Chalqueno Chapalote Bolita Cateto Sulino Dzit Bacal Gordo Pissccotunto Sabanero Serrano Tuson8-7-067-24-06B73 x LandracesNC33B115I137TN81-1MEF 156-55-2IL677AIa5125IA2132P39IL14HIL101F2EP1F7CO255NC366B52SC213RNC238GT112Mp339GA209M37WD940YT232U267YCI28AB2F2834TMo24WMS1334IDS28I-29SA244722SG18Sg1533HP301IDS91IDS69F6F44Ab28ACML328Oh603A441-5CML323SC55Mo18WNC264NC370NC320NC318NC334NC332CML92Tx303CML220CML218A272Tzi9CML77TZI8TZI10CML311CML349CML333CML158QCML154QCML281CML91parvi-03NC358NC356TX601NC340NC300NC350NC304NC338NC302NC354TZI18A6Ki44Ki43Ki11CML228Ki3Ki2007Ki21Ki2021Ki14CML238CML321CML157QCML247CML322CML332CML331CML261CML277CML341CML45CML11CML10Q6199CML314CML258CML5CML254CML61CML264CML9CML108CML103CML287Tzi11CML38CML69CML14CML52SC357L578T234N6E2558WM162WK64CI64CI44CI31ANC230CI66K55R109BMoGL317NC232VaW6CH701-30Va85CI90CM14H99Va99 PA91Ky226H95Oh40BOh43EVA26Pa762OH43A619Va22Va17Va14 Va59Va102Va35T8A654Pa880SD44CH9Pa875H49W64AWF9Mo1WOs420R168MS7138-11NC260Mo44CI21EHyKy21A661ND246WDA554CO125CO109B75DE-3DE-2DE1B57C123C103NC360NC364NC362NC342NC290ANC262NC344NC258CI91BCI187-2A682MO17K4NC222NC236CI3AK148Mt42MS153W401A556B77CM37CMV3OH7BW117HTCM7CO106B103B97R4Ky228B164Mo46Mo47Mo45Hi27Yu796-NSI205Tzi16Tzi25B79B105N7ASD40N28HTA641DE811H105WA214NH100A635A632A634B14AH91B68B64CM174CM105B104B84NC250H84B76B37N192A679B109NC294NC368NC326NC314NC328R229A680NC310NC324NC322NC330NC372B73HtrhmB73NC308NC312NC306NC268B46B10A239C49AC49A188W153RA659R177W22W182BCI-733-164226NC352NC336NC296NC346NC296ANC292SWEET CORNPOPCORNTROPICAL-SUBTROPICALSTIFF STALKNON STIFF STALKMIXEDLinkage Mapping Association Mapping Structured populationHigh powerLow resolutionAnalysis of 2 allelesModerate marker densityGenome scanUnstructured populationLow powerHigh resolutionAnalysis of many allelesHigh marker densityCandidate gene testing Nested Association Mapping (NAM)Structured sub-populations nested within an unstructured populationHigh PowerHigh resolutionAnalysis of many allelesModerate marker densityNAM Population DevelopmentThe 26 founder inbreds capture 80-85% of the diversity present in public maize inbreds (i.e. 302 assoc. pop.)TropicalCML103 CML228CML247CML277CML322CML333CML52CML69Ki11Ki3NC350NC358Tzi8Non-Stiff StalkB97 Ky21M162WMS71Oh43Oh7BMo17 (IBM) MixedM37W