DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits.docVIP

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DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits.doc

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DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits

Haseneyeretal.BMCPlantBiology2010,10:5 /1471-2229/10/5 RESEARCH ARTICLE OpenAccess DNApolymorphismsandhaplotypepatternsof transcriptionfactorsinvolvedinbarley endospermdevelopmentareassociatedwithkey agronomictraits GritHaseneyer1,4,5,SilkeStracke1,6,Hans-PeterPiepho2,SaschaSauer3,HartwigHGeiger4,AndreasGraner1* Abstract Background:Associationmappingisreceivingconsiderableattentioninplantgeneticsforitspotentialtofine mapquantitativetraitloci(QTL),validatecandidategenes,andidentifyallelesofinterest.Inthepresentstudy associationmappinginbarley(HordeumvulgareL.)isinvestigatedbyassociatingDNApolymorphismswith variationingrainqualitytraits,plantheight,andfloweringtimetogainfurtherunderstandingofgenefunctions involvedinthecontrolofthesetraits.WefocusedonthefourlociBLZ1,BLZ2,BPBFandHvGAMYBthatplayarole intheregulationofB-hordeinexpression,themajorfractionofthebarleystorageprotein.Theassociationwas testedinacollectionof224springbarleyaccessionsusingatwo-stagemixedmodelapproach. Results:Withinthesequencedfragmentsoffourcandidategenesweobserveddifferentlevelsofnucleotide diversity.TheeffectofselectiononthecandidategeneswastestedbyTajima’sDwhichrevealedsignificantvalues forBLZ1,BLZ2,andBPBFinthesubsetoftwo-rowedbarleys.Pair-wiseLDestimatesbetweenthedetectedSNPs withineachcandidategenerevealeddifferentintra-geniclinkagepatterns.Onthebasisofamoreextensive examinationofgenomicregionssurroundingthefourcandidategeneswefoundasharpdecreaseofLD(r20.2 within1cM)inallbutoneflankingregions. Significantmarker-traitassociationsbetweenSNPsiteswithinBLZ1andfloweringtime,BPBFandcrudeprotein contentandBPBFandstarchcontentweredetected.Mosthaplotypesoccurredatfrequencies0.05andtherefore wererejectedfromtheassociationanalysis.Basedonhaplotypeinformation,BPBFwasassociatedtocrudeprotein contentandstarchcontent,BLZ2showedassociationtothousand-grainweightandBLZ1wasfoundtobeasso- ciatedwithfloweringtimeandplantheight. Conclusions:DifferencesinnucleotidediversityandLDpatternwithinthecandidategenesBL