Genome mapping and molecular breeding in plants / [Vol. 1], Cereals and millets / Chittaranjan Kole (ed.) PDF
Preview Genome mapping and molecular breeding in plants / [Vol. 1], Cereals and millets / Chittaranjan Kole (ed.)
Genome 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 Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerial isconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broad- casting,reproductiononmicrofilmorinanyotherway,andstorageindatabanks.Duplicationof thispublicationorpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLaw ofSeptember9,1965,initscurrentversion,andpermissionsforusemustalwaysbeobtainedfrom Springer.ViolationsareliableforprosecutionundertheGermanCopyrightLaw. SpringerisapartofSpringerScience+BusinessMedia springer.com ©Springer-VerlagBerlinHeidelberg2006 Theuseofgeneraldescriptivenames,registerednames,trademarks,etc.inthispublicationdoesnot imply, even in theabsence of a specific statement, thatsuchnames are exempt from the relevant protectivelawsandregulationsandthereforefreeforgeneraluse. Editor:Dr.SabineSchreck,Heidelberg,Germany DeskEditor:Dr.JuttaLindenborn,Heidelberg,Germany Coverdesign:design&production,Heidelberg,Germany Typesettingandproduction:LE-TEXJelonek,Schmidt&VöcklerGbR,Leipzig,Germany 39/3100/YL 543210–Printedonacid-freepaper 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
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