13.2www.sss17.com

RESEARCHOpenAccessGeneticanalysisofanelitesuper-hybridriceparentusinghigh-densitySNPmarkersMeijuanDuan1,2,3,4,ZhizhongSun1,2,LipingShu5,6,YanningTan1,2,DongYu1,2,XuewuSun1,2,4,RuifenLiu1,2,4,YujieLi5,6,SiyuGong5,6andDingyangYuan1,2,4*AbstractBackground:Withanincreasingworldpopulationandagradualdeclineintheamountofarableland,foodsecurityremainsaglobalchallenge.
Continuedincreasesinriceyieldwillberequiredtobreakthroughthebarrierstograinoutput.
Inordertotransitionfromhybridricetosuper-hybridrice,breedingdemandscannotbeaddressedthroughtraditionalheterosis.
Therefore,itisnecessarytoincorporatehighyieldlocifromotherricegeneticgroupsandtoscientificallyutilizeintersubspecificheterosisinbreedinglines.
Inthisstudy,781linesfromasegregatingF2populationconstructedbycrossingtheindicavariety,"GiantSpikeRice"R1128astraitdonorwiththejaponicacultivar'Nipponbare',werere-sequencedusinghigh-throughoutmultiplexedshotgungenotyping(MSG)technology.
Incombinationwithhigh-densitysinglenucleotidepolymorphisms,quantitativetraitlocus(QTL)mappingandgeneticeffectanalysiswereperformedforfiveyieldfactors(spikeletnumberperpanicle,primarybranchesperpanicle,secondarybranchesperpanicle,plantheight,andpaniclelength)toexplorethegeneticmechanismsunderlyingtheformationofthegiantpanicleofR1128.
Also,theywerepreformedtolocatenewhigh-yieldingricegeneticintervals,providingdataforsuper-high-yieldingricebreeding.
Results:QTLmappingandgeneticeffectanalysisforfiveyieldfactorsinthepopulationgavethefollowingresults:49QTLsforthefiveyieldfactorsweredistributedon11of12chromosomes.
Thesuper-hybridlineR1128carriesmultiplemajorgenesforgoodtraits,includingSd1forplantheight,Hd1andEhd1forheadingdate,Gn1aforspikeletnumberandIPA1foridealplantshape.
Thesegenesaccountedfor44.
3%,21.
9%,6.
2%,12.
9%and10.
6%ofthephenotypicvariationintheindividualtraits.
SixnovelQTLs,qph1-2,qph9-1,qpl12-1,qgn3-1,qgn11-1andqsbn11-1arereportedhereforthefirsttime.
Conclusions:High-throughoutsequencingtechnologymakesitconvenienttostudyricegenomicsandmakestheQTL/genemappingdirect,efficient,andmorereliable.
Thegeneticregionsdiscoveredinthisstudywillbevaluableforbreedinginricevarietiesbecauseofthediversegeneticbackgroundsoftherice.
Keywords:Giantspikerice;Heterosis;MSG;Yieldcomponents;QTLmapping;EffectanalysisBackgroundRice(OryzasativaL.
)istheworld'smostimportantcerealcropandisthestaplefoodformorethanhalfoftheworld'spopulation(Mcleanetal.
2002).
Chinahaspioneeredtheadvantagesofheterosisinpromotingthesuccessfuluseofhybridricewhichhasresultedinasteadyincreaseinannualgrainproductionfrom0.
35billiontto0.
5billiont.
PercapitaannualgrainconsumptioninChinaisupto0.
4t.
Thisprogresshasreversedthefundamentalproblemofchronicfoodshortagesandrealizedthebasiccoordinationofgrainsupplyanddemand(Dengetal.
2010).
However,withanincreasingworldpopulationandgraduallydeterioratingenvironment,foodsecurityhasbecomeamajorchallengearoundtheworld,especiallyinAsiaandAfrica(Godfrayetal.
2010;Mcnallyetal.
2009;Sasson2012).
Greatcooperationanddedicationisneededtobreakthroughtheyieldbarrierbyincreasingthericeyieldperunitarea.
Sincethemid-1990s,ateam*Correspondence:yuandingyang@hhrrc.
ac.
cnEqualcontributors1StateKeyLaboratoryofHybridRice,HunanHybridRiceResearchCenter,Changsha410125,China2HunanAcademyofAgriculturalSciences,Changsha410125,ChinaFulllistofauthorinformationisavailableattheendofthearticle2013Duanetal.
;licenseeSpringer.
ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.
org/licenses/by/2.
0),whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.
Duanetal.
Rice2013,6:21http://www.
thericejournal.
com/content/6/1/21ofscientistsledbyYuanLongping,anacademic,hasachieved10.
5,12.
0and13.
5t/habyinsuper-hybridriceandisapproachingthetargetyieldof15.
0t/ha.
Thus,hybridricehasnowreachedthesuper-hybridbreedingstage.
Itisdifficulttomeetthedemandsofsuper-highyieldbydependingonheterosis.
Asignifi-cantbreakthroughinsuper-hybridricebreedingcanberealizedthroughmodificationofmorphologicaltraitsinthesuper-hybridparentandthescientificutilizationofheterosis(Chen2007;Chenetal.
2010).
Breedingpracticeshavedemonstratedthatthediscoveryofspecificgermplasmandinnovationinbreedingmate-rialsarecriticaltosuccessfulbreakthroughsinthedeve-lopmentofsuper-hybridrice(Cheng2000).
Exploitingheterosisbetweenricevarietiesisthemainstrategythatiscurrentlyusedinhybridricebreeding.
However,similargeneticbackgroundsandreducedgeneticdiversitycausedifficultiesinrestorerlinebreedinginhybridricecombi-nationfordrasticallyimprovingtheheteroticeffectandincreasinghybridriceyield.
Thissituationdoesnotmeanthattheimportanceofheterosisinriceisreduced,butratherthedifficultyinusingheterosishasincreased.
Sim-plyrelyingonheterosisbetweenvarietiescannotaddresstheneedsofsuper-hybridricebreeding.
Therefore,itisnecessarytopursueahigherlevelofheterosisbyusingthegeneticdifferencesthatexistinmoredistantly-relatedricegermplasm(subspecies,interspecificandintergeneric)inordertobreakthroughthebottleneckintraditionalriceheterotichybridapproaches,tomaximallyexploittheinteractionpotentialofriceyieldgenes(additive,domi-nance,over-dominanceandepistasis).
Thiscanalsobeusedtohelpbreedsuper-hybridriceparentallines,andtoacceleratethestepsrequiredforsuper-hybridricebreed-ing(Dengetal.
2010).
Riceyieldisessentiallydependentonfourprimaryfactors:(1)numberofspikeletsperpanicle,(2)grainweight,(3)grainfilling,and(4)thenumberofeffectivepanicles.
Therearealsosomesecondaryfactorssuchasplantheightandpaniclelengththateffectthericeyield.
Riceyieldisacomplexquantitativetrait,anditsincreaseisdependantonsynergyofallthesefactors(Gaoetal.
2011).
BreedingofdwarfriceinChinabeganinthelate1950sanddwarfinginthebasicproductionindicaricewasfinishedinthelate1960s.
Subsequently,breedersrebuilttheplantandleafshapesusingtheSd-1geneandexploredwaystofurtherincreasericepotentialyieldthroughgiantpaniclesandgrains(Liuetal.
2012b).
Overthepast20years,breedershavefocusedonincreasingthepotentialyieldinricebyincreasingthegiantpanicletypewhenmodifyingricevarieties.
OnestudymaintainedthatthepotentialyieldofearlyriceintheYangtzeRiverBasincanbeincreased15%–20%byreducingthenum-berofpaniclesandincreasingindividualpanicleweight(Zhuetal.
2007).
Constantgeneticrecombination(hybridizationandselection)allowsanewbalanceandcoordinationbetweenthenumberofpaniclesperplantandspikeletnumberperpanicleinricetobeattained,thusfulfillinganidealhigh-yieldingpurpose.
Theoptimalcombinationofmodificationforidealplantshapeandutilizationofheterosisareaninevitablepathforsuper-hybridricebreeding.
Themoleculardesignofthe"idealplantarchitecturewithgiantpanicle"and"erectsuper-hybridricewithgiantpanicle"isthedirectiontobetakeninfuturericebreedingefforts(Liuetal.
2012b).
Thesuper-hybridriceparentR1128isanoptimalres-torerlinewithgiantpanicles,whichwascreatedthrough-outthehybridizationofdistantly-relatedsubspeciesundertheabove-mentionedtheoreticalconceptandwasrecog-nizedas"GiantSpikeRice"byYuanLongping.
Thislinehasprominentfeaturesofhighgrainnumberperpanicle(uptoamaximumof980underthehigh-yieldingcultiva-tionregimeofhighfertilizerandlowdensityplanting,farhigherthanthestrongrestorerlines9311andMinghui63,whichaverage400–600),strongstem,highlodgingresistanceandhighseedsettingrate.
R1128alsoresolvesthecontradictionsofgiantpanicleandlowerseedsettingrateinpreviousgenerationswhenasignificantbreak-throughwasachievedincreatinghybridriceparentsthroughwidecrossesbetweensubspecies.
WiththerecentadvancesinDNAsequencingtechno-logyandfunctionalgenomics,morespeciesareresolvedandmorefunctionalgenesaremappedandcloned.
Inthisstudy,781linesfromthesegregatingindica-japonicaF2population(constructedbycrossingtheindicadonorparent,"GiantSpikeRice"R1128withthejaponicacultivarNippobare)werere-sequencedusinghigh-throughputmultiplexedshotgungenotyping(MSG)technology(Andolfattoetal.
2011).
Incombinationwithhigh-densitysinglenucleotidepolymorphism(SNP)(Lander1996)molecularmarkers,quantitativetraitlocus(QTL)mappingandgeneticeffectanalysiswereperfor-medonfiveyieldrelatedfactors.
Grainnumberperpanicle,primarybranchesperpanicle,secondarybranchesperpanicle,plantheight,andlengthofmainpanicleinordertoinvestigatethegeneticmechanismunder-lyingtheformationoftheR1128giantpanicleandtoidentifyandlocatethenewhigh-yieldingricegenelocustoprovideusefuldataforsuper-highyieldricebreeding.
ResultsSequencingandSNPidentificationWesequencedthecultivarR1128usingtheIlluminaHiseq2000platform,yieldingabout6.
17Gbasesofrawdata.
TheshortreadsweremappedbacktotheIRGSPv6ricegenomeusingSOAP2(version2.
20).
Thegenomecoveragewasabout87%andtheeffectivemappingdepthreached>16*.
About690,720SNPs,or1.
8SNPs/kb,wereDuanetal.
Rice2013,6:21Page2of15http://www.
thericejournal.
com/content/6/1/21identifiedbetweentheparentsusingastrictanalysispipeline(Table1).
Therestrictionenzymefragmentsrangingfrom400bpto600bpfor781F2individualsweresequencedandgeneratedatotalof107.
96Gbpofrawdata,whichisapproximately138.
23Mbpforeachline(Figure1B).
Thesequencedsitesaccountedfor8–12%ofthewholegenomeandonaverage,thedepthofeachsitewasapproximatelytwotosixtimesgreaterineachindividual(Figure1A).
PopulationSNPswerefilteredbythesitesandweredifferentbetweenthetwoparents.
TheSNPsthatwereobviouslyduetonoisewereremovedmanually.
Atotalof74,329SNPsor1SNPper5kbweredetectedfortheF2,andthedistributionofSNPswaseventhroughouttheentiregenome(Table1,Figure1CandAdditionalfile1).
Wecomparedthese74,329SNPstoriceSNPdatabasebuildbyOryzaSNPConsortium.
Atotalof9,377SNPscanbefoundinthisSNPdatabaseandalloftheseSNPsdifferfromthereferencegenomeallele.
WeaddtheSNPsinformationtothisricewholegenomeresequencinggeno-typedatafile(Additionalfile2).
RecombinationbreakpointdeterminationandBinmapconstructionInanF2population,thebreakpointsseparatehomozy-gousandheterozygousgenotypesandalsoseparateonehomozygousgenotypefromtheother.
Wedeterminedtherecombinationbreakpointsbycheckingthepositionswheregenotypeschangefromonetypetotheotherwhenplacedalongthechromosomes.
Atotalof22,594breakpointswereidentifiedforthe781individuals,foranaverageof29.
39perindividual(Additionalfile3andAdditionalfile4).
Afterwedeterminedtherecombinationbreakpointsforeachindividual,weconstructedaskeletonbinmap.
Atotalof6,819binsweredetectedforthe781F2progenyfortheminimum10kbintervals(Table2andAdditionalfile5).
Eachbin'sphysicallengthrangedfrom10.
01kbto3.
39Mb,averaging54.
6kb(Additionalfile6).
PhenotypicvariationanddistributionThefiveyieldcomponenttraits,whichincludedplantheight(PH),paniclelength(PL),grainnumber(GN),primarybranchnumber(PBN)andsecondarybranchnumber(SBN),wereinvestigatedbetweenR1128andNipponbareatChangshain2011.
TheGNofthesuperriceparentR1128wasnearlyfivetimesthatofNipponbare,reaching438.
Moreover,theincreaseinGNresultedfromanapparentincreaseinthePBNandSBN(Figure2).
ExtremevariationswerealsofoundintheyieldcomponentsPHandPL.
Alltraitvaluesweresignificantlydifferentatthe5%levelbetweenthetwoparents.
TherestorerlineR1128wasdistinctlydifferentfromthejaponicaricelineNipponbare,andprovidedanabundantsourceoftraitvariationforpopulationcon-structionandQTLmapping.
PhenotypicvaluesoftheyieldrelatedtraitsPL,GN,PH,PBNandSBNwereallfoundtobecontinuouswithnormaldistributionandthevaluesofpopulationskew-nessandkurtosiswerealllessthan1.
Bi-directionalitywasalsoobservedforalltraitsandthevaluesforthetwoparentswereallwithintherangeofthepopulation.
Thisindicatesthatyieldcomponenttraitswerequantita-tiveandtransgressivesegregationcouldbegeneratedfromgenerecombination.
Allcharactersinthepopula-tionmettherequirementsforQTLmapping(Figure2).
QTLidentificationandeffectcalculationsInthisstudy,fiveyieldrelatedtraitsincludingprimaryrachisbranch,secondaryrachisbranch,plantheight,grainnumberandmainpaniclelengthwereexaminedwiththebinmap.
ResultswithrespecttotraitQTLsidentifiedarepresentedinTable3.
Plantheight(PH)PlantheightintheR1128XNipponbareF2populationwasinfluencedby12genomicregionsoneightchromo-somes.
Thephenotypiceffect(R2)varianceexplainedbytheseQTLsrangedbetween1.
4%(qph1-1)and44.
3%(qph1-3).
OutoftheseQTLs,onlyqph1-3andqph10-1hadpositiveadditiveeffectswithvaluesof14.
98and5.
32,whichwerecontributedfromtheR1128alleles.
Qph1-3hadthehighestLODscore(97.
92)andthelargestpercentageofphenotypicvariation(44.
3%),follo-wedbyqph6-1(LOD=19.
37andR2=10.
9%).
PhenotypicvariationscontributedfromNipponbarealleleswerealsonoticedfor10QTLs(qph1-1,qph1-2,qph2-1,qph3-1,Table1NumberofSNPsperchromosomeintheR1128XNipponbareF2populationChromosomeNumberofhomozygousSNPsbetweenparentallinesNumberofSNPsinpopulationChr01659508063Chr02764386471Chr03709356926Chr04469886067Chr05537884482Chr06603847884Chr07621646107Chr08557067454Chr09508575228Chr10448125387Chr11631316388Chr12395673872Total69072074329Duanetal.
Rice2013,6:21Page3of15http://www.
thericejournal.
com/content/6/1/21qph3-2,qph4-1,qph6-1,qph6-2,qph9-1andqph12-1),showingnegativeadditiveeffectsrangingfrom1.
21to7.
42andexplaining1.
4%to10.
9%ofthephenotypicvariationinplantheight.
Viewedfromthestandpointofgeneinteraction(d/a),twoQTLs(qph3-1andqph3-2)manifestedmainlyadditiveeffectsandmostofthese12QTLsshowedpositiveornegativepartialdominance,whichincludedqph1-1,qph1-2,qph1-3,qph6-1,qph6-2,qph9-1,qph10-1andqph12-1.
Wealsoobservedthatqph2-1andqph4-1weretheonly2QTLsshowingnegativedominanceandpositiveoverdominance,respectively.
Paniclelength(PL)Paniclelength,oneofthemostimportantoftheyieldrelatedcharacters,wascontrolledby10QTLsthatwouldbedistributedonchromosomes1,2,3,4,6,8,10and12.
Amongthese,qpl6-2locatedatbin3807hadthehighestLODvalue(20.
28)andmorphologicalvariationscore(11.
5%)anddisplayedanegativeadditiveeffectmainlywiththepositiveallelefromNipponbare.
Consi-deredfromthestandpointofgeneinteraction,theother3QTLs(qpl3-1,qpl3-2,andqpl8-1)wereallmajorwithanegativeorpositiveadditiveeffectandexplained14.
4%ofthetotalphenotypicvariation.
qpl12-1,locatedinbin6738,hadapositiveoverdominanteffectalone,withaLODscoreof3.
14andR2=1.
9%.
TheremainingfiveQTLs(qpl1-1,qpl2-1,qpl14-1,qpl16-1andqpl10-1)thatcontrolthelengthofthemainpanicleshowmainlyposi-tiveornegativepartialdominanceeffects;amongthese,qpl6-1hasthehighestLODvalue(13.
37)whichexplains7.
7%ofthephenotypicvariation,andthepositivealleleoriginatedfromthefemaleparentNipponbare.
Grainnumber(GN)ElevenQTLsassociatedwithtotalGNpermainpaniclemappedtosixdifferentchromosomesinrice.
Conclu-sionsmaybedrawnthatthefiveQTLs,qgn1-1,qgn6-2,qgn6-3,qgn6-4andqgn8-1havelargeLODscoresabove15.
QTLqgn1-1hasthehighestLODscoreof23.
01andcontributionrateof12.
9%.
Withtheexceptionofqgn8-1,whichhasapartialdominantpositiveeffect,theotherfourgeneshaveadditiveeffects,andthepositiveallelesoriginatedinNipponbare.
FortheremainedsixQTLs,BACFigure1SequencingresultsfortheF2population.
(A)Populationcoveragedistribution.
Thehorizontalaxisshowsthecoverageandtheverticalaxisrepresentsthenumberofindividuals.
(B)Sequencingdepthdistribution.
Thehorizontalaxisshowsthesequencingdepthandtheverticalaxisrepresentsthenumberofindividuals.
(C)SNPdistributiononthe12ricechromosomes.
Table2NumberofbinsperchromosomeChromosomeNumberofbinsChr01979Chr02686Chr03700Chr04527Chr05541Chr06578Chr07603Chr08573Chr09364Chr10381Chr11517Chr12370Total6819Duanetal.
Rice2013,6:21Page4of15http://www.
thericejournal.
com/content/6/1/21thepositiveallelesofqgn1-2,qgn3-1andqgn3-2camefromthemaleparentR1128.
TheseQTLshowapartialpositivedominanteffect,apositiveoverdominanteffect,andapositivedominanteffect,respectivelyandexplain7.
8%ofthetotalphenotypicvariation.
Additionally,threeQTLs(qgn2-1,qgn6-1,qgn11-1)haveadditive,par-tialpositivedominant,andadditiveeffects,respectively.
ThepositiveallelescamefromNipponbare,andthetotalcontributionratewas6%.
Primarybranchnumber(PBN)AtotalofeightQTLsassociatedwithPBNweremappedintheF2populationandtheyweredistributedonchro-mosomes1,2,6,7,8and10.
TheQTLscontrollingthe0102030405060708051.
257.
363.
569.
675.
881.
988.
194.
2100.
4106.
5112.
7118.
8125.
0131.
1137.
3Plantheight/cmNumberoflines0102030405060708014.
015.
216.
517.
719.
020.
221.
522.
723.
925.
226.
427.
728.
930.
131.
4Paniclelength/cmNumberoflines02040608010032.
068.
1104.
1140.
2176.
2212.
3248.
4284.
4320.
5356.
5392.
6428.
7464.
7500.
8536.
9GrainnumberNumberoflines0204060801001206.
07.
38.
69.
911.
212.
513.
815.
116.
417.
719.
020.
321.
622.
924.
2PrimarybranchnumberNumberoflines02040608010013.
020.
427.
735.
142.
549.
857.
264.
671.
979.
386.
794.
0101.
4108.
8116.
1SecondarybranchnumberNumberoflinesACDEFP1P2P2P1P1P2P2P1P2P1P2P1BFigure2FieldperformancecomparisonbetweenparentsanddistributionofyieldcomponentsintheF2population.
(A)PanicleshapecomparisonbetweenR1128andNipponbare.
TheP1andP2representR1128andNipponbarerespectively.
Scalebar:3cm.
(B)Plantheight.
(C)Paniclelength.
(D)Grainnumberperpanicle.
(E)Primarybranchnumber.
(F)Secondarybranchnumber.
Duanetal.
Rice2013,6:21Page5of15http://www.
thericejournal.
com/content/6/1/21Table3QTLmappingandgeneticeffectanalysisTraitLODthresholdPosition;intervalQTLLocus;sizeLodAddDomD/[A]R2(%)IncludedQTLs/genes(Chromosome;cM)(peakbin;Kb)PH3.
21;17.
3-17.
6qph1-1bin132;14.
62.
352.
641.
490.
571.
4ph1.
1(Marrietal.
2005)1;22.
7-23.
2qph1-2bin172;13.
22.
572.
880.
880.
311.
51;131.
0-131.
5qph1-3bin807;19.
797.
9214.
985.
440.
3644.
3sd-1(Sasakietal.
2002)2.
92;87.
5-87.
7qph2-1bin1418;34.
02.
982.
712.
650.
981.
8Sn2a(Tanetal.
1996)3.
13;48.
3-50.
7qph3-1bin1846;10.
96.
154.
310.
50.
123.
6d88(Gaoetal.
2009)3;70.
7-71.
1qph3-2bin1943;40.
93.
33.
290.
170.
052OsApx1(Agrawaletal.
2003)2.
94;121.
9-122.
4qph4-1bin2728;106.
02.
831.
213.
833.
171.
7qPH1-4-1(Cuietal.
2004)2.
96;26.
6-27.
1qph6-1bin3619;57.
619.
377.
422.
580.
3510.
9qPH2-6-1(Cuietal.
2004);ph6(Xiaoetal.
1996)6;58.
1-58.
4qph6-2bin3845;78.
07.
735.
231.
180.
234.
5qIN3-6(Yamamotoetal.
2001)2.
89;0.
6-1.
5qph9-1bin5195;53.
04.
083.
492.
010.
582.
42.
610;47.
2-48.
0qph10-1bin5796;88.
310.
735.
322.
890.
546.
2OsCesA7(Tanakaetal.
2003)2.
812;66.
8-68.
0qph12-1bin6735;107.
23.
583.
152.
490.
792.
1nd1(Lietal.
2009a)PL3.
11;131.
3-131.
7qpl1-1bin808;23.
36.
410.
70.
40.
573.
8qp1-1(Hittalmanietal.
2002);p11.
1(Thomsonetal.
2003)32;22.
9-23.
2qpl2-1bin1175;25.
25.
040.
630.
390.
623qph-2(Pingetal.
2003)2.
93;48.
3-50.
7qpl3-1bin1846;10.
98.
380.
840.
060.
074.
9d88(Gaoetal.
2009)3;70.
7-71.
1qpl3-2bin1943;40.
96.
480.
740.
070.
093.
8OsApx1(Agrawaletal.
2003)2.
94;77.
7-78.
2qpl4-1bin2570;20.
33.
190.
470.
330.
71.
9pl4(Zhuangetal.
1997)2.
96;26.
6-27.
1qpl6-1bin3619;57.
613.
371.
040.
320.
317.
7qPH2-6-1(Cuietal.
2004);ph6(Xiaoetal.
1996)6;52.
7-53.
4qpl6-2bin3807;13.
120.
281.
350.
240.
1811.
5OsIAA23(Junetal.
2011);ph6(Xiaoetal.
1996)2.
98;87.
1-87.
4qpl8-1bin5156;37.
69.
70.
890.
110.
125.
7IPA1(Jiaoetal.
2010)2.
610;41.
4-41.
6qpl10-1bin5745;268.
25.
10.
590.
450.
763brd2(Hongetal.
2005)2.
812;68.
8-74.
3qpl12-1bin6738;11.
93.
140.
460.
471.
031.
9GN3.
11;18.
4-18.
7qgn1-1bin137;13.
423.
0137.
075.
390.
1512.
9Gn1a(Ashikarietal.
2005)1;127.
5-128.
0qgn1-2bin784;14.
58.
7422.
739.
10.
45.
1qLVBTS1-1(Cuietal.
2003)32;86.
0-86.
7qgn2-1bin1394;189.
63.
2915.
642.
960.
192qPN2(Yuanetal.
2003)3.
23;66.
6-67.
0qgn3-1bin1929;16.
92.
3612.
613.
611.
081.
43;137.
1-137.
5qgn3-2bin2208;23.
22.
212.
051.
010.
081.
3ps3(RedonaandMackill1998)2.
96;9.
7-10.
2qgn6-1bin3519;70.
93.
7616.
058.
970.
562.
2TNSP6(Zhuangetal.
2001)6;26.
2-26.
5qgn6-2bin3612;41.
016.
3632.
91.
590.
059.
4tns6(Linetal.
1995)6;32.
9-33.
3qgn6-3bin3660;135.
515.
6231.
375.
620.
188.
9OsJMT1(Kimetal.
2009)6;36.
5-36.
8qgn6-4bin3685;64.
215.
731.
355.
720.
189gp6(Huaetal.
2002)2.
78;67.
1-67.
8qgn8-1bin5104;14.
818.
7333.
2815.
650.
4710.
6IPA1(Jiaoetal.
2010)2.
711;26.
1-26.
5qgn11-1bin6104;17.
23.
0114.
040.
430.
031.
8PBN3.
21;18.
4-18.
7qpbn1-1bin137;13.
45.
550.
820.
120.
153.
3Gn1a(Ashikarietal.
2005)3.
12;79.
8-80.
4qpbn2-1bin1364;16.
66.
020.
850.
170.
23.
6np2.
2(Marrietal.
2005)2.
96;9.
4-9.
9qpbn6-1bin3517;37.
412.
411.
30.
040.
037.
2qNPB6-1(Cuietal.
2002)6;25.
5-26.
0qpbn6-2bin3607;95.
941.
172.
020.
960.
4821.
9Hd1(Yanoetal.
2000)6;36.
5-36.
8qpbn6-3bin3685;64.
231.
761.
80.
80.
4417.
4gp6(Huaetal.
2002)2.
97;65.
3-65.
7qpbn7-1bin4418;71.
02.
550.
390.
571.
481.
5OsFOR1(Jangetal.
2003)2.
88;68.
0-68.
4qpbn8-1bin5107;45.
014.
261.
330.
450.
348.
2IPA1(Jiaoetal.
2010)Duanetal.
Rice2013,6:21Page6of15http://www.
thericejournal.
com/content/6/1/21PBNonchromosome6wereuptothreemaximally(qpbn6-1,qpbn6-2andqpbn6-3);thehighestLODscorewasforqpbn6-2at41.
17,withaQTLcontributionrateof21.
9%.
ThepositivealleleswerefromtheNipponbareparentwithanegativepartialdominanteffect;theother2QTLshaveLODscoresof12.
41and31.
76,respect-ively,.
ThepositiveallelesalsocamefromNipponbarewithadditiveorpartialnegativedominanteffects.
TheQTLqpbn10-1withLODscore10.
57hasapositiveallelefromthepaternallineR1128onlyanditscon-tributionrateis6.
2%withanegativeoverdominanceeffect.
FortheremainingfourQTLs,qpbn1-1andqpbn2-1hadadditiveeffects,andqpbn7-1andqpbn8-1hadpositiveoverdominantandpositivepartialdomin-anteffects,respectively.
ThepositiveallelesofthesefourQTLscamefromNipponbareandhadacontri-butionrateof1.
5–8.
2%.
Secondarybranchnumber(SBN)EightQTLs,qsbn1-1,qsbn1-2,qsbn3-1,qsbn6-1,qsbn6-2,qsbn6-3,qsbn8-1andqsbn11-1,whichareassociatedwithSBN,mappedtofivechromosomes(1,3,6,8,11).
TheirLODvaluesrangefrom2.
40to25.
31,withphenotypiccontributionratesof1.
4%-14.
1%.
ThreeQTLs(qsbn1-2,qsbn3-1,qsbn8-1)havepartialpositivedominanteffects.
Amongthese,qsbn1-2andqsbn3-1possedpositivealleleswhichcamefromR1128.
Theqsbn8-1allelecamefromNipponbare;theotherfiveQTLs(qsbn1-1,qsbn6-1,qsbn6-2,qsbn6-3andqsbn11-1)showedadditiveeffectsandtheirpositivealleleswerefromNipponbare.
DiscussionR1128contributionanditsvalueinricebreedingTherestorerlineR1128resultedfromtakingfulladvan-tageofwidecrossesbetweenricesubspecies.
ThislinehasexcessiveGN,highlodgingresistanceandstrongcombiningability,therebycoordinatingthegiantpanicleandseedsettingdifficulties.
Thisnotonlyprovidesanimportanttechnicalrouteforsuper-hybridriceparentbreeding,butalsoprovidesabasistotestheterosistheory.
In2011,Liangyou1128(P88S/R1128),thesuper-hybridricecombinationbredfromthesuperrestorerlineR1128andtwo-linemalesterilelineP88S,wasidentifiedassingle-croppinglaterice(Xiangshenrice2011024)inHunanProvince.
Thisvarietyshowsahighandstableyield,goodplantshape,grainqualityandhighlodgingresistance(thelodgingresistancecoefficientisupto250goraboveatabout120cmPH).
Intheyears2009–2010,thelinewasputtotrialasseasonallatericeinHunanProvince.
Itsaverageyieldwas8.
52t/ha,6.
19%higheryieldthanShanyou63;yieldperdaywas0.
0672t/ha,0.
0018t/ha,higherthanthecontrol.
In2010,thesuperricecombinationwastestedinsmallareaplots(0.
12ha)totestitshigh-yieldingpotential.
Afterbeingharvestedbyexperts,theyieldwasupto14.
47t/ha(Liuetal.
2012a).
Accordingtoincompletestatistics,Liangyou1128,thecombinationofsuper-hybridrice,wasgrownpromotionallyover66,666.
67hectaresin2011/2012tolayafoundationforthestableandincreasingproductionandincomeoffarmers.
Afterattaining13.
89t/hainlargeplotslastyearandmeetingthegoalofthethirdstageaheadoftime,are-searchteamledbyYuanLongpingadvancedtothefourthstageof15t/haofsuper-hybridriceinlargeareaplots.
Threehybridricecombinations:YLiangyou1128(Y58S/R1128),Guangliangyou1128(Guangzhan63-2S/R1128)and4001S/R1128,wereallusingthesuper-hybridricerestorerlineR1128asaparentandweremadeforthepurposeofattaining15t/ha.
Itcanbeexpectedthatthetargetof15t/hacanbeachievedbyusingR1128incombinationunderthetechnicalguide-linesof"eliteseeds,correctmethod,suitablefieldandbetterecology"proposedbyYuanLongping.
MSGforidentificationofgeneticvariationMSG(multiplexedshotgungenotyping)isonemethodofreduced-representationsequencingandhassomeTable3QTLmappingandgeneticeffectanalysis(Continued)2.
610;47.
9-48.
6qpbn10-1bin5798;39.
810.
570.
831.
081.
36.
2Ehd1(Doietal.
2004)SBN3.
11;18.
4-18.
7qsbn1-1bin137;13.
425.
317.
980.
90.
1114.
1Gn1a(Ashikarietal.
2005)1;127.
5-128.
0qsbn1-2bin784;14.
58.
724.
622.
030.
445.
1qNSB1-1(Cuietal.
2002)3.
13;135.
2-135.
5qsbn3-1bin2186;373.
42.
952.
81.
20.
431.
8ps3(RedonaandMackill1998)2.
96;26.
2-26.
5qsbn6-1bin3614;107.
210.
215.
460.
90.
165.
9tns6(Linetal.
1995)6;29.
9-31.
2qsbn6-2bin3649;29.
511.
385.
590.
490.
096.
6qSPN-6(Heetal.
2001)6;36.
5-36.
8qsbn6-3bin3685;64.
210.
765.
440.
530.
16.
3gp6(Huaetal.
2002)2.
88;67.
1-67.
8qsbn8-1bin5104;14.
822.
347.
552.
620.
3512.
6IPA1(Jiaoetal.
2010)2.
911;26.
1-26.
5qsbn11-1bin6104;17.
22.
42.
570.
110.
041.
4Note:LODthresholdwascalculatedusingMapqtlsoftwarewith1000iterationsofthearrangementtest;R2:phenotypicvariationrate,D/[A]:additive(d/a=0-0.
2),partiallydominant(d/a=0.
2-0.
8),dominant(d/a=0.
81-1.
2),overdominant(d/a>1.
2);TheboldanditalictypeofQTLswererepresentednewone.
Duanetal.
Rice2013,6:21Page7of15http://www.
thericejournal.
com/content/6/1/21significantadvantagesforgenome-widegeneticmarkerdiscoveryandgenotyping.
MSGrequiresonlyasetofbar-codedadaptersandoneligationstep,followedbyfragmentsizeselection.
ItcostsmuchlessthanRAD(restrictionsiteassociatedDNA)(Bairdetal.
2008)duetoitssimpleprocedureandreducedrequirementsforlaboratoryequipment.
Librarypreparationforthe781individualsrequiredonlyfourdays,whichshowsthedramatichigh-throughputpotentialofthismethod.
Comparedtoarrays,MSGgivesmoreefficientandevenlydistributedgeneticmarkersforgenotyping.
Thefragmentselectionsizerangesfrom300bpto800bp,andcanbeadjustedfordifferentresearchmaterialsandobjectives.
SequencinganarrowsizerangeofDNAfrag-mentscangetenoughmarkersforhighlydivergentlines.
Inthisstudy,aboutone-tenthofthetotalSNPs(74329/690720)detectedbysequencing400bp–600bpfragmentsshowedhighresolutionforbreakpointdeterminationandQTLmapping.
Forlowdivergencelines,awiderrangefragmentsshouldbeselectedtogetmoreinformativemarkers.
Otherstudieshaveshownthatevendivergenceaslowas0.
5%betweenparentallinesallowedresolutionofhalfoftherecombinationbreakpointstowithin136kb,whichissufficientforQTLstudiesinvolvinggenotypingofhundredsofindividuals(Andolfattoetal.
2011;Mackay2001).
MSGreducesthegenomecomplexitysimilartoothermethodsthatarebasedonrestrictionenzymediges-tion.
Asaresult,dataanalysisismoreefficientandcanbedoneoncomputerswithmediumperformance.
Thegeno-typesofall781individualsweredeterminedinonlyoneweek,andappropriateindividualswerethenselectedforthehybridexperiment.
VerificationandanalysisofQTLmappingForty-nineQTLsforfivekeyyieldfactorsweremappedintheF2populationandwerefoundtobedistributedonall12chromosomesexceptforchromosome5.
Amongthese,14QTLsweremappedtochromosome6alone(Figure3).
TwelveassociatedgeneticintervalsweremappedforPH.
IncomparingQTLsdefinedinthisstudytopreviousresearch,qph1-3,withthehighestpeakvalueonchromo-some1,islocatedatthesamelocusastherice"GreenRevolution"genesd-1(Sasakietal.
2002).
LODinthepopulationreaches97.
92withacontributionrateof44.
3%asshowninFigure4A;qph1-1islocatedontheshortarmofchromosome1withina14.
6kbinterval,justintheareaofph1.
1andcomparedwiththemorefinelymappedre-gionby(Marrietal.
2005).
Thestudyof(Zhaoetal.
2009)consideredthatinheritanceofPHiscommonlycontrolledbyitsgroundinternodelength.
Examplescanbefoundinthisstudy:qph2-1mappedhereandthesecondinternodelengthlocusSn2amappedby(Tanetal.
1996)arelocatedinthesameinterval.
Additionally,qph6-2andqIN3-6(Yamamotoetal.
2001)onchromosome6arealsomappedtothesameinterval.
ThisindicatesthattheseareasmaybehavelocithatcontrolPHorinternodelength.
Theothertwogeneticintervals,qph3-2andqph4-1,werealsoreportedinthepreviousstudies.
Qph3-2iscoveringthecytoplasmascorbateperoxidasegeneOsApx1exactly;(Agrawaletal.
2003);qph4-1andqPH1-4-1areinthesameregion(Cuietal.
2004);qph3-1locatedontheshortarmofchromosome3islocalizedwithin10.
9kbwhiletheesterasegened88clonedby(Gaoetal.
2009)iswithinthisinterval.
Attentionshouldbepaidtothefreauently-appearinghighpeakvalueonchromosome6wheretheqph6-1LODscorereached19.
37atacontributionrate10.
9%.
ThelocusisincludedwithintheintervalbetweenqPH2-6-1mappedby(Cuietal.
2004)andph6mappedby(Xiaoetal.
1996).
TheLODscoresofqPH2-6-1andph6are22.
51and5.
36,respectively,explainingthephenotypicvariationratesof38.
4%and12.
1%.
TheabovelocihadsomevalueinricePHbreeding.
(Tanakaetal.
2003)hadstudiedandclonedtheOsCesA7gene,whichencodedacellulosesynthasecatalyticsubunitinvolvedinthebiosyn-thesisofthecellulose.
OsCesA7aftermutationcansignifi-cantlyreducethecellulosecontentinthestalk,makingthestembrittleandthinwhichwouldresultinadwarfplant.
Qph10-1locatedonchromosome10(peakvalueLOD=10.
37)inthisstudy,isclosetothegeneOsCesA7.
Ithasbeenspeculatedthatthevariationisduetothedifferentgeneticbackgroundandmappingapproaches,etc.
(Zhengetal.
2003).
Qph12-1istargetedintheregionwhichincludesricecellulosesynthasegenend1(Lietal.
2009a).
TheminorQTL(qph1-2andqph9-1)mappedinourpopulationhasnotbeenreportedpreviouslyandmayrepresentnewgeneticintervalslinkedtoPH.
Previousstudieshavedemonstratedthatplantheight,paniclelength,headingdateandflagleaflengthpresentasignificantpositivecorrelation;multipleQTLsaremappedtothesamearea,suchasplantheightandspikelength.
Thisindicatesthattherelationshipamongthequantitativetraitsisextremelyintricate;however,thefunctionaldirectiondoesnotchange(Zhangetal.
2006).
Thisstudyrevealedsuchcases:(Pingetal.
2003)mappedqph-2between5263536and30654749bponchromosome2with81indica-japonicaDHpopulations.
qpl2-1thatcontrolspaniclelengthinthispaperfallswithinthisinterval;qph3-1andqph3-2mappedforPHcharacteristicsthatarelinkedtobin1846(qpl3-1)andbin1943(qpl3-2)formainPLwhentheirpositiveallelesarederivedfromtheNipponbareparentwithpositiveeffects.
Therearealsoqpl6-1andqpl6-2withcontinu-ouspeakvaluesonchromosome6.
qpl6-1andqph6-1thataremappedtothesamebin(bin3619);OsIAA23(Junetal.
2011)isneartoqpl6-2withpeakvaluewithintheph6interval(6927624-29906021bp)(Figure4B).
Theextendedpeakonchromosome6makesitpossibleDuanetal.
Rice2013,6:21Page8of15http://www.
thericejournal.
com/content/6/1/21thatthenewmainQTLsexistwithinthegeneticintervalforPHandPL.
WhentheremainingQTLsformainPLarecomparedwithresultsfromotherstudies,qpl1-1(LOD=6.
41)fallswithinthesameintervalasqp1-1mappedby(Hittalmanietal.
2002).
Thislocuswasverifiedinp11.
1inaBC2F2populationthatwasconstruc-tedfromriceparentsJeffersonandO.
rufipogon(IRGC105491)by(Thomsonetal.
2003).
AlocusdistancethatismorefinelymappedthaninpreviousstudiesisconducivetocloningthisQTL;qpl4-1issimilartothelocusintervalmappedby(Zhuangetal.
1997).
qpl10-1onchromosome10wasmappedtobin5745whilethedwarfingstemgenebrd2(Hongetal.
2005)fallswithinthearea;thepeakvalueofqpl8-1wasmappedneartoIPA1(Jiaoetal.
2010)foridealplantarchitecture.
qpl12-1wasmappedtothelongarmofchromosome12,andthislocushasnotbeenreportedyet.
GNperpanicle,asakeyconstituentofriceyield,hasbeenstudiedextensively.
ThemainQTLsforgenesthatcontrolGNaremappedorclonedaccurately.
Incontrasttoapreviousstudy,atotalof11genomicintervalsassociatedwithtotalGNpermainpanicleweremappedinthisstudy,ofwhich,threehavebeencloned.
qgn1-1locatedonchromosome1andanalleleofGn1a(Ashikarietal.
2005)fromHabatakisharethesameregionwhichbecamethedominantQTLforincreasingthenumberofgrainsperpanicle.
TheLODscoreofqgn1-1inthepopulationwas23.
01,explaining12.
9%ofthephenotypicvariation;itcanbeseenfromFigure4Cthatchromosome6hasacontinuouspeak,withinwhichthemethyljasmonate(MeJA)biosynthesisgeneOsJMT1(Kimetal.
2009)islocatedatthesamepositionasqgn6-3.
Thecontributionrateofqgn6-3toGNperpanicleisupto8.
9%;chromosome8hasaprominentpeakwhereqgn8-1islocated.
Subjecttocomparison,thelocushasthesamepositionasgenesthatcontrolidealplanttypeinIPA1forricetillering,GNand1000-grainweight.
ThenextsixQTLs(qgn1-2,qgn2-1qgn3-2,qgn6-1,qgn6-2andqgn6-4)aresimilartolocireportedpreviously,withmoreaccurateintervals.
qgn1-2(qLVBTS1-1ofCuietal.
),qgn6-2(tns6ofLinetal.
)andqgn6-4(gp6ofHuaetal.
)havelargereffectvalues(Cuietal.
2003;Huaetal.
2002;Linetal.
1995;RedonaandMackill1998;Yuanetal.
2003;Zhuangetal.
2001).
Theseexplainatotalof23.
5%ofthephenotypicvariation,andprovideareferenceforriceGNbreeding.
However,wealsofoundtwonewQTLs,qgn3-1andqgn11-1forGN.
TheprimaryandsecondarybranchesinricepaniclesareimportantfactorsfordeterminingGN.
StudieshaveshownthattheGNperpaniclepresentsasignificantorverysignificantpositivecorrelation.
Somesuper-hybridricevarietieshavegiantpaniclesduetoalargernumberofprimaryandsecondarybranchesandalsohavehighergraindensity(WangandLi2005;Yangetal.
2000).
Inthisstudy,16QTLslinkedtoprimaryandSBNsweremapped;eightforeachcharacter.
ItcanbeseenfromFigure4DandEthatchromosomes1,6,and8havelociwithpeaksforprimaryandSBNs.
qpbn1-1forPBNandqsbn1-1forSBNwerelocatedinthesamebin137onchromosome1withQTLcontributionratesof3.
3%and14.
1%.
ThisisalsothelocationofGn1aforGN;qpbn6-3,qsbn6-3andqgn6-4werealsomappedbetweenthesameFigure3BinlinkagechromosomalmapshowinglocationsofQTLsrelatedtoriceyieldfactors.
ChromosomenumbersareindicatedaboveandBinnamesandgeneticdistance(cM)fromthedistalendoftheshortarmofeachchromosomeareshown.
ThelettersmarkedwithbluerepresentthepreviouslyknownQTLs/genesandtheoppositeweretheQTLsmappedinthisresearch,besidesthelettersmarkedwithredrespresentthenewQTLsforgrainyieldcomponents.
Duanetal.
Rice2013,6:21Page9of15http://www.
thericejournal.
com/content/6/1/21PositiononeachchromosomeLOD0102030405060708090chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12AChromosome1(Mb)LOD020406080100010203040sd1Chromosome6(Mb)LOD051015200102030qPH261qIN36Chromosome10(Mb)LOD05101501020OsCesA7Chromosome12(Mb)LOD0123450102030nd1PositiononeachchromosomeLOD0246810141822chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12BChromosome1(Mb)LOD0510010203040pl1.
1Chromosome3(Mb)LOD0510010203040D88OsApx1Chromosome6(Mb)LOD05101520250102030qPH261OsIAA23Chromosome8(Mb)LOD05100102030IPA1Chromosome10(Mb)LOD051001020brd2PositiononeachchromosomeLOD0510152025chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12CChromosome1(Mb)LOD0510152025010203040Gn1aqLVBTS11Chromosome6(Mb)LOD051015200102030tns6OsJMT1gp6Chromosome8(Mb)LOD051015200102030IPA1PositiononeachchromosomeLOD051015202530354045chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12DChromosome1(Mb)LOD0246810010203040Gn1aChromosome6(Mb)LOD0102030400102030qNPB61Hd1gp6Chromosome8(Mb)LOD0246810140102030IPA1Chromosome10(Mb)LOD02468101401020Ehd1PositiononeachchromosomeLOD051015202530chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12EChromosome1(Mb)LOD051015202530010203040Gn1aqNSB11Chromosome6(Mb)LOD0510150102030tns6qSPN6gp6Chromosome8(Mb)LOD05101520250102030IPA1Figure4Genome-widescanintheF2populationandQTLtraitmapping.
(A)Plantheight.
(B)Mainpaniclelength.
(C)Totalgrainnumberperpanicle.
(D)Primarybranchnumber.
(E)Secondarybranchnumber.
Duanetal.
Rice2013,6:21Page10of15http://www.
thericejournal.
com/content/6/1/21intervals36.
5-36.
8cM.
Thelocusissimilartogp6mappedby(Huaetal.
2002)forGN;IPA1(Jiaoetal.
2010)locatedonthelongarmofchromosome8,whichisacomplicatedgenethatcontrolsmultipleyieldtraitsinrice.
Inthepresentstudy,qpbn8-1forPBN,qsbn8-1forSBNandqgn8-1forGNareallclosetoIPA1.
(Endo-HigashiandIzawa2011)grewfourkindsofricelineswithdifferentfloweringstagesunderdissimilarphotoperiods.
There-sultsshowedthattheHd1andEhd1genescanreducethePBN,reducetheGNandcontrolthedependentonthefloweringstage.
Hence,twokeyricefloweringgenes,Hd1andEhd1,controlricepanicledevelopment.
Bothlociaffecttheexpressionofthefloweringlocusinleaf,possiblyhavingafurtheraffectonriceyieldinthefield.
TwoQTLs,qpbn6-2andqpbn10-1,withlargereffects,weremappedforPBN.
TheirLODscorespeakat41.
17and10.
57individually.
BothintervalsarelocatedneartothegenesHd1(Yanoetal.
2000)fortheheadingstageandEhd1(Doietal.
2004)forearlyheading.
TheseQTLsexplain21.
9%and6.
2%ofthephenotypicvariationseparately,similartotheirresults.
qpbn6-1mappedtochromosome6andqNPB6-1mappedby(Cuietal.
2002)fallwithinthesameintervalwhentheireffectvaluesarelargeramongtwodissimilarpopulations.
qpbn2-1fallswithinnp2.
2(Marrietal.
2005),andtheregulonOsFOR1(Jangetal.
2003)ofricefloweringorgansfallsjustwithintheqpbn7-1interval.
AdditionalQTLsforSBNareqsbn1-2,qsbn6-1andqsbn6-2,whichfallwithinthesameintervalsasqNSB1-1(Cuietal.
2002),tns6(Linetal.
1995)andqSPN-6(Heetal.
2001)respectively.
qsbn3-1islocatedinthere-gionforGN,whichwasmappedby(RedonaandMackill1998).
qsbn11-1onchromosome11couldbeanovelgen-eticregionthathasnotbeenreportedpreviously.
GeneclusteringistypicallyseeninpreliminaryQTLmappingstudies.
ItsignifiesthatQTLsforcorrelatedtraitsarelocatedinthesameorproximateintervalsonthesamechromosome.
Theirpositionsareoftenclosetooneanother,whileQTLsthatcontroldissimilartraitswithinthesameintervalandQTLthatcontrolthesametraitindifferentintervalsinthevariationofgeneticfunctionmode,effectdirectionandeffectsize(Duetal.
2008;Tengetal.
2002;Zhengetal.
2003).
ThisissubstantiatedinQTLmappinginthisstudy:withinin-tervalsof5–25Mbonchromosome6,fiveyieldfactors(PH,PL,GN,PBNsandSBNs),appearascontinuouspeaks;atotalof14QTLsweremapped,ofwhich,fourkeygenes,OsIAA23,Hd1,Ehd1,andOsJMT1,weredir-ectlymapped.
WebelievethatQTLswithinthisintervalwillberesolvedmoreaccuratelywiththedevelopmentofnewgenomesequencingtechnologyandhigh-densitySNPmarkers.
Sixnewintervals,qph1-2,qph9-1,qpl12-1,qgn3-1,qgn11-1andqsbn11-1areshowedforthefirsttimeinthisresearch.
Amongthose,qph9-1andqpl12-1havelagereffectvaluescomparedwiththeother.
Asthemainyieldrelatedfactors,weintendtodevelopCSSSLs(chromosomesinglesegmentsubstitutionlines)orNILs(near-isogeniclines)ofthetwoQTLswhichshouldbeusefultoplantheightandpanicletypeimprovement.
TheothernovelQTLsderivedfromhybridriceeliteparentR1128whichmayplayanimportanteffectinsuper-yieldricebreedingandcouldbeusedinricepyramidingorMAS(markerassistedselection)breedingtoincreasethegrainyields.
ConclusionsStudiesonricefunctionalgenomicshavebeengreatlyfacilitatedbytheuseofhigh-throughputsequencingtechnology.
Inthepresentstudy,multiplesequencingwasperformedonprogenyofanF2populationbasedonmaleparentR1128andfemaleparentNipponbare.
Mul-tiplesequencingwaspreformedbyusingMSGsequen-cingtechnology,whileQTLslinkedtoagronomictraitsweremappedandanalyzedfortheireffect.
Atotalof49QTLsforfivekeyyieldfactors,suchasPHandPLetal.
,weremapped,andaredistributedon11chromosomes(allexceptchromosome5).
Atotalof14QTLsweremappedonchromosome6alone;multiplemajorgenesforgoodtraitshavebeenpyramidedinR1128,includingSd1forplantheight,Hd1andEhd1forheadingdate,Gn1aforgrainnumberandIPA1foridealplantshape.
Thesegeneshaveindependentlyexplained44.
3%,21.
9%,6.
2%,12.
9%and10.
6%ofthephenotypicvariationsoftheirtraits.
Sixnovelloci,qph1-2,qph9-1,qpl12-1,qgn3-1,qgn11-1andqsbn11-1arereportedforthefirsttimeinthisstudy.
Thesuper-hybridriceparentR1128isbenefi-cialforricebreedingandtheinternationalresequencingvarityNipponbarehasthecleargenomebackgroundwhichisconducivetoricefunctionalgeneresearch.
ThegeneticbinmapconstructedbyR1128andNipponbareinthisstudyisnotonlyworthtoricegenefundamentalresearch,butalsovaluabletopracticalapplicationinricebreeding.
MethodsPlantmaterialandphenotypicevaluationInthisresearch,weused781F2(secondfilialgeneration)linesforthericeQTLmappingpopulation.
Thepopula-tionwasdevelopedfromacrossbetweenOryzasativassp.
indicacv.
R1128andssp.
japonicacv.
Nipponbarefollowedbyself-fertilizationoftheF1.
ThebreedingoftheindicarestorerlineR1128wasfromamultiplecrossbe-tweenSH527andaninbredF4linewhichwasgeneratedfromthecrossbetweenR855andatemporaryF4linenamed1033,whichwasintroducedfromAmerica.
TheresultingF1wascrossedwiththeF1fromMH63andR353followedbyselfingtotheF12(Liuetal.
2012a).
TheDuanetal.
Rice2013,6:21Page11of15http://www.
thericejournal.
com/content/6/1/21japonicavarietyNipponbareistheinternationalsequen-cedcultivar(Goffetal.
2002).
AllplantmaterialswerecultivatedatChangshainChinausingnormalfieldman-agementpractices.
Anarrayofmorphologicalcharactersincludingplantheight(PH),grainnumber(GN),paniclelength(PL),pri-marybranchnumber(PBN),secondarybranchnumber(SBN)ofthetwoparentallinesandtheF2populationwereinvestigatedatChangshain2011.
Theexaminationstandardwasreferredto(Zhaoetal.
2007)withlittleimprovement.
DNAisolationandMSGlibrarypreparationGenomicDNAwasextractedfromsmallsamples(0.
5g)ofyoungleavesfromtheR1128parentandtheF2pro-genyplantsusingCTAB.
Wholegenomere-sequencingwascarriedoutforR1128tovarifyitsidentification.
Genome-wideSNPdevelopmentandgenotypingfortheF2populationwereperformedusingMSG(multiplexedshotgungenotyping)asproposedby(Andolfattoetal.
2011),withsomemodifications.
Bar-codedadaptersweredesignedandmodifiedaccordingtothestandardIlluminaadapterdesignforpaired-endreadlibraries.
GenomicDNAofeachsample(1μg)wasdigestedwith1μlFastDigestTaqI(ThermoscientificFermentas)for10minat65°Cinavolumeof30μl.
Uniquebarcodeadapters(10μmol)weretheaddedtoeachsamplewell.
Theligationreactionwasincubated1hat22°CwithT4DNAligase(Enzymatics)andheatinactivatedat65°Cfor20min.
Twenty-fourligationproductsfordifferentsampleswerepooledinasingletubeand2μlchloroformwasaddedtoinactivetherestrictionenzyme.
DNAfrag-mentsbetween400–600bpwerethenselectedona2%agarosegelandpurifiedusingaQIAquickGelExtractionKit.
Alltheproductswereamplifiedwith10cyclesofPCR(Phusionhigh-fidelity,Finnzymes)ina50μlreactionwhichincluded25μlPhusionMasterMix,1μlofcom-monprimer(10μM)and1μlindexprimer.
TheamplifiedlibrarywaspurifiedusingaQIAquickPCRPurificationKit,quantifiedontheAgilent2100BioanalyzerandfinallysequencedonanIlluminaHiseq2000instrument.
SNPidentificationThericereferencegenomefromcultivarNipponbare(IRGSPv6)wasusedtoreadmappingwiththesoftwareSOAP2(version2.
20)(Lietal.
2009b).
SOAPsnp(version1.
01)wasusedtogeneratetheconsensussequencesforeachsample.
InputdataforSNPcallingwithrealSFS(version0.
983)waspreparedbySAMtools(version0.
1.
8).
PopulationSNPcallingwasperformedwithrealSFS,basedontheBayesianestimationofsitefrequencyateverysite.
Thelikelihoodsofgenotypesforeachindividualwereintegratedandsiteswithaprobabilityof>0.
95andapopulationwholedepthhigherthan40wereextractedascandidateSNPs.
PotentialSNPswerethenfilteredusingthefollowingcriteria:lociwith>70%missingdatathatalsoshowedseriousdistortedsegregationofthetwopar-entalgenotypeswereexcluded.
AlltheSNPswerefilteredusingaPERLscript.
TheSNPsgeneratedinthisstudywerecomparedtothericeSNPdatabasebuildbyOryzaSNPConsortium(website:http://oryzasnp.
plantbiology.
msu.
edu/).
OryzaSNPProjectSNPdatadownloadfromftp://ftp.
plantbiology.
msu.
edu/pub/data/Oryza_SNP/.
WeusetheSNPsidentifiedbyeitherthePerlegenSNPcallsorthemachinelearningSNPcallsasourreportedSNPdatasetbecauseitcontainsgenomewideSNPvariationfor20diversevarietiesandlandracesthatcapturetheimpressivegenotypicandpheno-typicdiversityofdomesticatedrice(Mcnallyetal.
2009).
ForR1128,IndelcallsweredonewithSOAPindel(version1.
08)andSV(structurevariation)wasidenti-fiedwithSOAPsv(version1.
02).
GenotypecallingandrecombinationbreakpointdeterminationWeconvertedtheSNPdataintoanotherformattosim-plifythegenotypecallinganalysis.
TheSNPtypefromNipponbarewascodedas"a",theR1128alleleswerecodedas"b"andtheheterozygoteswerecodedas"h",whilemissingdatawascodedas"-".
AnF2populationthatistemporaryandcollectivelyhasSNPsin50%heterozygousgenotype,theoretically.
Thegenotypesofthefemaleandmaleparentgenotypearedispersedirregularlyinheterozygousregions.
WhenSNPsdetectedfromtheF2populationwereplacedalongthechromosomes,inachromosomalregion,SNPsrepresentingoneparentorbothparents(heterozygous)werepredominantandthoserepresentingtheotherparentwerescatteringamongthem.
ItisnotaccuratetodeterminethegenotypeoftheF2populationbasedonindividualSNPs.
AslidingwindowapproachadoptedbyBinHan(Huangetal.
2009)withsomemodificationwasusedtoevaluateagroupofconsecutiveSNPsforgeno-typing.
Firstly,basedontheSNPdensity,wechosethewindowsizeof15SNPsforgenotyping,whichcoveredonaverage75kbor0.
3cMofricechromosomes.
WealsotestedtheeffectofdifferentwindowsizesonbinmapconstructionandQTLanalysisbyusingwindowsizesof7,11,19SNPs.
Thewindowsizesof7,11,and19yieldednearlyidenticalresultsasthesizeof15intheidentificationofthelargestQTLforplantheightandgrainnumberasthetraitexamples(Additionalfile7).
Evidently,thehighersequencingcoveragepermitstheuseoflargerwindowscoveringthesamephysicalandgeneticintervalsandconsequentlymoreaccuratemap-ping,sowechose15SNPsasouranalysisparameters.
Foreachsample,awindowof15SNPswithoutmissingdatawasusedforgenotypingcalling.
Ana/bratioofDuanetal.
Rice2013,6:21Page12of15http://www.
thericejournal.
com/content/6/1/2112:3orhigherwasrecognizedas"a",3:12orloweras"b"andanythinginbetweenas"h".
Wedeterminedthebreakpointsaccordingtoapub-lishedmethodforhigh-throughputgenotypingbyNGS(next-generationsequencing)withsomemodification(Daveyetal.
2011).
Recombinationbreakpointsweredeterminedbythejunctionoftwodifferentgenotypes.
Forthebreakpointsseparatingheterozygousfromhomozygous,whichisamajorkindofF2population,wepickedupthedivertlocusasrecombinationbreakpoint.
Forheterozygousfromhomozygous,therewereseveraltemporary"h"andthenchangedintoanothergenotype.
Thethirdchangedlocuswaschosenforthisbreakpoint.
BinmapconstructionandQTLanalysisAccordingtothebreakpointinformation,weusedaPERLscripttogeneratebininformationwithintervalslargerthan10kb.
QTLswereidentifiedbycompositeintervalmappingusingthesoftwareMapQTL5.
QTLmappinginthepresentexperimentwascarriedoutbycalculatingthethresholdlogarithmofoddsdifference(LOD)foreachtraitbyperformingatestwith1,000permutations.
Theexperi-mentalLODthresholdforeverytraitoneachchromosomewascalculatedindependentlyandthevaluecouldbeatthe5%levelofsignificance.
QTLwerenamedaccordingto(Mccouchetal.
1997)andtheQTLmappingresultswerecomprehensivelycomparedtotheOGRO(TheOverviewoffunctionallycharacterizedGenesinRiceonlinedatabase)(Yamamotoetal.
2012),theRiceGenomeAnnotationProject,theIRGSPandGramenedata.
ThedataforthepopulationandparentsfortraitswerecalculatedwithSPSSstatistics17.
0(P<0.
05)andMicrosoftExcel.
AdditionalfilesAdditionalfile1:TheSNPsinformationgeneratedfromF2population.
Thedocumentsincluding"chr01_filter.
ab"to"chr12_filter.
ab"arethesamplesgenotypewhichconvertedtobea\b\hformats.
Itismarked"a"thatthegenotypeofsampleisthesametoNipponbare,or"b"representstheR1128genotypeand"h"istheheterozygousgenotype;Thedeletionofsamplegentoypeismarkedas"-"specially.
DatafilesaregenerallyTXTwhichcompressedintoaZIPformat.
ForWindowsuser,"Editplus"or"UltraEdit"isrecommendedasthebrowserprogram.
Formatdescription(lefttoright).
1.
Chromosome.
2.
Position.
3.
GenotypeofNipponbare.
4.
GenotypeofR1128.
5.
Genotypeofsequencingsample.
Additionalfile2:TheSNPsinformationcomparedtothericeSNPdatabase.
Formatdescription(lefttoright).
1.
SNPID.
2.
Chromosome.
3.
Position.
4.
ReferenceSNP.
5.
TwentydiversericevarietiesandthelastoneisR1128.
Additionalfile3:Thegenomiclocationofthebreakpoints.
Thephysicalpositionandgenotypeofthebreakpointareconnectedwith"-",suchas"1140905-h".
Formatdescription(lefttoright).
1.
Individualsampleoneachchromosome.
2.
TheinitialGenotypeofNipponbare.
3.
Locationandgenotypeofbreakpointsofindividualsample.
Additionalfile4:Gentoypeofsequencingsamplescorrespondtoeachbinofchromosomes.
Formatdescription(lefttoright).
1.
Individualsample.
2.
Genotypeofsinglebin.
Additionalfile5:Ageneticlinkagemapconstructedwithindividualbinonchromosomes.
Additionalfile6:Thebinsizeandlocationforeachbin.
Formatdescription(lefttoright).
1.
Chromosome.
2.
Binname.
3.
Theinitialpositionofbin.
4.
Theterminationalpositionofbin.
5.
Thesizeofbin.
Additionalfile7:PlantheightandgrainnumberQTLsdetectedonchromosomeswhenusingdifferentwindowsizes.
CompetinginterestsTheauthorsdeclarethattheyhavenocompetinginterests.
Authors'contributionsSZcarriedoutthestatisticalanalysisanddraftedthemanuscript.
SLparticipatedinpreparationofdata.
TY,YD,SXandLRperformedtheF2populationconstruction,phenotypicevaluation,andleafsampling.
LYandGScarriedouttheDNAisolationandMSGlibrarypreparation.
YDandDMconceivedanddesignedtheexperimentsandrevisedthemanuscript.
Allauthorsreadandapprovedthefinalmanuscript.
AcknowledgmentsWethankDr.
QiujuXia,HongfengZouandZhiwuQuanforprovidinghelpfulproposalsofthisresearch.
WeespeciallythankDr.
GengyunZhangfortechnologysupportandcriticalreadingofthismanuscript.
ThisworkwassupportedbytheNationalKeyProgramsforTransgenicCrops(2011ZX08001-004),theNationalHighTechnologyResearchandDevelopmentProgramofChina(863Program)(2011AA10A107),MajorScienceandTechnologyProgramofHunan,China(2011FJ1002-2).
Authordetails1StateKeyLaboratoryofHybridRice,HunanHybridRiceResearchCenter,Changsha410125,China.
2HunanAcademyofAgriculturalSciences,Changsha410125,China.
3HunanAgriculturalUniversity,Changsha410125,China.
4LongPingBranchofGraduateSchoolofCentralSouthUniversity,Changsha410125,China.
5BeijingGenomicsInsititute(BGI),Shenzhen518083,China.
6GuangdongProvincialKeyLaboratoryofCropGeneticResourcesResearchandApplication(NO.
2011A091000047),Shenzhen518083,China.
Received:1February2013Accepted:9August2013Published:15August2013ReferencesAgrawalG,JwaN,IwahashiH,RakwalR(2003)ImportanceofascorbateperoxidasesOsAPX1andOsAPX2inthericepathogenresponsepathwaysandgrowthandreproductionrevealedbytheirtranscriptionalprofiling.
Gene322:93–103AndolfattoP,DavisonD,ErezyilmazD,HuTT,MastJ,Sunayama-MoritaT,SternDL(2011)Multiplexedshotgungenotypingforrapidandefficientgeneticmapping.
GenomeRes21:610–617AshikariM,SakakibaraH,LinS,YamamotoT,TakashiT,NishimuraA,AngelesER,QianQ,KitanoH,MatsuokaM(2005)Cytokininoxidaseregulatesricegrainproduction.
Science309:741–745BairdNA,EtterPD,AtwoodTS,CurreyMC,ShiverAL,LewisZA,SelkerEU,CreskoWA,JohnsonEA(2008)RapidSNPdiscoveryandgeneticmappingusingsequencedRADmarkers.
PLoSOne3:e3376ChenLY(2007)Practiceandcreativeidealsonsuperhybridricebreeding.
JHunanAgricUniv(NaturalSciences)33:21–25ChenLY,LeiDY,TangWB,XiaoYH(2010)ThoughtsandPracticeofSomeProblemsaboutResearchandApplicationofTwo-LineHybridRice.
ChinJRiceSci24:641–646ChengS(2000)Currentstatusandprospectinthedevelopmentofbreedingmaterialsandbreedingmethodologyofhybridrice.
ChinJRiceSci14:165CuiK,PengS,XingY,YuS,XuC(2002)Geneticanalysisofthepanicletraitsrelatedtoyieldsinksizeofrice.
ActageneticaSinica29:144Duanetal.
Rice2013,6:21Page13of15http://www.
thericejournal.
com/content/6/1/21CuiK,PengS,XingY,YuS,XuC,ZhangQ(2003)Moleculardissectionofthegeneticrelationshipsofsource,sinkandtransporttissuewithyieldtraitsinrice.
TheorApplGenet106:649–658CuiK,PengS,YingY,YuS,XuC(2004)Moleculardissectionoftherelationshipsamongtillernumber,plantheightandheadingdateinrice.
PlantProdSci7:309–318DaveyJW,HohenlohePA,EtterPD,BooneJQ,CatchenJM,BlaxterML(2011)Genome-widegeneticmarkerdiscoveryandgenotypingusingnext-generationsequencing.
NatRevGenet12:499–510DengHF,ZhuYG,XiaoCH,TangSQ,HuaZT,ZhengJK,WangF,WangSH,JiangL,HeQ,ZhangWH,YuanLP(2010)AdvancesofResearchonStrongHeterosisHybridRiceinChina.
HybridRice25:1–4DoiK,IzawaT,FuseT,YamanouchiU,KuboT,ShimataniZ,YanoM,YoshimuraA(2004)Ehd1,aB-typeresponseregulatorinrice,confersshort-daypromotionoffloweringandcontrolsFT-likegeneexpressionindependentlyofHd1.
GenesDev18:926–936DuJH,FanYY,WuJR,ZhuangJY(2008)DissectionofQTLsforYieldTraitsontheShortArmofRiceChromosome6.
ScientiaAgriculturaSinica41:939–945Endo-HigashiN,IzawaT(2011)FloweringtimegenesHeadingdate1andEarlyheadingdate1togethercontrolpanicledevelopmentinrice.
PlantCellPhysiol52:1083–1094GaoZ,QianQ,LiuX,YanM,FengQ,DongG,LiuJ,HanB(2009)Dwarf88,anovelputativeesterasegeneaffectingarchitectureofriceplant.
PlantMolBiol71:265–276GaoJ,XuJD,YiL,YuanSJ(2011)ResearchProgressofYieldRelatedTraitsofRice.
ShandongAgricSci9:57–60GodfrayHCJ,BeddingtonJR,CruteIR,HaddadL,LawrenceD,MuirJF,PrettyJ,RobinsonS,ThomasSM,ToulminC(2010)Foodsecurity:thechallengeoffeeding9billionpeople.
Science327:812–818GoffSA,RickeD,LanTH,PrestingG,WangR,DunnM,GlazebrookJ,SessionsA,OellerP,VarmaH(2002)Adraftsequenceofthericegenome(OryzasativaL.
ssp.
japonica).
Science296:92–100HeP,LiJ,ZhengX,ShenL,LuC,ChenY,ZhuL(2001)ComparisonofmolecularlinkagemapsandagronomictraitlocibetweenDHandRILpopulationsderivedfromthesamericecross.
CropSci41:1240–1246HittalmaniS,ShashidharH,BagaliPG,HuangN,SidhuJ,SinghV,KhushG(2002)Molecularmappingofquantitativetraitlociforplantgrowth,yieldandyieldrelatedtraitsacrossthreediverselocationsinadoubledhaploidricepopulation.
Euphytica125:207–214HongZ,Ueguchi-TanakaM,FujiokaS,TakatsutoS,YoshidaS,HasegawaY,AshikariM,KitanoH,MatsuokaM(2005)Thericebrassinosteroid-deficientdwarf2mutant,defectiveinthericehomologofArabidopsisDIMINUTO/DWARF1,isrescuedbytheendogenouslyaccumulatedalternativebioactivebrassinosteroid,dolichosterone.
PlantCell17:2243–2254HuaJP,XingYZ,XuCG,SunXL,YuSB,ZhangQ(2002)Geneticdissectionofanelitericehybridrevealedthatheterozygotesarenotalwaysadvantageousforperformance.
Genetics162:1885–1895HuangX,FengQ,QianQ,ZhaoQ,WangL,WangA,GuanJ,FanD,WengQ,HuangT(2009)High-throughputgenotypingbywhole-genomeresequencing.
GenomeRes19:1068–1076JangS,LeeB,KimC,KimSJ,YimJ,HanJJ,LeeS,KimSR,AnG(2003)TheOsFOR1geneencodesapolygalacturonase-inhibitingprotein(PGIP)thatregulatesfloralorgannumberinrice.
PlantMolBiol53:357–372JiaoY,WangY,XueD,WangJ,YanM,LiuG,DongG,ZengD,LuZ,ZhuX(2010)RegulationofOsSPL14byOsmiR156definesidealplantarchitectureinrice.
NatGenet42:541–544JunN,GaohangW,ZhenxingZ,HuanhuanZ,YunrongW,PingW(2011)OsIAA23‐mediatedauxinsignalingdefinespostembryonicmaintenanceofQCinrice.
PlantJ68:433–442KimEH,KimYS,ParkSH,KooYJ,DoChoiY,ChungYY,LeeIJ,KimJK(2009)Methyljasmonatereducesgrainyieldbymediatingstresssignalstoalterspikeletdevelopmentinrice.
PlantPhysiol149:1751–1760LanderES(1996)Thenewgenomics:globalviewsofbiology.
Science274:536–539LiM,XiongG,LiR,CuiJ,TangD,ZhangB,PaulyM,ChengZ,ZhouY(2009a)Ricecellulosesynthase‐likeD4isessentialfornormalcell‐wallbiosynthesisandplantgrowth.
PlantJ60:1055–1069LiR,YuC,LiY,LamTW,YiuSM,KristiansenK,WangJ(2009b)SOAP2:animprovedultrafasttoolforshortreadalignment.
Bioinformatics25:1966–1967LinHX,QianHR,ZhuangJY,LuJ,MinSK,XiongMZ,HuangN,ZhengKL(1995)IntervalmappingofQTLsforyieldandotherrelatedcharactersinrice.
RiceGenetNewsl12:251–253LiuH,DengZQ,DengLF,DengXL(2012a)BreedingandApplicationofNewStrongHeterosisHybridRiceCombinationLiangyou1128.
HybridRice27:17–19LiuJ,TaoH,ShiS,YeW,QianQ,GuoL(2012b)GeneticsandBreedingImprovementforPanicleTypeinRice.
ChinJRiceSci26:227–234MackayTFC(2001)QuantitativetraitlociinDrosophila.
NatRevGenet2:11–20MarriPR,SarlaN,ReddyLV,SiddiqE(2005)IdentificationandmappingofyieldandyieldrelatedQTLsfromanIndianaccessionofOryzarufipogon.
BMCgenetics6:1–14MccouchSR,ChenX,PanaudO,TemnykhS,XuY,ChoYG,HuangN,IshiiT,BlairM(1997)Microsatellitemarkerdevelopment,mappingandapplicationsinricegeneticsandbreeding.
PlantMolBiol35:89–99McleanJ,DaweD,HardyB,HettelG(2002)RiceAlmanac.
SourceBookfortheMostImportantEconomicActivityinEarth,3rdedition.
CABIPublishing,Oxon,UKMcnallyKL,ChildsKL,BohnertR,DavidsonRM,ZhaoK,UlatVJ,ZellerG,ClarkRM,HoenDR,BureauTE(2009)GenomewideSNPvariationrevealsrelationshipsamonglandracesandmodernvarietiesofrice.
ProcNatlAcadSci106:12273–12278PingL,LikhuangZ,YingkguoZ(2003)CharacterizationofQTLsforHarvestIndexandSourceKsinkCharactersinaDHPopulationofRice(OryzasativaL.
).
JGenetGenomics30:1118–1126RedonaE,MackillD(1998)Quantitativetraitlocusanalysisforricepanicleandgraincharacteristics.
TheorApplGenet96:957–963SasakiA,AshikariM,Ueguchi-TanakaM,ItohH,NishimuraA,SwapanD,IshiyamaK,SaitoT,KobayashiM,KhushG(2002)Amutantgibberellin-synthesisgeneinrice.
Nature416:701–702SassonA(2012)FoodsecurityforAfrica:anurgentglobalchallenge.
AgrFoodSecur1:1–16TanZ,ShenL,KuangH,LuC,ChenY,ZhouK,ZhuL(1996)IdentificationofQTLsforlengthsofthetopinternodesandothertraitsinriceandanalysisoftheirgeneticeffects.
ActaGenetSin23:439–446TanakaK,MurataK,YamazakiM,OnosatoK,MiyaoA,HirochikaH(2003)Threedistinctricecellulosesynthasecatalyticsubunitgenesrequiredforcellulosesynthesisinthesecondarywall.
PlantPhysiol133:73–83TengS,QianQ,ZengD,KunihiroY,HuangD,ZhuL(2002)QTLanalysisofricepedunclevascularbundlesystemandpanicletraits.
ActaBotanicaSinica44:301–306ThomsonM,TaiT,McclungA,LaiX,HingaM,LobosK,XuY,MartinezC,MccouchS(2003)Mappingquantitativetraitlociforyield,yieldcomponentsandmorphologicaltraitsinanadvancedbackcrosspopulationbetweenOryzarufipogonandtheOryzasativacultivarJefferson.
TheorApplGenet107:479–493WangYB,LiW(2005)EffectsontheDifferentModelofPanicleYieldsandYieldComponentsofDistributionPatternofRice.
JLiaoningAgricColl7:6–8XiaoJ,LiJ,YuanL,TanksleyS(1996)IdentificationofQTLsaffectingtraitsofagronomicimportanceinarecombinantinbredpopulationderivedfromasubspecificricecross.
TheorApplGenet92:230–244YamamotoT,Taguchi-ShiobaraF,UkaiY,SasakiT,YanoM(2001)MappingQuantitativeTraitLociforDays-to-heading,andCulm,PanicleandInternodeLengthsinaBC1F3PopulationUsinganEliteRiceVariety,Koshihikari,astheRecurrentParent.
BreedSci51:63–71YamamotoE,YonemaruJ,YamamotoT,YanoM,ZangY,WangQ,XueC,LiM,WenR,XiaoW(2012)OGRO:TheOverviewoffunctionallycharacterizedGenesinRiceonlinedatabase.
Rice5:1–10YangHJ,YangRC,LiYZ,JiangZW,ZhengJS(2000)Yieldpotentialandyieldcomponentsofsuperhigh-yieldingricecultivars.
FujianJAgricuSci15:1–8YanoM,KatayoseY,AshikariM,YamanouchiU,MonnaL,FuseT,BabaT,YamamotoK,UmeharaY,NagamuraY(2000)Hd1,amajorphotoperiodsensitivityquantitativetraitlocusinrice,iscloselyrelatedtotheArabidopsisfloweringtimegeneCONSTANS.
PlantCell12:2473–2483YuanAP,CaoLY,ZhuangJY,LiRZ,ZhengKL,ZhuJ,ChengSH(2003)AnalysisofadditiveandAEinteractioneffectsofQTLscontrollingplantheight,headingdateandpaniclenumberinrice(OryzasativaL.
).
JGenetGenomics30:899–906ZhangQJ,LiangYS,YeSP,DengQM,WangLX,LiP,YuDR,ZouJSLCG(2006)QTLAnalysisofAgronomicTraitswithSequencedRiceVarieties.
ActaAgronmicaSinica32:1503–1510Duanetal.
Rice2013,6:21Page14of15http://www.
thericejournal.
com/content/6/1/21ZhaoFM,ZhuHT,DingXH,ZengR,ZhangZM,LiWT,ZhangGQ(2007)DetectionofQTLsforTraitsofAgronomicImportanceandAnalysisofTheirStabilitiesUsingSSSLsinRice.
ScientiaAgriculturaSinica40:447–456ZhaoFM,ZhangGQ,ZengRZ,YangZL,ZhuHT,ZhongBQ,LingYH,HeGH(2009)AdditiveEffectsandEpistasisEffectsofQTLforPlantHeightandItsComponentsUsingSingleSegmentSubstitutionLines(SSSLs)inRice.
ActaAgronomicaSinica35:48–56ZhengJS,JiangLR,ZengJM,LinWX,LiYZ(2003)QTLAnalysisofHeadingDate,PlantHeightandYieldComponentsinF2PopulationDerivedfromMinghui86*Jiafuzhan.
MolPlantBreed1:633–639ZhuXD,ZhangGP,YaoHG,ChenHQ,TaoLX,TangSQ(2007)YieldandAgronomicCharactersComparisonbetweenEarlyRiceofZhejiang.
ZhejiangAgricSciences1:69–73ZhuangJY,LinHX,LuJ,QianHR,HittalmaniS,HuangN,ZhengKL(1997)AnalysisofQTL*environmentinteractionforyieldcomponentsandplantheightinrice.
TheorApplGenet95:799–808ZhuangJY,FanYY,WuJL,XiaYW,ZhengKL(2001)ComparisonoftheDetectionofQTLforYieldTraitsinDifferentGenerationsofaRiceCrossUsingTwoMappingApproaches.
JGenetGenomics28:458–464doi:10.
1186/1939-8433-6-21Citethisarticleas:Duanetal.
:Geneticanalysisofanelitesuper-hybridriceparentusinghigh-densitySNPmarkers.
Rice20136:21.
Submityourmanuscripttoajournalandbenetfrom:7Convenientonlinesubmission7Rigorouspeerreview7Immediatepublicationonacceptance7Openaccess:articlesfreelyavailableonline7Highvisibilitywithintheeld7RetainingthecopyrighttoyourarticleSubmityournextmanuscriptat7springeropen.
comDuanetal.
Rice2013,6:21Page15of15http://www.
thericejournal.
com/content/6/1/21