玉米穗行数全基因组关联分析

作物学报ACTAAGRONOMICASINICA2014,40(1):1−6:[e-mail](31201219)(973)(2011CB100106)*(Correspondingauthors):,E-mail:[e-mail];,E-mail:[e-mail]:E-mail:[e-mail]():2013-06-19;Accepted():2013-09-16;Publishedonline():2013-10-22.URL::10.3724/SP.J.1006.2014.00001玉米穗行数全基因组关联分析张焕欣翁建峰*张晓聪刘昌林雍洪军郝转芳李新海*/,100081:,203,2007;41101(SNP)9(P0.0001)SNP,1.021.107.038.029.0610.038SNP(QTL)SNPLD4,F-boxkn1AP2,:;;;Genome-wideAssociationAnalysisofKernelRowNumberinMaizeZHANGHuan-Xin,WENGJian-Feng*,ZHANGXiao-Cong,LIUChang-Lin,YONGHong-Jun,HAOZhuan-Fang,andLIXin-Hai*InstituteofCropScience,ChineseAcademyofAgriculturalSciences/NationalEngineerLaboratoryofCropMolecularBreeding,Beijing100081,ChinaAbstract:Kernelrownumber(KRN)isoneofgrainyieldcomponentsinmaize(ZeamaysL.).Investigationofitsgeneticarchi-tecturewillhelpdevelophigh-yieldvarietiesinmaize.Inthisstudy,theKRNinapanelof203maizeinbredlineswasdetectedinUrumqiofXinjiang,GongzhulingofJilin,andSanyaofHainanin2007,andusedtoperformthegenome-wideanalysisforKRNusingMaizeSNP50BeadChip.AtotalofnineSNPswerefoundtobesignificantlyassociatedwithKRNatathresholdofP0.0001,whichwereonchromosomeBins1.02,1.10,7.03,8.02,9.06,and10.03,respectively.EightoftheseSNPswerelocatedintheQTLintervalsreportedpreviously.Meanwhile,fourcandidategeneswerescanned,encodingauxinsignalingF-boxcontainingprotein,kn1protein,AP2domaincontainingproteinandleucine-richrepeattransmembraneproteinkinaserespectively.Insum-mary,theseidentifiedgenesandSNPswillofferessentialinformationforcloningyield-relatedgenesinmaize.Keywords:Maize;Kernelrownumber;Genome-wideassociationanalysis;Candidategene(kernelrownumber,KRN),[1],,[2],QTL[3],,QTL10Ma[4]3×87-1294(recombinantinbredline,RIL)13QTL,13458910Lu[5]478×340150F2:313QTL,7.03340QTLqkrn717.86%Guo[6]58×7-2231F2:3QTL,24087QTL[7]478×319×2F2:35.046.05−6.077.0210.03QTL[8]3518410QTL,622Meta-QTLQTLQTL,,,QTL,,QTL,(genome-wideassociationstudy,GWAS),[9-10]Huang[11]950GWAS,3210Weng[12]41101SNP284,105,qHS2.091Mb[13]Tian[14]Buckler[15]Brown[16]5000RIL,,203,,1材料与方法1.1203,2007,(XJ)(JL)(HN)4.5m,0.6m,20,2,10,CTAB[17]203DNA,0.8%NanoDrop2000DNA,DNASNPIlluminaMaizeSNP50BeadChip,56110SNP,B73SNPIllumina,IlluminaBeadStation500GSNPWeng[12],41101SNP1.2SAS9.1.3(SASInc.,Cary,NC)PROCUNIVARIATEPROCGLMPROCCORRKnapp[18]h2=σg2/(σg2+σgl2/n+σe2/nr),σg2,σgl2,σe2,n,r1.3STRUCTUREV2.3[19],50000.2SNP,Weng[12]LancasterPBBSSSPA6SPAGeDi[20],5000SNP1.4TASSELV3.0[21](mixed-linearmodel,MLM),,SNPP0.0001,SNP1.51994—2013QTL;MaizeGDBGWASSNPQTL,1.6GWAS,SNP60bp,B73RefGen_v2(MGSC)(=LAST_UI)Weng[12],LD27.7kb,30.0kb2结果与分析2.1313.2913.8613.61,13.87%1:313.84%14.67%,81.07%,Lu[5]Pearson,3(1)表1203份自交系穗行数统计分析Table1Statisticsonkernelrownumberevaluatedon203inbredlinesinthreeenvironmentsCorrelationcoefficientEnvironmentMeanSDCV(%)XinjiangJilinh2(%)Xinjiang13.291.8413.87Jilin13.861.9213.840.67**Hainan13.611.9914.670.59**0.50**81.07**P=0.01SD:standarddeviation;CV:variablecoefficient;**SignificanceatP=0.01.2.2TASSELV3.0MLM,20339(P0.0001)SNP,1.021.107.038.029.0610.03,,1.107.0323SNP,15.00%(2)11.10PZE1012200142(21),SNPPZE-1012199996kbTASSELV3.0,3QQ(2),2.39(P0.0001)SNP图1穗行数全基因组关联分析Fig.1Genome-wideassociationstudyofkernelrownumberwithmixedlinearmodelXJJLHNXJ,JL,andHNindicateexperimentsatXinjiang,JilinandHainan,respectively.Blackhorizontallineindicatesthegenome-widesignificancethreshold.图23个环境下全基因组关联分析的QQ图Fig.2Quantile-quantileplotforkernelrownumberinthreeenvironmentsP,PThehorizontalaxisshows−lgtransformedexpectedP-values,andtheverticalaxisshows–lgtransformedobservedP-values.,4(2)GRMZM2G398848F-box(auxinsignalingF-boxcontainingprotein)GRMZM2G017087(knotted1,kn1),[23],GRMZM2G069146AP2(AP2domaincontainingprotein)GRMZM2G151567(leucine-richrepeattransmembraneproteinkinase)440表2与穗行数显著关联的SNP位点(P0.0001)Table2SNPsidentifiedtobeassociatedwithkernelrownumber(P0.0001)PP-valuer2(%)SNPGenotypeMAFBinPhysicalpositionCandidategeneXJJLHNXJJLHNReferencePZE-101030429AA/CC0.111.0218,624,531GRMZM2G3988489.10E-059.96Guo,etal.,2011[6]PZE-101220014AA/GG0.061.10271,334,722GRMZM2G0170879.52E-061.30E-0612.8015.00Ma,etal.,2007[4]PZE-101219999AA/GG0.331.10271,341,306GRMZM2G0170878.50E-0510.33Ma,etal.,2007[4]SYN17065AA/GG0.427.03140,572,9666.76E-0511.53Lu,etal.,2011[5]PZE-107084987AA/CC0.457.03140,711,7201.44E-0510.70Lu,etal.,2011[5]PZE-107085390AA/GG0.387.03141,138,454GRMZM2G0691467.77E-0510.49Lu,etal.,2011[5]PZE-108018598AA/GG0.178.0218,896,2762.85E-059.70Liu,etal.,2007[22]PZE-09090136AA/GG0.069.06138,014,7924.51E-059.60PZE-110033446AA/GG0.1710.0363,031,153GRMZM2G1515674.22E-059.83Lu,etal.,2011[5],Tan,etal.,2011[7]QTLSNPMAF:minorallelefrequencies.ThereexistsconsistencybetweenSNPandQTLintervalreportedinthereferences.XJ,JL,andHNin-dicateexperimentsatXinjiang,JilinandHainan,respectively.3讨论3.1GWAS,SNP,,GWASQTL[9-12,15,24-26],GWAS203,39(P0.0001)SNPMassman[27]5cMSNPQTL,1.10PZE-101219999PZE