Table Of ContentGenome Mapping and Molecular Breeding in Plants
Volume1
SeriesEditor:ChittaranjanKole
VolumesoftheSeries
GenomeMappingandMolecularBreedinginPlants
Volume1
CerealsandMillets
Volume2
Oilseeds
Volume3
Pulses,SugarandTuberCrops
Volume4
FruitsandNuts
Volume5
Vegetables
Volume6
TechnicalCrops
Volume7
ForestTrees
Chittaranjan Kole (Ed.)
Cereals and Millets
With25Illustrations,3inColor
123
ChittaranjanKole
DepartmentofHorticulture
316TysonBuilding
ThePennsylvaniaStateUniversity
UniversityPark,PA16802
USA
e-mail:[email protected]
LibraryofCongressControlNumber:2006926542
ISBN-10 3-540-34031-9 SpringerBerlinHeidelbergNewYork
ISBN-13 978-3-540-34031-7 SpringerBerlinHeidelbergNewYork
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Preface to the Series
Genomesciencehasemergedunequivocallyastheleadingdisciplineofthisnew
millennium.Progressinmolecularbiologyduringthelastcenturyhasprovided
criticalinputsforbuildingasolidfoundationforthisdiscipline.However,ithas
gained fast momentum particularly in the last two decades with the advent of
geneticlinkagemappingwithRFLPmarkersinhumansin1980.Sincethenithas
been flourishingat a stupendouspace withthedevelopment of newly emerging
tools and techniques. All these events are due to the concerted global efforts
directedatthedelineationofgenomesandtheirimprovement.
Geneticlinkagemapsbasedonmolecularmarkersarenowavailableforalmost
allplantsofsignificantacademicandeconomicinterest, andthelistofplantsis
growingregularly.Alargenumberofeconomicgeneshavebeenmapped,tagged,
cloned,sequenced,orcharacterizedforexpressionandarebeingusedforgenetic
tailoring of plants through molecular breeding. An array of markers in the ar-
senal from RFLP to SNP; tools such as BAC, YAC, ESTs, and microarrays; local
physicalmapsoftargetgenomicregions;andtheemploymentofbioinformatics
contributingtoallthe“-omics”disciplinesaremakingthejourneymoreandmore
enriching.Mostnaturally,theplantswecommonlygrowonourfarms,forests,or-
chards,plantations,andlabshaveattractedemphaticattention,anddeservedlyso.
Thetwo-wayshuttlingfromphenotypetogenotype(orgene)andgenotypte(gene)
tophenotypehasmadethecanvasmuchvaster.Onecouldhaveeasilycompiledthe
vitalinformationongenomemappingineconomicplantswithinsome50pagesin
the1980sorwithin500pagesinthe1990s.Inthemiddleofthefirstdecadeofthis
century,even5,000pageswouldnotsuffice!Clearlygenomemappingisnolonger
a mere “promising” branch of the life science; it has emerged as a full-fledged
subject in its own right with promising branches of its own. Sequencing of the
Arabidopsisgenomewascompletein2000.Theearly21stcenturywitnessedthe
completegenomesequenceofrice.Manymoreplantgenomesarewaitinginthe
wingsofthenationalandinternationalgenomeinitiativesonindividualplantsor
families.
Thehugevolumeofinformationgeneratedongenomeanalysisandimprove-
mentisdispersedmainlythroughoutthepagesofperiodicalsintheformofreview
papersorscientificarticles.Thereisaneedforareadyreferenceforstudentsand
scientistsalikethatcouldprovidemorethanjustaglimpseofthepresentstatus
ofgenomeanalysisanditsuseforgeneticimprovement.Ipersonallyfeltthegap
sorely when I failed to suggest any reference works to students and colleagues
interested in the subject. This is the primary reason I conceived of a series on
genomemappingandmolecularbreedinginplants.
Thereisnotasingleorganismonearththathasnoeconomicworthorconcern
forhumanity.Informationongenomesoflowerorganismsisabundantandhighly
usefulfromacademicandappliedpointsofview.Informationonhigheranimals
including humans is vast and useful. However, we first thought to concentrate
only on the plants relevant to our daily lives, the agronomic, horticultural and
technical crops, and forest trees, in the present series. We will come up soon
withcommentariesonfoodandfiberanimals,wildlifeandcompanionanimals,
laboratory animals, fishes and aquatic animals, beneficial and harmful insects,
VI PrefacetotheSeries
plant- and animal-associated microbes, and primates including humans in our
next“genomeseries”dedicatedtoanimalsandmicrobes.Inthisseries,82chapters
devoted to plants or their groups have been included. We tried to include most
oftheplantsinwhichsignificantprogresshasbeenmade.Wehavealsoincluded
preliminaryworksonsomeso-calledminorandorphancropsinthisseries.We
would be happy to include reviews on more such crops that deserve immediate
nationalandinternationalattentionandsupport.Theextentofcoverageinterms
ofthenumberofpages,however,hasnothingtodowiththerelativeimportanceof
aplantorplantgroup.Nordoesthesequenceofthechaptershaveanycorrelationto
theimportanceoftheplantsdiscussedinthevolumes.Asimpleruleofconvenience
hasbeenfollowed.
Ifeelmyselffortunatetohavereceivedhighlypositiveresponsesfromnearly
300scientistsofsome30-pluscountrieswhocontributedthechaptersforthisse-
ries.Scientistsactivelyinvolvedinanalyzingandimprovingparticulargenomes
contributedeachandeverychapter.Ithankthemallprofoundly.Imadeaconsci-
entiousefforttoassemblethebestpossibleteamofauthorsforcertainchapters
devoted to the important plants. In general, the lead authors of most chapters
organizedtheirteams.Iextendmygratitudetothemall.
Thenumberofplantsofeconomicrelevanceisenormous.Theyareclassified
fromvariousangles.Ihavepresentedthemusingthemostconventionalapproach.
The volumes thus include cereals and millets (Volume I), oilseeds (Volume II),
pulse, sugar and tuber crops (Volume III), fruits and nuts (Volume IV), vegeta-
bles (Volume V), technical crops including fiber and forage crops, ornamentals,
plantationcrops,andmedicinalandaromaticplants(VolumeVI),andforesttrees
(VolumeVII).
A significant amount of information might be duplicated across the closely
relatedspeciesorgenera,particularlywhereresultsofcomparativemappinghave
beendiscussed.However,somereaderswouldhavelikedtohavehadachapteron
a particular plant or plant group complete in itself. I ask all the readers to bear
withmeforsuchredundancy.
Obviouslythecontentsandcoverageofdifferentchapterswillvarydepending
on the effort expended and progress achieved. Some plants have received more
attention for advanced works. We have included only introductory reviews on
fundamentalaspectsonthemsincereviewsintheseareasareavailableelsewhere.
On other plants, including the “orphan” crop plants, a substantial amount of
informationhasbeenincludedonthebasicaspects.Thisapproachwillbereflected
intheillustrationsaswell.
Itismainlymyresearchstudentsandprofessionalcolleagueswhosparkedmy
interestinconceptualizingandpursuingthisseries.Ifthisseriesservesitspurpose,
thenthemajorcreditgoestothem.Iwouldneverhaveventuredtotakeupthis
hugetaskofeditingwithouttheirconstantsupport.Workingandinteractingwith
manypeople,particularlyattheLaboratoryofMolecularBiologyandBiotechnol-
ogyoftheOrissaUniversityofAgricultureandTechnology,Bhubaneswar,India
asitsfounderprincipalinvestigator;theIndo-RussianCenterforBiotechnology,
Allahabad,Indiaasitsfirstprojectcoordinator;thethen-USSRAcademyofSci-
encesinMoscow;theUniversityofWisconsinatMadison;andThePennsylvania
State University, among institutions, and at EMBO, EUCARPIA, and Plant and
AnimalGenomemeetingsamongthescientificgatheringshavealsoinspiredme
andinstilledconfidenceinmyabilitytoaccomplishthisjob.
I feel very fortunate for the inspiration and encouragement I have received
frommanydignifiedscientistsfromaroundtheworld,particularlyProf.Arthur
PrefacetotheSeries VII
Kornberg,Prof.FranklinW.Stahl,Dr.NormanE.Borlaug,Dr.DavidV.Goeddel,
Prof. Phillip A. Sharp, Prof. Gunter Blobel, and Prof. Lee Hartwell, who kindly
opinedontheutilityoftheseriesforstudents,academicians,andindustryscientists
ofthisandlatergenerations.Iexpressmydeepregardsandgratitudetothemall
forprovidinginspirationandextendinggenerouscomments.
IhavebeenespeciallyblessedbyGodwithanaffectionatestudentcommunity
andverycordialresearchstudentsthroughoutmyteachingcareer.Iamthankful
toallofthemfortheirregardsandfeelingsforme.Iamgratefultoallmyteachers
and colleagues for the blessings, assistance, and affection they showered on me
throughoutmycareeratvariouslevelsandplaces.Iamequallyindebtedtothefew
criticswhohelpedmetobecomeprofessionallysounderandmorallystronger.
MywifePhullaraandourtwochildrenSouravandDevleenahavebeenofgreat
help to me, as always, while I was engaged in editing this series. Phullara has
takenpains(“pleasure”shewouldsay)allalongtoassumemostofmydomestic
responsibilitiesandtoallowmetodevotemaximumpossibletimetomyprofes-
sional activities, including editing this series. Sourav and Devleena have always
shownmaturityandpatienceinallowingmetoremaingluedtomyPCor“printed
papers”(“P3”astheywouldsay).Forthisseries,theyassistedmewithInternet
searches,maintenanceofallhardandsoftcopies,andvarioustimelyinputs.
Somefiguresincludedbytheauthorsintheirchapterswerepublishedelsewhere
previously.Theauthorshaveobtainedpermissionfromtheconcernedpublishers
orauthorstousethemagainfortheirchaptersandexpresseddueacknowledge-
ment.However,asaneditorIrecordmyacknowledgementstoallsuchpublishers
andauthorsfortheirgenerosityandgoodwill.
Ilookforwardtoyourvaluablecriticismsandfeedbackforfurtherimprove-
mentoftheseries.
Publishingabookserieslikethisrequiresdiligence,patience,andunderstand-
ing on the part of the publisher, and I am grateful to the people at Springer for
havingallthesequalitiesinabundanceandfortheirdedicationtoseeingthisseries
throughtocompletion.Theirprofessionalismandattentiontodetailthroughout
theentireprocessofbringingthisseriestothereadermadethemagenuineplea-
suretoworkwith.Anyenjoymentthereadermayderivefromthisbooksisduein
nosmallmeasuretotheirefforts.
UniversityPark, ChittaranjanKole
Pennsylvania,
10January2006
Preface to the Volume
Cereals and millets form the leading group of economic plant species. Many of
themhaveagloriouspastwithrecordsoftheirdomesticationintheearliestcivi-
lizationsandarementionedinancientwritingstheworldover.Theyarethestaple
foodformostoftheearth’spopulationandhaveattractedmostoftheattentionof
plantscientists.Someofthemhavecontributedimmenselytothediscoveryorre-
inforcementofmanyconceptsingeneticsandstrategiesofbreeding.Forexample,
maizewasamodelplantingeneticsandbreedinginthelastcenturyandcouldbe
calledthe“plantDrosophila”.Itledtoconceptssuchaslinkagemapping,cytoplas-
micinheritance,somaticcrossover,mutation,chromosomalaberration,heterosis,
and,mostimportantly,transposableelements.Inthemoderneraalso,maizeand
rice were among the first plant species to have molecular genetic linkage maps.
Theso-calledgrassfamilywaselegantlyusedtoelucidategenomehomologyand
synteny,withriceatthecenterofthecircle.Rice,withitssmall,simplegenome,
isamodelplanttodayandhasprideofplaceinbeingthefirstcropplanttohave
its complete genome mapped.Thanks tothe Rockefeller Foundation, enormous
progress hasbeen madein ricegenome research, particularlyin thedeveloping
nations of Asia and Africa, which in fact laid the foundation for biotechnology
researchinthesecountriesandfacilitatedinfrastructureandhumanresourcede-
velopment.Theliteratureonthemajorcerealcropssuchasrice,wheat,maize,and
barleyisvoluminous.Othercerealslikeoat,rye,sorghum,andthemilletsstandin
sharpcontrast.Wehavemilestogotodepicttheirgenomesandimproveuponthem
consideringthepreferenceandpotentialofthesecropsinsomeedaphoclimates.
Deliberations on genome mapping and molecular breeding in some cereals,
particularlyrice,wheat,andmaize,wouldrequireatleastacompletevolumefor
each crop. It is widely recognized that a hundred pages or so on each of these
cerealscannotdothemjustice.Theauthorshaverightlydevotedmorepagestothe
advancedstudiesonthesecrops;reviewsonthebasicstudiesonthemarewidely
available.Bycontrast,roadmapsforgenomeresearchonothercerealsandmillets
havebeenthoroughlydelineatedbytheauthors.
Theauthorsofthisvolume’schaptershavemadetremendouscontributionsto
thestudyofthecroptowhichtheirrespectivechaptersaredevoted,aswellasto
thestudyofrelatedcrops.Thismadethedeliberationsnotjustcomprehensivebut
philosophicalaswell.Thelong,evenlifetime,experienceofmostofthemmadethe
experimentsandexamplescitedespeciallypertinent.Iwasglued,Imustconfess,
to the manuscripts during the many long days (and nights) spent as I mentally
preparedmyselftoeditthechaptersoftheseesteemedscientists.Evenduringthe
reviewofthesereviews,Iwasastudentfirst,aneditorlater,andareaderlast!Iam
verygratefultothemforgivingmethisuniqueopportunity.
Weareallawareofthefastpaceatwhichtheideas,strategies,anddatabases
oncerealsandmilletsarebeinggenerated.Theauthorstookpains(andpleasure!)
toupdatetheirchapters atleast twoor threetimes. Finallywehadthefinalized
chapters in hand, knowing full well that, regardless of when the volume was
published,itwouldbemissing“theverylatest”.Andsoitgoesforallthesciences;
otherwisetheywouldnotbecalledscience.
X PrefacetotheVolume
Editingthisvolumehasgoneverysmoothlythankstoallthekindheartedand
highlyprofessionalauthors.Manyofthecontributingauthorsinthisvolumeare
my personal friends as well. My own works on molecular mappingstarted with
cerealcrops,andIretainanostalgicloveforthem.Manyofmyresearchstudents
worked with me on rice, and some of them are pursuing their own research on
this crop. Editing this volume was therefore highly enriching and enjoyable for
me thanks to the interactions and intellectual exchanges from the authors, old
colleagues,andresearchstudents.
Ilookforwardtoreceivingsuggestionsfromyou,thereader,foranupdated
secondeditionofthisvolume.
UniversityPark, ChittaranjanKole
Pennsylvania,
10January2006
Contents
Contributors ....................................................... XVI
Abbreviations...................................................... XXI
1 Rice
P.K.Subudhi,T.Sasaki,G.S.Khush .................................... 1
1.1 Introduction................................................... 1
1.1.1 TaxonomyandOriginofCultivatedRice ................... 1
1.1.2 DispersalofCultivatedRice .............................. 2
1.1.3 VarietalDiversityofRice................................. 3
1.1.4 RiceVarietalImprovement ............................... 4
1.1.5 Rice-BreedingChallengesinthe21stCentury............... 5
1.2 ConstructionofMolecularLinkageMapsinRice ................... 6
1.3 MolecularMappingofSimple
andComplexTraitsinRice ...................................... 16
1.3.1 DiseaseResistance ...................................... 17
1.3.2 InsectResistance........................................ 20
1.3.3 TraitsRelevantforHybridRiceBreeding ................... 22
1.3.4 GrainQuality........................................... 26
1.3.5 AbioticStressTolerance.................................. 27
1.3.6 ImportantAgronomicTraits.............................. 37
1.3.7 QTL×EnvironmentInteraction .......................... 44
1.3.8 UtilizationofWildSpeciesforMapping
andIntrogressionofAgronomicTraits..................... 45
1.4 MolecularCharacterizationofRiceGermplasm .................... 45
1.5 ProgressinMarker-AssistedBreeding ............................ 46
1.5.1 MASforDiseaseResistance .............................. 47
1.5.2 MASforInsectResistance................................ 47
1.5.3 MASforGrainQuality................................... 50
1.5.4 MASinHybridRiceBreeding............................. 50
1.5.5 GenePyramiding ....................................... 51
1.5.6 MASforOtherTraitsandQTL ............................ 51
1.5.7 MASforIntrogressionofAlienGenes...................... 52
1.6 Map-BasedCloningofRiceGenes
andQTL ...................................................... 52
1.7 AdvancedWorks ............................................... 55
1.7.1 RicePhysicalMaps ...................................... 55
1.7.2 ToolsforRiceFunctionalGenomics ....................... 56
1.7.3 DNAMicroarray ........................................ 56
1.7.4 InsertionalMutagenesis.................................. 57
1.8 FutureScopeofWork........................................... 58
References .......................................................... 60
2 Wheat
R.K.Varshney,H.S.Balyan,P.Langridge ............................... 79
2.1 Introduction................................................... 79
2.2 MolecularMarkers–TypesandAvailability ....................... 80
