Mapping and Validation of qHD7b: Major Heading-Date QTL Functions Mainly under Long-Day Conditions

Abstract

Heading date (HD) is one of the agronomic traits that influence maturity, regional adaptability, and grain yield. The present study was a follow-up of a previous quantitative trait loci (QTL) mapping study conducted on three populations, which uncovered a total of 62 QTLs associated with 10 agronomic traits. Two of the QTLs for HD on chromosome 7 (qHD7a and qHD7b) had a common flanking marker (RM3670) that may be due to tight linkage, and/or weakness of the statistical method. The objectives of the present study were to map QTLs associated with HD in a set of 76 chromosome segment substitution lines (CSSLs), fine map and validate one of the QTLs (qHD7b) using 2,997 BC5F2:3 plants, and identify candidate genes using sequencing and expression analysis. Using the CSSLs genotyped with 120 markers and evaluated under two short-day and two long-day growing conditions, we uncovered a total of fourteen QTLs (qHD2a, qHD4a, qHD4b, qHD5a, qHD6a, qHD6b, qHD7b, qHD7c, qHD8a, qHD10a, qHD10b, qHD11a, qHD12a, and qHD12b). However, only qHD6a and qHD7b were consistently detected in all four environments. The phenotypic variance explained by qHD6a and qHD7b varied from 10.1% to 36.1% (mean 23.1%) and from 8.1% to 32.8% (mean 20.5%), respectively. One of the CSSL lines (CSSL52), which harbored a segment from the early heading XieqingzaoB (XQZB) parent at the qHD7b locus, was then used to develop a BC5F2:3 population for fine mapping and validation. Using a backcross population evaluated for four seasons under different day lengths and temperatures, the qHD7b interval was delimited to a 912.7-kb region, which is located between RM5436 and RM5499. Sequencing and expression analysis revealed a total of 29 candidate genes, of which Ghd7 (Os07g0261200) is a well-known gene that affects heading date, plant height, and grain yield in rice. The ghd7 mutants generated through CRISPR/Cas9 gene editing exhibited early heading. Taken together, the results from both the previous and present study revealed a consistent QTL for heading date on chromosome 7, which coincided not only with the physical position of a known gene, but also with two major effect QTLs that controlled the stigma exertion rate and the number of spikelets in rice. The results provide contributions to the broader adaptability of marker-assisted breeding to develop high-yield rice varieties.

Full text

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Plants2022,11,2288.https://doi.org/10.3390/plants11172288www.mdpi.com/journal/plants
Article
MappingandValidationofqHD7b:MajorHeading‐DateQTL
FunctionsMainlyUnderLong‐DayConditions
AmirSohail
1
,LiaqatShah
1,2
,LingLiu
1
,AnowerulIslam
1,3
,ZhengfuYang
1,4
,QinqinYang
1
,GalalBakrAnis
1,5
,
PengXu
1
,RiazMuhammadKhan
1,6
,JiaxinLi
1
,XihongShen
1
,ShihuaCheng
1
,LiyongCao
1,7
,YingxinZhang
1,
*
andWeixunWu
1,
*
1
StateKeyLaboratoryofRiceBiology,ChinaNationalRiceResearchInstitute,Hangzhou310006,China
2
DepartmentofAgriculture,MirChakarKhanRindUniversity,Sibi82000,Pakistan
3
DepartmentofAgriculturalExtension,MinistryofAgriculture,Dhaka1215,Bangladesh
4
StateKeyLaboratoryofSubtropicalSilviculture,ZhejiangA&FUniversity,Hangzhou311300,China
5
RiceResearchandTrainingCenter,FieldCropsResearchInstitute,AgricultureResearchCenter,
Kafrelsheikh33717,Egypt
6
CerealCropsResearchInstitute(CCRI)PirsabakNowshera,AgricultureResearchSystemKhyber
Pakhtunkhwa24100,Pakistan
7
NorthernCenterofChinaNationalRiceResearchInstitute,Shuangyashan155600,China
*Correspondence:wuweixun@caas.cn(W.W.);zhangyingxin@caas.cn(Y.Z.)
Abstract:Headingdate(HD)isoneoftheagronomictraitsthatinfluencematurity,regional
adaptability,andgrainyield.Thepresentstudywasafollow‐upofapreviousquantitativetraitloci
(QTL)mappingstudyconductedonthreepopulations,whichuncoveredatotalof62QTLs
associatedwith10agronomictraits.TwooftheQTLsforHDonchromosome7(qHD7aandqHD7b)
hadacommonflankingmarker(RM3670)thatmaybeduetotightlinkage,and/orweaknessofthe
statisticalmethod.TheobjectivesofthepresentstudyweretomapQTLsassociatedwithHDina
setof76chromosomesegmentsubstitutionlines(CSSLs),finemapandvalidateoneoftheQTLs
(qHD7b)using2,997BC
5
F
2:3
plants,andidentifycandidategenesusingsequencingandexpression
analysis.UsingtheCSSLsgenotypedwith120markersandevaluatedundertwoshort‐dayandtwo
long‐daygrowingconditions,weuncoveredatotaloffourteenQTLs(qHD2a,qHD4a,qHD4b,
qHD5a,qHD6a,qHD6b,qHD7b,qHD7c,qHD8a,qHD10a,qHD10b,qHD11a,qHD12a,andqHD12b).
However,onlyqHD6aandqHD7bwereconsistentlydetectedinallfourenvironments.The
phenotypicvarianceexplainedbyqHD6aandqHD7bvariedfrom10.1%to36.1%(mean23.1%)and
from8.1%to32.8%(mean20.5%),respectively.OneoftheCSSLlines(CSSL52),whichharboreda
segmentfromtheearlyheadingXieqingzaoB(XQZB)parentattheqHD7blocus,wasthenusedto
developaBC
5
F
2:3
populationforfinemappingandvalidation.Usingabackcrosspopulation
evaluatedforfourseasonsunderdifferentdaylengthsandtemperatures,theqHD7bintervalwas
delimitedtoa912.7‐kbregion,whichislocatedbetweenRM5436andRM5499.Sequencingand
expressionanalysisrevealedatotalof29candidategenes,ofwhichGhd7(Os07g0261200)isawell‐
knowngenethataffectsheadingdate,plantheight,andgrainyieldinrice.Theghd7mutants
generatedthroughCRISPR/Cas9geneeditingexhibitedearlyheading.Takentogether,theresults
fromboththepreviousandpresentstudyrevealedaconsistentQTLforheadingdateon
chromosome7,whichcoincidednotonlywiththephysicalpositionofaknowngene,butalsowith
twomajoreffectQTLsthatcontrolledthestigmaexertionrateandthenumberofspikeletsinrice.
Theresultsprovidecontributionstothebroaderadaptabilityofmarker‐assistedbreedingto
develophigh‐yieldricevarieties.
Keywords:rice(OryzasativaL.);quantitativetraitlocus;chromosomesegmentsubstitutionlines;
qHD7b;fine‐mapping


Citation:Sohail,A.;Shah,L.;Liu,L.;
Islam,A.;Yang,Z.;Yang,Q.;Anis,
G.B.;Xu,P.;Khan,R.M.;Li,J.;etal.
MappingandValidationofqHD7b:
MajorHeading‐DateQTLFunctions
MainlyUnderLong‐DayConditions.
Plants2022,11,2288.https://doi.org/
10.3390/plants11172288
AcademicEditors:KassaSemagn
andTikaAdhikari
Received:28June2022
Accepted:30August2022
Published:1September2022
Publisher’sNote:MDPIstays
neutralwithregardtojurisdictional
claimsinpublishedmapsand
institutionalaffiliations.

Copyright:©2022bytheauthors.
LicenseeMDPI,Basel,Switzerland.
Thisarticleisanopenaccessarticle
distributedunderthetermsand
conditionsoftheCreativeCommons
Attribution(CCBY)license
(https://creativecommons.org/license
s/by/4.0/).

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1.Introduction
Riceisastaplefoodformorethan50%oftheworld’spopulation,withitsproduction
expectedtoincreasebyabout25%in2030tokeeppacewithpopulationgrowth.Riceisa
facultative,short‐daycropthatflowersearlierundershort‐day(SD)conditionsandlater
underlong‐day(LD)conditions[1].Headingdate(HD)isacrucialtraitaffectingrice
adaptiontodiversecultivationareas,croppingseasons,maturity,andgrainyield[2].The
developmentofearly‐orlate‐maturingcultivarsdependsonecologicalconditions.Inthe
regionswheregrowingseasonsareshort,theaimistodevelopearlymaturingvarieties
toescapefrostdamage,buttheremaybeayieldpenalty.However,intheregionswhere
growingseasonsarelong,theaimistodeveloplate‐maturingvarietieswithallofthe
assimilatesefficientlytransmittedtothegrains,therebyenhancinggrainweightandyield.
Generally,therewasatrade‐offbetweenfloweringtimeandyield,whichaimedto
maximizeproduction[3].
Numerousstudieshavebeenconductedtomapandcharacterize712HDgenesand
quantitativetraitloci(QTLs)thathavebeendocumentedintheGramenedatabase
(http://archive.gramene.org/qtl/(accessedon29August2022)).TheE1/Ghd7wasthefirst
HDQTLreportedinrice,whichpossessesafunctionaldominantE1alleleandanon‐
functionale1allele[4].TheallelicvariationofGhd7contributestothegeographic
distributionofcultivatedrice[5],whichhasbeeninvestigatedforphotoperiodsensitivity
andregionaladaptability[6].ThefunctionalGhd7alleles(e.g.,Ghd7‐1,Ghd7‐2,andGhd7‐
3)delayheading,whilethenon‐functionalalleles(e.g.,Ghd7‐0andGhd7‐0a)shorten
headingdateinthedifferentgeneticbackgroundsofrice.BoththeGhd7‐1andGhd7‐3
alleleswerefoundinricevarietiesgrowninthetropics,subtropics,andareaswithhot
summersandlonggrowingseasonsinChinaandSoutheastAsia.TheGhd7‐2allelewas
foundintemperatejaponicavarietiesfromJapanandnorthernChinaandhadasmaller
phenotypiceffectthanGhd7‐1[7].Se1/Hd1wasthefirstclonedheading‐dateQTL,an
orthologofArabidopsisCONSTANSthatpromotesandsuppressesfloweringundershort‐
andlong‐daygrowingconditions,respectively[8].Headingdate6(Hd6)[9],Headingdate
3a(Hd3a)[10],Earlyheadingdate1(Ehd1)[11],Daystoheading8(DTH8)/Ghd8[12],Heading
date17(Hd17)[13],RICEFLOWERINGLOCUST1(RFT1)[14],andDaystoheading2
(DTH2)[3]areotherHDQTLsinricethathavebeenclonedusingamap‐basedapproach.
Theanalysisofthesegenesexhibitedtwomainphotoperiodicfloweringpathwaysinrice:
Hd1‐Hd3aandGhd7‐Ehd1‐Hd3a/RFT1.MajorQTLsassociatedwiththelateheading,such
asGhd7,Hd1,DTH8/Ghd8,andDTH7/Ghd7.1[5,15],showedastrongcorrelationwithan
increaseingrainyield,whichsuggeststhattheuseofsuchtypesofHDQTLscan
significantlyinfluencerice’sproductivityandadaptabilitytospecificgrowingconditions.
Recentprogressinmoleculartechnologyandstatisticalmethodologyhasprovided
researchersanopportunitytomapandcharacterizeHDQTLsindiversetypesof
populations,includingF2,recombinantinbredlines(RILs),anddoubledhaploidlines
(DHLs)inrice[16,17].However,thesepopulationsmaynotbeidealfortheprecise
mappingofQTLsduetothesimultaneoussegregationofmultiplelocioriginatingfrom
thetwoparents.Moreover,itwouldbemorechallengingtodeterminetheactualgenetic
actionsoftheQTLsanddifferentiatetheQTLeffectsfrombackgroundnoise[18,19].
Chromosomesegmentsubstitutionlines(CSSLs)aregeneticstocksthatconsistof
overlappingsegmentsofthecompletegenomeofanygenotype.CSSLshavebeenwidely
usedtomapQTLsaccurately,evaluategeneinteractions,discovernewalleles,and
comparethephenotypiceffectofgenesorQTLs[19,20].FurtherfinemappingofQTLsof
interestcanbedonebyconstructingsegregatingpopulationsobtainedfromcrossingone
oftheCSSLsandtheirrecurrentparent[21].
Inapreviousstudy,ourgroupidentified9HDQTLsinaRILpopulation(FigureS1)
and2BCF1populationsderivedfromacrossbetweenXieqingzaoB(XQZB)and
Zhonghui9308(ZH9308),whichindividuallyaccountedfor2.6–18.6%ofthephenotypic
variance[22].ThreeofthenineHDQTLsweremappedonchromosome7between
RM3670andRM2markers(qHD7a),betweenRM5436andRM3670(qHD7b),andbetween

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RM118andRM3555(qHD7c),explaining18.6%,12.1%,and5.6%,respectively.TheqHD7a
andtheqHD7bQTLwerephysicallylocatedbetween13439924–16022676bpand9075636–
13439924bp,respectively.RM3670,locatedat13439924bp,wasacommonflanking
markerinbothqHD7aandqHD7b,suggestingthatthetwoQTLsareeithertightlylinked
orthestatisticalmethodwronglyidentifiedthemastwoindependentQTLs.Bothissues
mayberesolvedusingCSSLs,whichformthebasisofthepresentstudy.Therefore,the
objectivesofthepresentstudyweretounderstandthephenotypicvariationoftheCSSLs
forheadingdate,finemaptheHDQTLonchromosome7,andidentifycandidategenes
associatedwithHDundershort‐andlong‐dayrice‐growingconditions.Furthermore,we
werealsointerestedindeterminingtheproportionofphenotypicvarianceexplainedby
oneoftheQTLsonchromosome7,validatingandfinemappingitspositionusingthe
BC5F2:3populationderivedfromacrossbetweenoneoftheCSSLsandtherecurrent
parent,identifyingcandidategenesnearthetargetQTL,anddeterminingitsactualeffect
inmutantsgeneratedthroughCRISPR/Cas9geneediting.
2.Results
2.1.PhenotypicandGenotypicAnalysisofCSSLs
Seventy‐sixCSSLsandthetwoparentswereevaluatedforHDundernaturalSD
(NSD)atHainanin2015‐2016andundernaturalLD(NLD)atHangzhouin2014‐2015for
twoseasons.TheXQZBmaturedabout32and20daysearlierthantheZH9308inthe
HangzhouandHainangrowingconditions,respectively(Figure1A,B;Table1).Thedays
toheadingof76CSSLsexhibited59to122daysinNLDsandfrom93to124daysinNSDs
(Figure1C–F;Table1).Overall,HDshowedcontinuousvariationinbothgrowing
conditionsbutskeweddistribution(Table1,Figure1).Thebroad‐senseheritabilitywas
computedfromallfourenvironments,Hainan,andHangzhou,andwere0.83,0.82,and
0.79,respectively(Table1).PC1andPC2fromtheprincipalcomponentanalysis(PCA)
accountedfor75.7%and15.5%,respectively(FigureS2),withmostCSSLsshowingan
averageheadingdateclusteredtogetherattheorigin.Highly‐significantpositive
correlationswereobservedamongthetestedenvironmentsforheadingdate(FigureS2).
Table1.Summaryofheadingdatesofparentsand76chromosomesegmentsubstitutionlines
(CSSLs)evaluatedundertwonaturalshort‐dayconditionsatHainanandlong‐dayconditionsat
Hangzhou.
Parentsb76CSSLsa
Year/LocationZH9308XQZBMinMaxMeanSDKurtosisSkewnessH
2014Hangzhou91.83±1.11**60.17±1.1060.40119.2287.128.895.21−0.230.79
2015Hangzhou88.33±0.50**56.67±0.5457.67124.2888.219.424.45–0.33
2015Hainan110.99±1.52**91.00±1.3196.57124.94110.873.944.330.630.82
2016Hainan109.67±1.24**91.44±1.6790.00122.80103.596.101.540.36
Combined
TraitMinMaxMeanσ2Gσ2GxEσ2ECVH2
HD80.77119.7897.4534.8624.918.983.080.83
aValuesforCSSLsareminimum(Min),maximum(Max),mean,standarddeviation(SD),and
repeatability(H2).bDataofparentsarepresentedasmean±SDwith**indicatingsignificant
differencesbetweenZH9308andXQZBatthep<0.01.

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Figure1.ComparisonofZH9308andXQZBparentswith**indicatingsignificantdifferencesatp<
0.01(A–B)andheadingdatedistributionofthe76chromosomesegmentsubstitutionlines(CSSLs)
basedonthebestlinearunbiasedprediction(BLUP)evaluatedattheHangzhouandHainan
growingconditions(C–F).
2.2.QTLAnalysisoftheCSSLs
ThegeneticlinkagemapoftheCSSLpopulationwasconstructedusing87simple
sequencerepeats(SSRs)and33insertion/deletion(InDel)markersthatfollowedthe1:1
Mendeliansegregationpattern(FigureS3).Atotalof120markersweredistributedacross
thewholegenomewithtotalcoverageof1311.02cmusingtheKosambifunctionof
IciMappingsoftware(FigureS3;TableS1).Inclusivecompositeintervalmapping
conductedontheBLUPHDdataofthefourenvironmentsusingaLODthresholdvalue
≥2.5identified14QTLsassociatedwithheadingdateonChr2(qHD2a),Chr4(qHD4aand
qHD4b),Chr5(qHD5a),Chr6(qHD6aandqHD6b),Chr7(qHD7bandqHD7c),Chr8
(qHD8a),Chr10(qHD10aandqHD10b),Chr11(qHD11),andChr12(qHD12aandqHD12b)

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(Table2).Theproportionofphenotypicvariance(PVE)explainedbyeachQTLranged
from0.4%to36.1%,andtheadditiveeffectfrom–15.4to18.2.OfthefourteenQTLs,only
qHD6aandqHD7bwereconsistentlydetectedinallfourenvironments,from10.1%to
36.1%(mean23.14%)andfrom8.1%to32.8%(mean20.5%),respectively.Theremaining
12QTLsweredetectedonlyin1or2environments(Table2).WethenfocusedonqHD7b
forfurtherresearchduetoitsconsistentdetectionnotonlyinallfourenvironmentsinthe
presentstudy,butalsointwotypesofmappingpopulationsinourpreviousstudy[23].
ThefavorableallelesofallQTLwithanegativeadditiveeffectoriginatedfromtheXQZB,
whilethosewithapositivealleleoriginatedfromZH9308.TheXQZBalleleattheqHD7b
leadstoearlyheadingunderbothNSDandNLDconditions(Figure1A,B;Table2).
Table2.ChromosomallocationsofputativeHDQTLsunderfourdifferentenvironmentsusing76
CSSLpopulations.
QTLsYear/locationaChr.Region(cM)FlankingmarkersLODbPVE(%)cAddd
qHD2a2015HZ219.77RM6424‐InD312.802.542.37
qHD4a2014HZ46.58InD62‐RM120538.899.8713.13
2015HZ410.54RM1205‐RM59796.464.501.75
qHD4b2015HZ421.08RM3839‐RM24111.339.148.79
qHD5a2014HZ525.20RM3638‐RM68412.590.45–0.47
2016HN514.52InD79‐RM36382.917.78–3.91
qHD6a2014HZ66.58RM5754‐RM596349.6719.0318.21
2015HN65.27RM510‐RM575411.1236.146.78
2015HZ66.58RM5754‐RM596313.1410.139.90
2016HN65.27RM510‐RM57548.8325.018.67
qHD6b2014HZ611.85RM20069‐InD943.770.330.36
qHD7b2014HZ727.69RM3859‐RM587554.4226.54–15.44
2015HN727.69RM3859‐RM58753.248.10–2.61
2015HZ727.69RM3859‐RM587526.5632.84–12.90
2016HN727.69RM3859‐RM58757.5520.33–6.76
qHD7c2015HZ721.13RM1132‐RM4552.562.790.88
qHD8a2014HZ87.91RM5556‐RM2252946.4016.12–12.03
2015HZ87.91RM5556‐RM2252915.9113.30–8.22
qHD10a2015HZ102.63InD133‐InD13512.279.14–13.28
2015HN102.63InD133‐InD1356.6718.74–7.37
qHD10b2016HN106.58RM6142‐RM56203.608.89–5.96
qHD11a2014HZ1110.54RM7463‐RM2665218.141.94–7.76
2015HZ1117.16RM26652‐InD1512.513.10–2.72
qHD12a2014HZ122.63InD156‐RM700315.422.21–6.10
qHD12b2014HZ1223.82InD165‐RM13002.850.43–0.44
aYear/Locationreferstotheyearoftheexperiment(2014,2015,and2016)followedbythelocation
(Hangzhou—HZ/Hainan—HN).bLogarithmofodd,ctheproportionofthephenotypicvariance
explainedbytheQTLeffect,dthesignoftheadditiveeffectsshowstheparentaloriginofthe
favorablealleles(negative=XQZBandpositive=ZH9308).
2.3.PhotoperiodicResponseofqHD7b
TheCSSL52isoneofthechromosomesegmentsubstitutionlines,whichcontainstwo
segmentsfromXQZBintheZH9308backgroundandharborstheearlyheadingalleleat
theqHD7bregionflankedbyRM3859andRM5875markers(FigureS4).ZH9308and
CSSL52wereevaluatedforfiveconsecutiveseasonsunderNLDandNSDconditionswith
differentdaylengthsandtemperatures(Figure2A–D).ThereweresignificantHD
differences(p<0.01)betweentheparentsinallthestudiedenvironments(Figure2E–G).
ZH9308headed24.6–26.4dayslaterthanCSSL52atHangzhouNLDconditions(Figure

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2E,G).AtHainanNSDconditions,ZH9308headed6.2–10.4dayslaterthanCSSL52(Figure
2F,G).Similarly,ZH9308hadahigherplantheightthanCSSL52underallfive
environments(Figure2H).Takentogether,ZH9308headedlaterthanCSSL52underboth
SDandLDconditions,andthephenotypicdifferencesofdaystoheadingweremore
significantunderLDconditions.Duetolongerdaystoheading,ZH9308alsoexhibiteda
tallerPH,longerpaniclelength,morenumbersofinternodes,longerinternodelength,a
greaternumberofpaniclesperplant,andamoresignificantnumberofgrainsinthemain
paniclethanCSSL52(FiguresS5andS6).

Figure2.ComparisonofheadingdateandplantheightofZH9308andCSSL52underfive
environmentalconditions.(A–D)Dailyphotoperiod(A,B)andmeantemperature(C,D)under
HangzhouandHainanconditionsin2020duringtherice‐growingseason.(E,F)Thephenotypeof
ZH9308andCSSL52underHangzhou(E)andHainan(F).ThephotowastakenattheCSSL52
headingstagein(E)andtheCSSL52maturationstagein(F).(G,H)Daystoheading(G)andplant

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height(H)comparisonbetweenparentsfrom2019–2021underNLDconditionsinHangzhouand
NSDconditionsinHainan.Theasterisks**indicatesignificancebetweentheparentsatthep<0.01,
accordingtoStudent’st‐test.
Headingdateshowedahighly‐significantpositivePearsoncorrelationwithplant
height(r=0.83,p<0.01),paniclelength(r=0.86,p<0.01),andnumberofgrainsinthe
mainpanicle(r=0.79,p<0.01)(TableS2).Plantheightshowedhighpositivecorrelations
withthepaniclelength(r=0.83,p<0.01)andnumberofgrainsinthemainpanicle(r=
0.80,p<0.01).Similarly,therewasalsoasignificantpositivecorrelationbetweenpanicle
lengthandnumberofgrainsinthemainpanicle(r=0.76,p<0.01)(TableS2).
2.4.QTLMappinginBC5F2:3Population
TheqHD7bwasinitiallydelimitedtothe7.1MbregionbetweentheRM3859and
RM5875markers(Table1).WeusedaBC5F2populationtovalidateandfinemapthe
qHD7bQTL,whichwasdevelopedbycrossingCSSL52thathastheearly‐headingallele
withtheZH9308parentandthenbackcrossingtheprogeniesfivetimeswiththeZH9308
todevelopasecondaryF2(BC5F2)populationforfinemappingqHD7b(FigureS7).
Usingalinkagemapof9markersneartheqHD7bQTLandheadingdataofasubset
of501BC5F2plants(Figure3)evaluatedfortwoconsecutiveseasonsunderHangzhou
NLDandtwoseasonsunderHainanNSDconditions(FigureS8),wemappedtheqHD7b
QTLbetweentheInDel4373andInDel3markers.TheQTLwasdetectedinallfour
environments(seasons)andwasbetween10.8%and41.1%ineachenvironment(mean=
26.0%),andhadaLODscorerangingfrom4.9to62.7(mean=33.8).UnderHangzhou
conditions,however,theqHD7bhadaverylargeeffect(31.5–41.1%)andmoresignificant
LODscores(59.8–62.7)thanintheHainanconditions(PVE=10.8–21.2%,LOD=4.9–7.5),
whichwasabouttwo‐foldgreaterinthemeanphenotypiceffectandnearlyten‐foldlarger
inthemeanLODscore(TableS3).Wethenclassifiedthe501BC5F2aslateandearly
headingandcalculatedthemeandifferenceinheadingdate.Theaveragedifference
betweentheearlyandlatesegregatingprogenieswas9.6and25.5daysunderNSDand
NLD,respectively(FigureS8).AChi‐squareanalysisperformedontheBC5F2population
fittheexpected3(late):1(early)ratio(386:115;χ2=0.52,p=0.47),indicatingthatqHD7b
behavesasasingledominantgenethatismorefunctionalunderLDconditionsthanSD
conditions.
2.5.FineMappingofqHD7b
TonarrowdowntheconfidenceintervaloftheqHD7bidentifiedusingthe501BC5F2
plants,weusedatotalof2997BC5F2:3individualsgenotypedwith7markersthatwere
polymorphicbetweentheZH9308andCSSSL52,aswellasthetwoflankingInDels
(InDel4373andInDel3)identifiedduringtheinitialmapping.Thegenotypedatarevealed
14homozygousrecombinants(Figure3D)thatbelongto4groups(G1=3plants,G2=5
plants,G3=4plants,andG4=2plants).TherecombinantplantsinG1hadthesame
headingdate(86.0d)astheZH9308parent(85.2d),whiletheremainingthree
recombinantgroupshadnearlythesameheadingdate(56.2–58.0d)astheCSSL52parent
(58.8d).Inthefinemapping,InDel4477,locatedat9075693bp,wastheclosestmarkerto
qHD7b,whileRM5436andRM5499weretheflankingmarkerslocatedat9075636bpand
9988139bponchromosome7.IncontrasttotheG1recombinantsthathadtheZH9308
parentgenomebetweenRM5436andRM5499attheqHD7binterval,theremainingthree
groupsofrecombinants(G2toG4)allinheritedtheCSSL52genome.Thephysicalinterval
betweenRM5436andRM5499markersspans912.7kb(Figure3D),whichwasconfirmed
using20BC5F3:4progenyfromeachrecombinantgroup.

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Figure3.CoarsemappingandfinemappingofqHD7bonchromosome7.(A)ThepositionofqHD7b
basedon76CSSLsgenotypedwith12molecularmarkersonchromosome7.(B)Thepositionof
qHD7bbasedon501BC
5
F
2
plantsgenotypedwith7markerslocatedbetweenRM3859andRM5875
(theflankingmarkersidentifiedusingtheCSSLs).(C)FinemappingofqHD7busingBC
5
F
2:3
plants
genotypedwith7markersthatmappedbetweenInDel4373andInDel3(theflankingmarkers
identifiedusingthe501BC
5
F
2
plants).(D)Genotypesandphenotypesofthetwoparents(ZH9308
andCSSL52)and14homozygousrecombinantlinesusedforfinemappingofqHD7b.TheZH9308
andCSSL52genotypicmarkersarerepresentedbywhiteandblackbars,respectively.The14
homozygousrecombinantsbelongtofourgroups(G1=3plants,G2=5plants,G3=4plants,and
G4=2plants).Thesuperscriptedletters(aandb)indicatestatisticallysignificantdifferencesinthe
headingdatesofrecombinantsrelativetotheparents.(E)Approximately29openreadingframes
(ORFs)werelocatedbetweenthetwoflankingmarkersidentifiedduringthefinemapping(RM5436
andRM5499),whicharesummarizedinTableS4.(F)SequencecomparisonbetweenZH9308and
CSSL52with5.984‐kbdeletioninCSSL52atOs07g0261200using7markers(M1toM7).Thedeleted
regioninCSSL52issignificant,andsevenmolecularmarkers(Ghd7‐M1toGhd7‐M7)linkedwith
qHD7bareamplifiedinZH9308.
2.6.CandidateGeneAnalysisofqHD7bandValidationUsingCRISPR/Cas9
Acandidategenesearchusingthephysicalpositionofthetwoflankingmarkers
identifiedduringthefinemapping(RM5436andRM5499)intheGramenedatabase
(https://www.gramene.org/(accessedon29August2022))usingtheOryzasativajaponica
groupreferencegenomeidentified29predictedgenes,ofwhich18hadOryzaindica
homologuesthatfellwithinthe912.7‐kbregion(7:9075636‐9988139)ofqHD7b(Figure3E
andTableS4).ORF4(Os07g0261200)isphysicallylocatedat9,152,377bponchromosome
7,encodestheCCTmotiffamilyprotein,andhasbeenannotatedasGhd7(Os07g0261200).
WethensequencedOs07g0261200inthetwoparentsusingsevenmarkers(M1toM7),
whichrevealeda5.984‐kbdeletionintheORF4regionintheCSSL52parentbutnotin

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ZH9308(Figure3F).TheexpressionlevelsofOs07g0261200inCSSL52werealsonearly
zeroascomparedwithZH9308,whichalsosuggeststhatGhd7isaprobableputative
candidategeneforqHD7b(FigureS9).
Tovalidatethemutantphenotype,weknockedoutGhd7intheNipponbaregenetic
backgroundutilizingtheCRISPR/Cas9system(Figure4A).TheHDofthewildtypewas
9.4dayslaterthantheghd7mutantunderNLDconditionsinHangzhou(Figure4B,C)and
2.0dayslaterunderNSDconditionsinHainan(Figure4C).Thewild‐typeshowed
significantdifferenceswiththeghd7mutantforHD,plantheight,andthenumberof
grainsperpanicle(Figure4D,E).

Figure4.Headingdateofwild‐type(WT)andghd7mutantintheNipponbaregeneticbackground.
(A)SchematicoftheGhd7genewiththesgRNA:Cas9targets(green)andcorresponding
protospacer‐adjacentmotifsequences(underlined).Theinsertionnucleotideisshownasaredletter.
(B)ThephenotypeofWTandmutantghd7attheheadingstageunderHangzhouconditions.(C)
DaystoheadingofWTandghd7undernaturallong‐dayHangzhouandnaturalshort‐dayHainan
conditions.(DandE)ComparisonoftheWTandghd7mutantforplantheight(D)andthenumber
ofgrainsinthemainpanicle(E)undernaturallong‐dayconditions.Thedataareexpressedasmean
values±SD.Theasterisks**indicatesignificancebetweenWTandghd7mutantatthep<0.01,as
determinedbyStudent’st‐test.
3.Discussion
Headingdateisoneofthemostimportantagronomictraitsandvarieswidelyinrice
dependingonthegeneticdifferencesamonggenotypes,environmentalconditions,day
length,temperature,andtheirinteractions[23].Aclearunderstandingofthegenetic
driversofheadingdatesisessentialforcultivatingriceindifferentgeographicalregions
andseasons[24].Numerousgeneticmappingstudieswereconductedtoidentifygenes
andQTLsassociatedwithheadingusingbi‐parentalpopulations,suchasF2,backcross,
doubledhaploidlines,RILs,andCSSLs[25,26].Hundredsofgenomicregionsrelatedto
HDhavebeenreportedinrice;however,fewhavebeenmappedandcloned[27].qHD7b
wasidentifiedusingtwotypesofpopulationsthatwere76CSSLsandaBC5F2population.
Using76CSSLlines,thepresentstudyconfirmedtheqHD7bQTLthatwepreviously
reportedbetweenmarkersRM5436,locatedat9075636bp,andRM3670,locatedat
13439924bp[22].However,thephysicalintervaloftheQTLwasaboutdoubleinthe

Plants2022,11,228810of15
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CSSLs(7120.8kb)ascomparedwiththepreviousstudy(4,364.3kb),whichislikelydue
tothesmallpopulationsizeoftheCSSLs.Theuseof501BC5F2plantsreducedthephysical
confidenceintervaloftheQTLto1245.9kb,followedby912.7kbwhenitwasfine‐mapped
using2997BC5F2:3plants(Figure3).RM5436andRM5499weretheflankingmarkersof
theqHD7bQTLafterfinemapping,whichwerealsopreviouslyreportedasflanking
markersforamajorQTL(qSSP7),therebycontrollingthenumberofspikeletsperpanicle
[28],andanothermajorQTL(qSE7),therebyinfluencingthestigmaexertionrate[29]in
rice.AcandidategenesearchconductedusingthephysicalintervaloftheqHD7b
(7:9075636‐9988139)andtheOryzasativajaponicagroupreferencegenomeinGramene
identifiedatotalof29candidategenes.Ghd7(Os07g0261200)isoneofthe29candidate
genes,whichhasbeenextensivelystudiedforitseffectoninfluencingheadingdate,grain
yield,plantheight,andotheragronomictraitsinrice[7,30].However,othermultiple
genesshouldalsobeexploredinthefuture.
OneofthechallengesinQTLmappingisidentifyingQTLsthatareconsistently
detectedacrossdifferentenvironments,whichwasnotthecaseforqHD7b.ThisQTLwas
consistentlydetectedinallenvironmentsregardlessofthetypeofmappingpopulations,
butitseffectandLODscorestendtobeveryerratic.TheLODscorefortheqHD7bvaried
from3.2to54.4inthe76CSSLsandfrom4.9to62.7inthe501BC5F2plants,whilethe
phenotypicvarianceexplainedbytheQTLvariedfrom8.1%to32.8%intheCSSLsand
from10.8%to41.1%intheBC5F2plants(Table2andTableS3).Apreviousstudyshowed
thattheQTLeffectdetectedbythedifferentmappingpopulationsandenvironmental
conditionsisnotnecessarilythesame[31].Inourcase,thediscrepanciesmaybedueto
differencesinthepopulationsizeand/orthetypeofmappingpopulations.CSSLsare
powerfulforQTLdiscoverystudiesduetothepresenceofmultipleoverlappingsegments
andseveralrecombinationevents[32].Still,thesmallsizeofthepopulationinthecurrent
studymayaffecttheQTLresults.TheBC5F2populationsize,ontheotherhand,wasideal
forQTLdiscoverystudiesintermsofpopulationsizebuthaslimitedrecombination
frequency,whichmakesitinferiorintermsofmappingresolutions.Thetwophenotyping
locationswerealsodifferentinbothtemperatureanddaylength,withHangzhou’s
showingahighertemperatureandlongerdaylengththanHainan(Figure2A–D),which
resultedinacleardifferenceinphenotypebetweentheparentsinHangzhou’sthan
Hainan(Figure2E–H)[33].Asaresult,theproportionofphenotypicvarianceexplained
byqHD7bwasverylowinHainaninboththeCSSLandBC5F2populations(Table2and
TableS3).Liuetal.[23]alsoreportedrelativelyloweffectsforqHD1binHainanthanin
Hangzhou.Thedifferencesinheadingdatesbetweenthewild‐typeandtheghd7mutant
werealsosmallerinHainanthanintheHangzhougrowingconditions,andrecentstudies
alsosupportthisresult[34].TheseresultssuggestqHD7basamajorHDQTLfunction,
mainlyunderLDconditions.
OursequencingresultrevealedthatattheGhd7locus,theqHD7bXQZBallelebelongs
toGhd7‐0,whichisnon‐functional,andtheqHD7bZH9308allelebelongstoGhd7‐4,whichis
functionaltogetherwithGhd7‐1,Ghd7‐2,andGhd7‐3[35].Thenon‐functionalMinghui63
alleleofGhd7showednon‐significantphenotypedifferencesunderSDconditions[7].
However,underSDconditions,theqHD7bXQZBallelefloweredearlierthantheqHD7bZH9308
allele(Figure2G).Thesephenotypicdifferencesmaybecausedbybackground
differences,indicatingqHD7balsofunctionsinSDconditions,buttheeffectissmallerthan
thatinLDconditions.ThetwoflankingmolecularmarkersforqHD7b(RM5436and
RM5499)andthesevenmolecularmarkersthatmappedwithintheQTLconfidence
interval(Ghd7‐M1locatedat9,150,263toGhd7‐M7locatedat9,155,572bp)cancontribute
towardstheeffortinthebreedingofricevarietiesusingmarker‐assistedselection(MAS).
Forexample,qHD7bZH9308couldbeusefulinbreedinglate‐maturingcultivars.Whenthe
ricecultivarswithGhd7‐0a,Ghd7‐0,andGhd7‐2allelesoriginatingfromnorthernChina
wereintroducedtosouthernChina,theirheadingdatewouldbesignificantlyearlier.The
qHD7bZH9308allelecouldbeintroducedintothesecultivarstoprolongtheirheadingdate
tomakethemhavedelayedheadingandincreasetheiryield.Onthecontrary,qHD7bXQZB

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couldbeusefulinbreedingearly‐maturingcultivars.WhenthericecultivarswithGhd7‐
1,Ghd7‐3,andGhd7‐4allelesoriginatingfromthetropicalandsubtropicalregionswere
introducedtonorthernChina,theirgrainscouldn’treachmaturityduetolaterheading.
TheqHD7bXQZBallelecouldbeintroducedintothesecultivarstomakeearlyheadingto
matureandharvestintime.
4.MaterialsandMethods
4.1.PopulationDevelopmentandPhenotyping
Thepresentstudywasconductedusingthreepopulations.Oneofthepopulations
wasdevelopedbycrossing134RILswithZhonghui9308(ZH9308),whichwasthen
backcrossedthreetimes,andselfedsixtimestoformBC4F6generation.TheRILswere
initiallydevelopedfromacrossbetweenanearly‐headingXieqingzaoB(XQZB)donor
parentandalate‐headingZH9308recipientparentandparentallinesofXieyou9308(an
indica‐japonicasubspeciessuperhybridricewith87.5%indicaand12.5%japonicagenome)
[22].Seventy‐sixofthe134BC4F6lineswereselectedtorepresentCSSLsforQTLmapping,
andthegenotypesofthe76CSSLswerealsoinvestigated[36].Thesecondpopulationwas
developedbycrossingoneoftheCSSLs(CSSL52)thatexhibitedearlyheadingwiththe
ZH9308parentandthenbackcrossingtheprogeniesfourtimeswiththeZH9308to
developasecondaryBC5F2populationforvalidationandaBC5F2:3populationforthefine‐
mappingoftheqHD7bQTL(FigureS1).
Asetof76CSSLsalongwithparentallines,ZH9308andXQZB,wereevaluatedfor
headingdatethroughaRandomizedCompleteBlock(RCB)designconsistingof3
replications,with4rows×8plantsforeachlineatHangzhouandHainanfor4seasons.
Eachplotconsistedof4rowsof1.32squaremeterswith16.5cm×26.5cmspacingbetween
plantsandrows.TheBC5F2population,alongwithZH9308andCSSL52parents,was
evaluatedfortwoyearsunderNLD(daylength>14h)conditionsinHangzhou,Zhejiang
Province(120.0°E,30.15°N),andNSD(daylength<12h)conditionsinLingshui,Hainan
Province(110.0°E,18.5°N).HDwasrecordedasthenumberofdaysfromthesowingdate
totheemergenceofthefirstheading.Plantheight(PH)wasmeasuredfromtheground
leveltothetipofthepanicleatfullphysiologicalmaturity.Internodelengthwasrecorded
asthelengthbetweentwonodes.Numberofpaniclesperplantwasrecordedasthe
numberofallpaniclesperplant.Paniclelength(PL)wasrecordedfromthenecktothe
apexofthepanicle.Thenumberofgrainsinthemainpaniclewasrecordedasthefilled
grainnumbersofthemainpanicle.Paddyfieldmanagementfollowedconventional
practices[37].
4.2.TestofDayLengthResponseinGrowthChambers
Toinvestigatethephotoperiodicresponse,ZH9308andCSSL52plantsweregrown
underCLD(14hlight,30°C/10hdarkness,25°C)andCSD(10hlight,30°C/14h
darkness,25°C).Thehumiditywas75%,andthelightintensitywas300μmolm−2s−1[38].
4.3.MolecularMarkersDevelopmentandDNAExtraction
PolymorphismsbetweenZH9308andCSSL52werescreenedusing
Insertion/Deletion(InDel)andSimpleSequenceRepeat(SSR)markers[39].Todetermine
thecandidategenesofqHD7bQTL,thesequencebetweenRM3859andRM5875was
downloadedfromtheEnsemblePlants(http://plants.ensembl.org/index.html(accessedon
29August2022))andGramenewebsite(https://www.gramene.org/(accessedon29
August2022))usingtheOryzasativajaponicagroupreferencegenomebyablastsearchof
theprimersequences.NewInDelmarkersintheQTLregionweredesignedbasedon
differencesingenomicsequencebetweenIndicaandJaponicausingthePrimerPremier
5.0software(PREMIERBiosoftInternational,CA,USA).ThemarkersarelistedinTables
S5andS6.Themarkersthatamplifiedthemutatedregionbetweenparentsarelistedin
TableS7.

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GenomicDNAwasextractedfromthefreshleavesofparentsandthesecondaryF2
(BC5F2)populationusingthecetyltrimethylammoniumbromide(CTAB)method
describedbyLuoetal.[40].Apolymerasechainreaction(PCR)wasperformedina12μL
volumethatconsistedof5μLofmastermix,3μLofddH2O,2μLof10pmolμL−1primers
(1μLforwardprimerandreverseprimers),and2μLoftemplategenomicDNA(200ng).
ThePCRamplificationprotocolconsistedofapre‐denaturationstep(95°Cfor3min),
followedby32cycles(denaturationat95°Cfor15s,annealingat55°Cfor15s,and
extensionat72°Cfor5s),andfinalextension(72°Cfor10min).ThePCRproductswere
separatedusinggelelectrophoresison8%non‐denaturingpolyacrylamidegeland
visualizedwithsilvernitratestainingusingaformaldehydesolution[41].
4.4.RNAExtractionandqRT‐PCR
ThetotalRNAwasextractedfromleavesofZH9308andCSSL52usinganRNAprep
PurePlantkit(TiangenBiotechCo.Ltd.,Beijing,China).Atotalof50μLof
complementaryDNA(cDNA)wassynthesizedusing5μgofRNAwithReverTraAce®
qPCRRTMasterMixwithgDNARemover(ToyoboCo.Ltd.,Osaka,Japan).Real‐time
quantitativeRT‐PCR(RT‐qPCR,20μLreactionvolume)wasperformedusing0.5μLof
cDNA,0.2μMofeachgene‐specificprimer,andTBGreenPremixExTaqII(TakaraBio,
Inc.,Kusatsu,Shiga,Japan)inaLightCycler®480II(Roche).ThericeUbqgene
(Os03g0234350)wasexploitedastheendogenouscontrol.TheprimersforqRT‐PCRwere
designedusingGeneScript(https://www.genscript.com/tools/real‐time‐pcr‐taqman‐
primer‐design‐tool)andaredisplayedinTableS7.
4.5.Generationofghd7MutantUsingCRISPR/Cas9System
TheCRISPR/Cas9systemwasusedtoknockoutGhd7accordingtothemethodsas
describedpreviously[42].The18‐bpsgRNA:Cas9targetsequenceofGhd7wasintroduced
intothepCas9‐sgRNAvectorattheAarIsite.Thefinalvectorwastransformedinto
NipponbareusingAgrobacterium‐mediatedtransformation[43].Theprimersusedare
displayedinTableS7.
4.6.StatisticalAnalysis
Theexperimentaldesignineachenvironmentwasarandomizedcompleteblock
designwiththreereplicationsperenvironment/location.Thebestlinearunbiased
prediction(BLUP)valueswereobtainedthroughMETA‐Rv6.03[44],usingthelinear
model:
Yik=μ+Repi+Genk+εik(withintheenvironment)
Yijk=μ+Repi(Envj)+Envj×Genk+Genk+Envj+εijk(acrossenvironments)
whereYikisthetraitofinterest,μisthemeaneffect,Repiistheeffectoftheithreplicate,
Genkistheeffectofthekthgenotype,εikistheerrorassociatedwiththeithreplication,and
thekthgenotype,whichisassumedtobenormallyandindependentlydistributed.For
acrossenvironments,Yijkisthetraitresponse,Envjisthejthenvironment,Repi(Envj)is
theeffectofithreplicationinthejthenvironment,andEnvj×Genkistheenvironmentand
genotypeinteraction.Theresultinganalysisproducedtheadjustedtraitphenotypic
valuesintheformofBLUPwithinandacrossenvironments.TheBLUPmodelconsiders
genotypesasrandomeffects.Broadsenseheritability(H2)andrepeatability(H)were
calculatedaccordingtoAlemuetal.[45]usingMETA‐Rsoftware.
H= σ 2g
σ 2g + σ 2e /reps (within the environment)
H= σ
2
g
σ 2g + σ 2 ge /env + σ 2 e/(reps × env) (across environment)

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whereσ
2gandσ
2earethegenotypicanderrorvariance,σ
2geisthegenotypeby
environmentinteractionvariance,repisthenumberofreplicates,andenvisthenumber
ofenvironments.
QTLanalysiswasperformedusingtheinclusivecompositeintervalmapping(ICIM)
functionimplementedinQTLIciMappingsoftware[46].ALODthresholdvalue≥2.5
indicatesthepresenceofQTL(selectedby1000permutationteststoobtaina0.05genome‐
wideprobabilitylevelofTypeIerror,withasearchstepof1cm).QTLswerenamedby
placinga“q”atthebeginningofthetrait“HD”,followedbythechromosomenumber.
FormorethanoneQTLonthesamechromosome,asecondidentifierwasplacedafterthe
chromosomenumberreportedpreviously[47].
5.Conclusions
Atotaloffourteensignificant(LOD≥2.5)HDQTLs(qHD2a,qHD4a,qHD4b,qHD5a,
qHD6a,qHD6b,qHD7b,qHD7c,qHD8a,qHD10a,qHD10b,qHD11a,qHD12a,andqHD12b)
weredetectedinthe76CSSLpopulationsconcerningthepositionandintrogression
segmentsunderfourdifferentenvironments.WefocusedonqHD7bforfurtherresearch
duetoitsstability.AsecondaryF2(BC5F2)populationwasdevelopedbybackcrossing
CSSL52withrecurrentparentZH9308,andqHD7bwasnarroweddowntothe912.7‐kb
region,flankedbymarkersRM5436andRM5499using2995individualsfromthe
secondaryF2:3(BC5F2:3)population.TheCSSL52alleleattheqHD7blocusnegatively
regulatesHDunderSDandLDconditions.Sequencingandexpressionanalysis
demonstratedthatOs07g0261200encodesGhd7,asuitablecandidategeneforqHD7b.The
ghd7mutantgeneratedthroughCRISPR/Cas9promotedtheheadingdateandvalidated
Ghd7asaputativecandidategeneforHD.FurtherstudyonqHD7bwillcontributetoMAS
andthedevelopinglate‐maturingvarietiesthatcanbeusedindiversegeographical
regions.
SupplementaryMaterials:Thefollowingsupportinginformationcanbedownloadedat:
www.mdpi.com/article/10.3390/plants11172288/s1,FigureS1:BreedingschemeforQTL
identificationandfinemapping,FigureS2:GGEBiplotofdaystoheadingfrom76CSSLstestedin
fourenvironments,FigureS3:Linkagemapof76CSSLsderivedfromZH9308×XQZBusing120
polymorphicmarkers,FigureS4:AschematicrepresentationofZH9308,XQZB,andCSSL52plants
toshowdifferencesonchromosome7nearqHD7b,FigureS5:Agronomictraitphenotypesof
ZH9308andCSSL52,FigureS6:MeasurementofagronomictraitsofZH9308andCSSL52,Figure
S7:PhenotypesandgenotypesofZH9308,CSSL52,andsecondaryF2(BC5F2)population,FigureS8:
FrequencydistributionofheadingdateinthesecondaryF2(BC5F2)populationunderHainanand
Hangzhouconditions,FigureS9:TheexpressionlevelsofOs07g0261200inZH9308andCSSL52,
TableS1:Chromosome‐wiseSNPmarkersandgeneticmaplengthofriceCSSLpopulation,Table
S2:Pearsoncorrelationcoefficientsamongheadingdateandyield‐relatedtraits,TableS3:
EvaluationofheadingdateQTLqHD7bunderHainanandHangzhouconditions,TableS4:
Candidategeneswithin912.7‐kbphysicalregionsofqHD7bonchromosome7,TableS5:
PolymorphicDNAmarkersusedinheading‐dateQTLanalysisin76CSSLsandthesecondaryF2
(BC5F2)population,TableS6:DNAmarkersusedinQTLanalysisandfinemappingofqHD7b,Table
S7:Markersusedforsequencing,qRT‐PCR,andCRISPR.
AuthorContributions:Conceptualization,W.W.,Y.Z.,S.C.andL.C.;methodology,W.W.;software,
A.S.;investigation,A.S.,L.S.,L.L.,A.I.,Z.Y.,Q.Y.,G.B.A.,P.X.,R.M.K.,J.L.andX.S.;resources,Y.Z.;
writingoriginaldraftpreparation,A.S.;writingreviewandediting,A.S.andW.W.;supervision,
W.W.;projectadministration,W.W.;fundingacquisition,W.W.Allauthorshavereadandagreed
tothepublishedversionofthemanuscript.
Funding:ThisresearchwassupportedbygrantsfromtheNationalKeyR&DProgramofChina
(2020YFE0202300), theNationalNaturalScienceFoundationofChina(31871604,32071996,and
31961143016),theFundamentalResearchFundsofCentralPublicWelfareResearchInstitutions
(CPSIBRF‐CNRRI‐202102),HainanYazhouBaySeedLab(B21HJ0219),andtheAgriculturalScience
andTechnologyInnovationProgramoftheChineseAcademyofAgriculturalSciences(CAAS‐
ASTIP2013‐CNRRI).

Plants2022,11,228814of15
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InstitutionalReviewBoardStatement:Notapplicable.
InformedConsentStatement:Notapplicable.
DataAvailabilityStatement:Notapplicable.
ConflictsofInterest:Theauthorsdeclarenoconflictofinterest.
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