Poster Print Size: Exploing Trait Correlaons for Next...
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ExploiBngTraitCorrelaBonsforNext-GeneraBonGrainYieldandEnd-UseQualityImprovementofU.S.HardWinterWheat
ScogHaley1,JessicaMoore1,SusanLatshaw1,CraigMorris2,JessePoland31SoilandCropSciencesDept.,ColoradoStateUniversity,FortCollinsCOUSA
2USDA-ARSWesternWheatQualityLaboratory,PullmanWAUSA3Dept.ofPlantPathology,KansasStateUniversity,ManhaganKSUSA
ScogD.Haley,Ph.D.WinterWheatBreederColoradoStateUniversityemail:[email protected]:wheat.colostate.edu
Contact1. ButlerD,CullisB,GilmourA,GogelB(2009)ASReml-Rreferencemanual,Version3.hgp://www.vsni.co.uk/soHware/asreml-r/.2. EndelmanJ(2011)RidgeregressionandotherkernelsforgenomicselecFonwithRpackagerrBLUP.ThePlantGenome4:250-255.3. GlaubitzJC,CasstevensTM,LuF,HarrimanJ,ElshireRJ,SunQ,BucklerES(2014)TASSEL-GBS:Ahighcapacitygenotypingby
sequencinganalysispipeline.PLoSONE9(2):e90346.4. JiaY,JanninkJL(2012)MulFple-traitgenomicselecFonmethodsincreasegeneFcvaluepredicFonaccuracy.GeneFcs192:
1513-1522.5. MoneyD,GardnerK,MigicovskyZ,SchwaningerH,ZhongG-Y,MylesS(2015)LinkImpute:fastandaccurategenotypeimputaFonfor
nonmodelorganisms.G3:Genes,Genomes,GeneFcs5(11):2383-2390.6. PolandJA.,BrownPJ,SorrellsME,JanninkJ-L(2012)Developmentofhigh-densitygeneFcmapsforbarleyandwheatusinganovel
two-enzymegenotyping-by-sequencingapproach.PloSONE7:e32253.7. RCoreTeam(2016)R:AlanguageandenvironmentforstaFsFcalcompuFng.,R3.3.2ed.RFoundaFonforStaFsFcalCompuFng,
Vienna,Austria.hgps://www.r-project.org.
References
GrainyieldandqualityimprovementareimportantwheatbreedingobjecFves.EarlypredicFonofbreedingvaluesviagenomicselecFon(GS)mayfostermorerapidgeneFcgainsinappliedculFvardevelopmentprograms.Whole-genomesinglenucleoFdepolymorphisms(SNPs)discoveredusinggenotyping-by-sequencing(GBS)wereusedtoassesspredicFonaccuracyinsingle-traitandmulF-traitpredicFonmodelsforend-usequalityandfield-basedtraits.Single-traitcross-validaFonaccuraciesforqualitytraitsrangedfrom0.31forgrainproteinto0.64formixographmixingFme,yetfewimprovementswereobservedformulF-traitGSforqualitytraits.MulF-traitGSforgrainyieldwithsecondarytraitsgrainproteinandgrainproteindeviaFonwashighlyeffecFveatincreasingGSpredicFonaccuracy,withaccuraciesover0.70.MulF-traitGSshowspromiseforleveragingphenotypesfromappliedculFvardevelopmentprogramstoincreasetherateofgainthroughbreeding.
AbstractGBS-BasedSNPMarkerDiscovery• Over24,000SNPswereidenFfiedintheSNPdiscoveryamongthetotal
of11,528individualsinthepanel(Fig.4).OverallalowercoverageoftheDgenomewasobserved,ashasbeenreportedpreviously.
• FollowingmeanimputaFonusingrrBLUP,9,488SNPswereretainedforGSanalysiswiththetestindividuals.
PredicFonAccuracy• StrongposiFveandnegaFvephenotypiccorrelaFonswereobserved
withinthepanelfortheend-usequalitytraits(Fig.5).RelaFvelyfewimprovementsinpredicFonaccuracywereobserved,however,withincorporaFonofasecondarytraitinthemodel(Table1).MixingFmeandtolerancewerenotableexcepFons.
• Single-traitGSpredicFonaccuraciesforyield,grainprotein,andgrainproteindeviaFonwerelowtomoderate(Fig.6).IncorporaFonofgrainproteinandgrainproteindeviaFonassecondarytraitssignificantlyimprovedGSpredicFonaccuracyforgrainyield.AddiFonofagroupof245unphenotypedindividualsintothemodel(“forward”,Fig.6)resultedinasimilarpredicFonaccuracyaswiththeoriginalpanel.
RaBonaleandObjecBves
Phenotypes• Laboratoryend-usequalitydataandyieldtrialdatafromtheCSU
WheatBreedingProgramsince2006wereassembledforanalysis.• End-usequalitycharacterisFcsincludedgrainhardnessandprotein,
breakflouryield,mixographmixingFmeandtolerance,andpup-loafbakewaterabsorpFonandloafvolume(3,743records).
• Yield,grainprotein,andgrainproteindeviaFon(residualsfromproteinvsyieldregression)wereobtainedfromyieldtrials(6,819records).
GBS-SNPMarkerDiscovery• GBSlibrarieswereconstructedusinggenomicDNAextractedina96-
wellformatusingtheKingFisherFlexPurificaFonSystem(ThermoFisherScienFfic,Waltham,MA)andtherestricFonenzymesPstIandMspIusingaprotocolmodifiedfromPolandetal.(2012).
• Sequencingwasperformedat96-and192-plexonanIlluminaHi-Seq2500(Univ.Missouri,ColumbiaMO),and384-plexonanIlluminaHi-Seq4000(Univ.Illinois,UrbanaIL).
• SNPcallsweremadewiththeTASSEL-GBSv2Pipeline(Glaubitzetal.2014)usingtheInternaFonalWheatGenomeSequencingConsorFumWholeGenomeAssemblyv0.4asareference.SNPswerefilteredforF>0.9andthensubjecttoLD-kNNiimputaFon(Moneyetal.2015).
StaFsFcalAnalysis• Bestlinearunbiasedpredictors(BLUPs)forgenotypes(n=771for
qualitytraits,n=681forfieldtraits)foreachphenotypewereobtainedusingtheASreml-Rpackage(VSNIntl.Ltd.,HemelHempsteadUK;Butleretal.2009)inR(RCoreTeam2016)basedonanacross-locaFonmodelwithgenotypes,years,andlocaFonsasrandomeffects.
• Single-traitGSwasdoneusingtherrBLUPpackage(Endelman2011)inRandmulF-traitGS(JiaandJannink2012)wasdoneusingtheASreml-Rpackage.TheGinverserelaFonshipmatrixwascalculatedinrrBLUP(max.missingvalue=0.3)foruseinthecalltoASreml-R.
MaterialsandMethodsSecondaryTrait
PrimaryTrait
SingleTraitGS
MixingTime
FlourYield
MixingTolerance
GrainHardness
LoafVolume
BakeAbsorpFon
GrainProtein 0.23 0.21 0.24 -0.14 0.27 0.24 0.24
BakeAbsorpFon 0.31 0.25 0.15 0.32 0.25 0.21 ---
LoafVolume 0.50 0.39 -0.04 0.30 0.12 --- 0.28
GrainHardness 0.53 0.17 -0.28 0.15 --- 0.54 0.36
MixingTolerance 0.54 0.65 0.43 --- 0.50 0.49 0.33
FlourYield 0.62 -0.01 --- 0.05 0.25 0.65 -0.21
MixingTime 0.64 --- 0.40 0.74 0.56 0.65 0.36
Sincetheearly1980s,thelandareaplantedtoU.S.hardwinterwheatandtheshareofU.S.wheatinexportmarketshavedeclineddramaFcally.Improvedprofitabilityofothercrops,staFcdomesFcflourconsumpFon,andincreasinglycompeFFveglobalmarketsarefactorsunderlyingthesetrends.Inordertoreversethesetrends,modernapproachesmustbeimplementedthatfosterincreasedratesofgeneFcgainforproducFon-relatedtraitssimultaneouslywithimprovedfuncFonalvalueforend-usequality.UsingamulF-year,mulF-environmentpanelofgenotypesandphenotypescollectedwithinanappliedwheatculFvardevelopmentprogram,ourobjecFveswereto:
a)esFmatesingle-traitGSpredicFonaccuraciesforproducFon-relatedandquality-relatedcharacterisFcs,and
b)assesstheuFlityofmulF-traitGSforincreasingpredicFonaccuracyofkeytargettraits.
ResultsandDiscussion
Figure1.Combineharvestoffieldyieldtrials.
Figure2.ComputerizedmixographfordoughmixingproperFes.
Figure3.Pup-loafbaketestforloafvolumeandwaterabsorpFon.
Table1.GenomicselecFonpredicFonaccuraciesforend-usequalitytraits.HighlightedcellsrepresentincreasedmulF-traitGSaccuracyrelaFvetosingle-traitGSaccuracy.
Figure4.DistribuFonofGBS-basedSNPsacrossthewheatgenome.
Figure5.PhenotypiccorrelaFonsamongend-usequalitytraits.
Figure6.GenomicselecFonpredicFonaccuraciesforgrainyieldandrelatedtraitsgrainproteinandgrainproteindeviaFon(GPD).