Control of grain size shape and quality by OsSPL16 in rice.docx
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Control of grain size shape and quality by OsSPL16 in rice.docx
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ControlofgrainsizeshapeandqualitybyOsSPL16inrice
Controlofgrainsize,shapeandqualitybyOsSPL16inrice
∙ShaokuiWang1,2
∙KunWu1
∙QingboYuan1
∙XueyingLiu1
∙ZhengbinLiu1
∙XiaoyanLin2
∙RuizhenZeng2
∙HaitaoZhu2
∙GuojunDong3
∙QianQian3
∙GuiquanZhang2
∙XiangdongFu1
∙Affiliations
∙Contributions
∙Correspondingauthors
Journalname:
NatureGenetics
Volume:
44,
Pages:
950–954
Yearpublished:
(2012)
DOI:
doi:
10.1038/ng.2327
Received
21February2012
Accepted
30May2012
Publishedonline
24June2012
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Grainsizeandshapeareimportantcomponentsofgrainyieldandqualityandhavebeenunderselectionsincecerealswerefirstdomesticated.Here,weshowthataquantitativetraitlocusGW8issynonymouswithOsSPL16,whichencodesaproteinthatisapositiveregulatorofcellproliferation.Higherexpressionofthisgenepromotescelldivisionandgrainfilling,withpositiveconsequencesforgrainwidthandyieldinrice.Conversely,aloss-of-functionmutationinBasmatiriceisassociatedwiththeformationofamoreslendergrainandbetterqualityofappearance.ThecorrelationbetweengrainsizeandallelicvariationattheGW8locussuggeststhatmutationswithinthepromoterregionwerelikelyselectedinricebreedingprograms.Wealsoshowthatamarker-assistedstrategytargetedateliteallelesofGS3andOsSPL16underlyinggrainsizeandshapecanbeeffectivelyusedtosimultaneouslyimprovegrainqualityandyield.
Ataglance
1.Figure1:
MappingandcloningofqGW8.
(a)Parentalgrains.Scalebar,3mm.(b)QTLlocationsforgrainlength(GL)andwidth(GW).(c)Inthefine-scalemapgeneratedfromanalysisof2,000F2segregants,theQTLfallsintheintervalbetweenRM502andPSM736.NumbersbelowthelineindicatethenumberofrecombinantsbetweenqGW8andthemarkershown.(d)GenotypingofprogenyhomozygousforqGW8delimitedthelocustoan~7.5-kbstretchflankedbyRM502andPSM711.Grainwidth(mean±standarderror(SE),n=30)ofrecombinantBC5F4lines(L1–L6),aBC6F3line(L178)andthetwoparentalvarieties(H,HJX74;B,Basmati385).FilledandopenbarsrepresentchromosomalsegmentshomozygousforBasmati385andHJX74alleles,respectively.(e)MappingofallelicvariationtotheBasamti385OsSPL16proteinsequence.
Seelarger
2.Figure2:
TheeffectofqGW8oncellproliferationandgrainsize.
(a–d)GrainsfromtransgenicNIL-GW8(a),NIL-gw8(b),NIL-gw8(c)andBasmati385(d)plants.Scalebars,2.5mm.(e)ExpressionofOsSPL16inNIL-GW8andNIL-gw8.R,root;C,culm;L,leafblade;SAM,shootapexmeristem;BM,branchmeristem;YP1–Y22,youngpanicles,wherethenumberindicatesthelengthofthepanicleincentimeters.Expressionlevelsareshownasrelativenumberofcopiesper1,000copiesofriceactin3.Dataaregivenasmean±s.e.m.(n=4).(f)SpikeletsofNIL-GW8andNIL-gw8plantsbeforeanthesis.Scalebar,2.5mm.(g)Cross-sectionsofspikelethullsindicatedbythedashedlineinf.Scalebar,0.5mm.(h)Magnifiedviewofthecross-sectionboxeding.Scalebar,100μm.(i–k)Totallength(i),cellnumber(j)andcelllength(k)intheouterparenchymalayerofthespikelethullsformedbyNIL-GW8andNIL-gw8.Dataaregivenasmean±s.e.m.(n=12).Student'sttestswereusedtogeneratePvalues.
Seelarger
3.Figure3:
ContrastingphenotypeandgrainyieldofNIL-GW8andNIL-gw8plants.
(a)Matureplantappearance.Scalebar,10cm.(b)NIL-GW8andNIL-gw8grains.Scalebar,2.5mm.(c)Plantheight.(d)Tillernumber.(e)Paniclelength.(f)Numberofsecondarybranchesperpanicle.(g)Numberofgrainsperpanicle.(h)Grainlength.(i)Grainwidth.(j)1,000-grainweight.(k)Grainyieldperplot.Allphenotypicdatainc–kweremeasuredfromplantsgrownwith20×20cmspacinginpaddiesundernormalcultivationconditions.Datarepresentmean±s.e.m.(n=120).Student'sttestswereusedtogeneratePvalues.
Seelarger
4.Figure4:
ImprovinggrainsizeandshapebyQTLpyramiding.
(a)AppearanceofthegrainformedbyBasmati385andvariousNILs.Scalebar,3mm.(b)TheQTLcontentoftheNILs.ChromosomalsegmentshomozygouswithrespecttoBasmati385areshownasfilledbars,andthosehomozygouswithrespecttoHJX74areshownasemptybars.(c)Grainwidth.(d)Grainlength.(e)1,000-grainweight.Datainc–earegivenasmean±s.e.m.(n=40).(f)PolymorphismattheOsmiR156targetsitewithinOsSPL16intheAmol3variety.(g)ExpressionanalysisofOsSPL16inNIL-gw8Amol.AbbreviationsasinFigure2.Relativeexpressionisshownasthenumberofcopiesper1,000copiesofriceactin3.Dataaregivenasmean±s.e.m.(n=4).(h)GrainsfromNIL-gw8Amolplants.Scalebar,2.5mm.(i–k)ContrastbetweenNIL-GW8andNIL-gw8Amolwithrespectto1,000-grainweight(i),thenumberofgrainsperpanicle(j)andgrainyieldperplot(k).Allphenotypicdataweremeasuredfromfield-grownplantsundernormalcultivationconditions.Dataaregivenasmean±s.e.m.(n=120).Student'sttestswereusedtogeneratePvalues.
Seelarger
Main
∙Main
∙Methods
∙References
∙Acknowledgments
∙Authorinformation
∙Supplementaryinformation
Riceisamajorcomponentofthedietofoverhalfoftheworld'spopulation.Simultaneousimprovementofyieldandend-usequalityremainsachallengeforricebreedersbecauseyieldandqualityaretypicallynegativelycorrelatedwithoneanother1.Grainsizeisaprimebreedingtarget,asitaffectsbothyieldandquality.Geneticcontrolofthischaracterhasbeenextensivelyinvestigatedoverthelastdecade.Recently,severalgeneshavebeenshowntocontrolgrainsize:
GS3andDEP1regulategrainlength2,3,4,andGW2,qSW5andGS5regulategrainwidth5,6,7.However,manyofthegeneticdeterminantsarecurrentlyexplainedonlybyquantitativetraitloci(QTLs),withoutanyunderstandingofthenatureoftheencodedgeneproduct.
Slendergrains(havingalength-to-widthratioofthreeandabove)arepreferredbythemajorityofconsumers2,8.ThetraditionalindicaBasmativarieties,suchasBasmati385,formaparticularlyslendergrain,whichcombineadistinctaromawithexcellentcookingquality8buttypicallyshowonlyamodestlevelofproductivity9.Incontrast,thehigh-yieldindicavarietyHJX74producesshort,widegrains(Fig.1a).Weconstructedasetof153singlesegmentsubstitutionlines(SSSLs)bycrossingBasmati385(donorparent)andHJX74(recurrentparent),eachlinecontainingonlyonechromosomesegmentfromthedonorsubstitutedintotheHJX74geneticbackground10,11(OnlineMethods).Ananalysisoftheselinesidentifiedfourgenomiclocationswheredonoralleleswereresponsibleforlongergrainsandfourwheretheywereresponsibleforslenderness(Fig.1b).AsubsequentQTLanalysisshowedthepresenceofamajorgrain-widthlocus(qGW8)withinageneticwindowonthelongarmofchromosome8definedbythemarkersRM80andRM447(SupplementaryTable1).Amajorgrain-lengthQTL(qGL3.2)wasdetectedonchromosome3betweenRM282andPSM127,whichisthesameQTLasthepreviouslyreportedqGS3(ref.2)(SupplementaryTable1).Theinheritancepatternsof327F2plantsbredfromthecrossbetweenaselectedSSSLandHJX74indicatedthatasemidominantqGW8allelefromHJX74controlsgrainwidth(SupplementaryFig.1andSupplementaryTable2).
Figure1:
MappingandcloningofqGW8.
(a)Parentalgrains.Scalebar,3mm.(b)QTLlocationsforgrainlength(GL)andwidth(GW).(c)Inthefine-scalemapgeneratedfromanalysisof2,000F2segregants,theQTLfallsintheintervalbetweenRM502andPSM736.NumbersbelowthelineindicatethenumberofrecombinantsbetweenqGW8andthemarkershown.(d)GenotypingofprogenyhomozygousforqGW8delimitedthelocustoan~7.5-kbstretchflankedbyRM502andPSM711.Grainwidth(mean±standarderror(SE),n=30)ofrecombinantBC5F4lines(L1–L6),aBC6F3line(L178)andthetwoparentalvarieties(H,HJX74;B,Basmati385).FilledandopenbarsrepresentchromosomalsegmentshomozygousforBasmati385andHJX74alleles,respectively.(e)MappingofallelicvariationtotheBasamti385OsSPL16proteinsequence.
∙Fullsizeimage(101KB)
∙Figuresindex
∙Next
Alocalizedhigh-resolutionmapconstructedonthebasisoftheanalysisof2,000F2segregantsallowedtheplacementofqGW8betweenRM502andPSM736(Fig.1c).Theprogenytestingofhomozygousrecombinantplantsallowedthisregiontobenarrowedtoan~7.5-kbstretchflankedbyRM502andPSM711(Fig.1d),asegmentthatcontainsonlythepromoterregionandthepredictedfirstexonoftheLOC_Os08g41940ORF.ThecandidategeneOsSPL16encodessquamosapromoter-bindingprotein–like16,whichbelongstotheSBPdomainfamilyoftranscriptionfactors12,13,14,15,16andshareshomologywiththeproductoftga1,adomesticationsyndromegeneassociatedwiththeformationofnakedgrainsinmaize17(SupplementaryFig.2).SequencecomparisonofOsSPL16inHJX74andBasmati385revealedsixpolymorphisms:
a10-bpindelinthepromoterregion(c.–32_–23delGAGCTGAGCT),anin-frame3-bpindelinexon1(c.327_328insGCG),onesynonymouspolymorphism(c.36T>C)andthreemissensepolymorphisms(c.236T>C,c.818A>Candc.1089T>G)(Fig.1e).
Wedevelopedanear-isogenicline(NIL),NIL-gw8,whichcarriesan~407-kbsegmentincludingtheBasmati385qgw8alleleintheHJX74background,whereasitsmatchingline,NIL-GW8,carriesthehomologoussegmentfromHJX74.TheconstitutiveexpressionofasmallinterferingRNA(siRNA)directedatOsSPL16ledtonovisiblechangeinphenotypeatthewhole-plantorpanicle-architec
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