Chapter21
Sugarcane:AMajorSourceofSweetness,Alcohol,andBio-energy
AngéliqueD’Hont,GlauciaMendesSouza,MarceloMenossi,
MichelVincentz,Marie-AnneVan-Sluys,JeanChristopheGlaszmann,andEugênioUlian
AbstractSugarcaneisanimportanttropicalcrophavingC4carbohydratemetabolismwhich,alliedwithitsperennialnature,makesitoneofthemostpro-ductivecultivatedplants.Itismostlyusedtoproducesugar,accountingforalmosttwothirdsofworldproduction.Recentlyithasgainedincreasedattentionbecauseofitsimportantpotentialforbio-fuelproduction.However,sugarcanehasoneofthemorecomplexcropgenomes,whichhaslonghamperedthedevelopmentofsugarcanegeneticstosupportbreedingforcropimprovementprograms.SugarcanebelongstothegenusSaccharumL,partofthePoaceaefamilly(Grasses)andtheAndropogonaetribe,whichencompassesonlypolyploidspecies.Withtheadventofmoleculargenomics,thesugarcanegenomehasbecomelessmysterious,althoughitscomplexityhasbeencon?rmedinmanyaspects.Shortcutstogenomicanalyseshavebeenidenti?edthankstosyntenyconservationwithothergrasses,inparticularsorghumandrice.Overtime,newtoolshavebecomeavailableforunderstandingthemolecularbasesbehindsugarcaneproductivityandarenewedinteresthassurfacedinitsgeneticsandphysiology.
21.1Introduction
21.1.1Economic,Agronomic,andSocietalImportance
ofSugarcane
Sugarcanehasbeenthemainplantsourceofsweetenerforhumansforseveralmil-lennia.Itisabletopartitioncarbontosucroseinthestem,avegetativeorgan,incontrastwithothercultivatedgrassesthatusuallyaccumulatetheirreserveproducts
A.D’Hont
CIRAD,(CentredeCoopérationInternationaleenRechercheAgronomiquepourleDéveloppement),UMR1096,AvenueAgropolis,TA40/03,F-34398Montpellier,Francee-mail:angelique.dhont@cirad.fr
P.H.Moore,R.Ming(eds.),GenomicsofTropicalCropPlants??CSpringer2008
483
484A.D’Hontetal.
inseeds.Thisalmostuniquefeaturewasselectedbymanwho?rstuseditssoftwateryculmforchewing.
SugarcanebelongstothegenusSaccharumL.,whichispartofthePoaceaefamily(Grasses)andtheAndropogonaetribe.Thereference,domesticatedspeciesforsugarcaneisSaccharumof?cinarum(alsocallednoblecane).S.of?cinarumisagroupofthick,juicycanesthatwereinitiallycultivatedinSoutheastAsiaandthePaci?cIslandsbeforespreadingovertheinter-tropicsbetween1500and1000BC(DanielsandRoach1987).InChinaandIndia,S.of?cinarumcrossedwithwildrelativestoformthenaturalhybridsS.sinense(Chinesecanes)andS.barberi(NorthIndiancanes)thatwerethenselectedandcultivated.Sugarextractionprobablyde-velopedinIndiaandChinafromsuchhybrids(DanielsandDaniels1975).SugarmanufacturingappearedinPersiaaround500AD.AfewclonesofS.barberiorhybridsbetweenS.of?cinarumandS.barberiwereprobablytakenfromIndiaviaPersiainthe6thcentury,arrivingintheMediterraneanandSpainbythe8thcentury.FromtherethePortuguesetookittoMadeirainthe15thcentury,fromwhenceitspreadtootherislandsandWestAfrica.SugarcanereachedtheAmericasin1493whenColumbustookittotheDominicanRepublic,andthePortugueseplanteditinBrazilintheearly16thcentury.Inthe16thcentury,sugarproductionforworldtradeprogressivelychangedfromcottageindustriesbasedonS.sinenseandS.barberi,toplantationandfactoryindustriesbasedonselectedclonesofS.of?cinarum(DanielsandRoach1987).Neartheendofthe19thcentury,S.spontaneum,awildspeciesproducingnosugar,withthinstalks,aswellasafew“NorthIndian”sugarcaneswereusedinJavaandIndiainbreedingprogramsaimedatovercomingdiseasesusceptibilitiesaffectingS.of?cinarum.Interspeci?chybridizationwasthemajorbreakthroughinmodernsugarcanebreeding.Hybridizationnotonlysolvedmanyofthediseaseproblemsbutitalsoprovidedincreasedyields,improvedratooningability,andadaptabilityforgrowthundervariousabioticstresses(Roach1972).Allmodernsugarcanecultivarshavebeenderivedessentiallyfromafewroundsofintercrossingfromthose?rstinterspeci?chybrids(Arceneaux1967;Price1965).Commercially,sugarcaneispropagatedvegetativelyviastemcuttings.Germina-tionofthelateralbudsproducesnewplantsthatbranchintostoolsconsistingofalargenumberoftillers.Undergoodgrowthconditions,theplantwillgrow4–5me-tersin12months,withtheextractableculmsmeasuring2–3metersandcontaining13–16%sucrose.Becauseitisaperennialcrop,afterharvestandundertherightgrowingconditions,undergroundbudswillsproutgivingrisetoanewcrop.Inmostsituations,fourtosixcropsareharvestedbeforetheyieldsbecomeeconomicallyunsustainableandthe?eldisrenewedwiththeplantingofanewcrop.
Sugarcaneiscurrentlycultivatedonmorethan20millionhectaresintropicalandsubtropicalregionsoftheworld,producingupto1.3billionmetrictonsofcrushablestems.Itismostlyusedtoproducesugar,accountingforalmosttwo-thirdsofworldproduction.Recently,ithasgainedincreasingattentionsinceoneofitsproducts,ethanol,hasbeenpublicizedasanimportantsourceofrenewablebio-fuel,whichcouldturnitintoaglobalcommodityandanimportantenergysource.Ethanolisanalcoholthatcanbeproducedfromavarietyofagriculturalproductsandby-productsandisprobablythebestknownbiofuel.Brazilalreadydivertshalfofitssugarcane
21Sugarcane:AMajorSourceofSweetness,Alcohol,andBio-energy485
productiontoethanolproductionanditwillneedtobuildmorethan70newmillsandturnmorethan2.5millionhectaresoflandovertosugarcaneproductiontomeetthedemandforinternalethanolconsumption(Pessoaetal.2005).Inaddition,newtechnologiesareemergingtoconvertcellulosicresidueslikebagasseandotheragri-culturalbyproducts,suchassugarcanetrash(dryandgreenleavesandplanttopsleftinthe?eldduringharvest),intovaluablecommoditiesthatwouldbedegradedintosmallsugarmoleculesviaeitherenzymaticorphysical-chemical(orboth)processestobefermentedintoethanol.Thesetechnologiesareallinthescale-upphaseandinthenextfewyearswillbecomecommercialrealities,changingthefateofcellulosicresidues.
Theeconomicimportanceofsugarcaneanditsmainproductstomanycountriesintropicalandsub-tropicalregionsoftheworldhasnotalwaysbeenmetwithsignif-icantinvestmentsfortheresearchanddevelopmentofnewtechnologiestosupportthebreedingprogramsanddevelopsugarcanegenetics.Oneofthereasonsforthisisprobablythecomplexnatureofthesugarcanegenomeandthedif?cultiesfacedinselectingnew,moreproductivecultivarsinlongselectionprogramsthatcouldtakeupto15years.Withtheadventofgenomics,newtoolshavebecomeavailableandarenewedinterestinsugarcanegeneticshassurfaced(reviewedbyD’HontandGlaszmann2001;Butter?eldetal.2001;GrivetandArruda2001;Mingetal.2006).
21.1.2OriginandDiversityoftheSugarcaneComplex
Thetaxonomyofthesugarcanecomplex,basedonmorphology,chromosomenum-bers,andgeographicaldistribution,hasbeencontroversialsincetheoriginalclassi-?cationofSaccharumof?cinarumbyLinnaeusin1753(DanielsandRoach1987;Daniels1996;Irvine1999).Recentmoleculardataarebeginningtohelptracethedomesticationandearlyevolutionofsugarcane(reviewbyGrivetetal.2004,2006)(Fig.21.1).
AcontributionbyvariousgeneraotherthanSaccharum,particularlyErianthus(2n=20,30,40and60),Miscanthus(2n=38,40,76),Sclerostachya(2n=30),andNarenga(2n=30),totheemergenceofsugarcanehasbeenhypothesizedbyseveralsugarcanespecialists(reviewinDanielsandRoach1987).However,re-centmoleculardatadonotappeartocon?rmthesehypotheses.CurrentextantspeciesofthegeneraSaccharum,Erianthus,andMiscanthusareclearlydistinctaccordingtoisozyme,nuclear,andcytoplasmicrestrictionfragmentlengthpoly-morphism(RFLP)data(Glaszmannetal.1989,1990;Burnquistetal.1992;Luetal.1994a;D’Hontetal.1993,1995;Besseetal.1997),ampli?edfragmentlengthpolymorphism(AFLP)andsimplesequencerepeat(SSR)data(Selvietal.2004;Caietal.2005),andsequencedata(Hodkinsonetal.2002).Inaddition,repeatedspecies-speci?csequenceswithmultipledispersedlociinthegenomewereclonedinMiscanthusandErianthusandhybridizedontheDNAofrepresentativesoftradi-tionalcultivarsandwildSaccharum,andnotraceoftheseMiscanthusorErianthusspeci?csequenceswasfoundinanyoftheindividualstested(Alixetal.1998,1999).Restrictionfragmentanalysisofthechloroplastgenome(Sobraletal.1994)
486
Several Million yearsSeveral thousand yearsA.D’Hontetal.
Saccharum
S. spontaneum(2n=40 to 128)S. sinense
(2n=116 to 120)S. barberi(2n=81 to 124)Modern cultivars(2n=100 to 130)S. robustum(2n=60, 80 + up to 200)S. officinarum(2n=80)S. edule(2n=60 to 122)Miscanthus(2n=38, 40, 76)Erianthus(2n=20, 30, 40 and 60)CultivatedWildFig.21.1Scenariocompatiblewithavailablemoleculardataforsugarcaneevolutionanddomes-tication(AdaptedfromGrivetetal.2005)
andanalysisofthenuclearrepeatedsequences(Alixetal.1998,1999)suggestedthatSaccharumismorecloselyrelatedtoMiscanthusthantoErianthus.
ThesedatasupporttheviewthatthegenusSaccharumisawell-de?nedlineagethathasdivergedoveralongperiodofevolutionfromthelineagesleadingtotheErianthusandMiscanthusgenera(Grivetetal.2006).ThuscultivatedsugarcanesprobablyemergedfromwildSaccharumspecies,andsecondaryintrogressionswithothergeneraarenotlikelypathways.However,thisdoesnotmeanthatnaturalin-tergenerichybridizationsareimpossibleandmaynotaccountforsomelocalpecu-liarities.Arti?cialintergenerichybridswiththesegenerahavebeenproduced(Chenetal.1993;D’Hontetal.1995;Piperidisetal.2000).
TheSaccharumgenusincludessixpolyploidtaxonomicgroupsoftenaffordedspeciesstatus:twowildspecies,S.spontaneum(2n=40to128)andS.robustum(2n=60,80andupto200);threegroupsofearlycultivars,S.of?cinarum(2n=80),S.barberi(2n=81–124),andS.sinense(2n=116–120);andthemarginalsterilegroup,S.edule(2n=2n=60to122)(reviewinDanielsandRoach1987;Sreeni-vasanetal.1987).
S.spontaneumischaracterizedbythinstalkswithnoorverylittlesugarandhasahugegeographicdistributionfromEastAfricatoSoutheastAsiawithaprobable
21Sugarcane:AMajorSourceofSweetness,Alcohol,andBio-energy487
continentalAsiaorigin.S.robustumischaracterizedbylong,thickstalkswithlit-tleornosugarandhasbeenreportedasoccurringinnaturalpopulationsintheIndonesianislandsofKalimantan,Sulawesi,andMaluku,inNewGuinea,andintheBismarck,Solomon,andVanuatuarchipelagos.Thesetwowildspeciesdisplaydifferentstructuralorganizationsoftheirmonoploidgenome(basicsetofchromo-some).Thiswassuggestedbythepresenceofpolyploidchromosomeseriesbasedonmultiplesofeightandten,respectively.Thishasbeencon?rmedbycytogeneticmappingoftheribosomalRNAs45Sand5Sby?uorescentinsituhybridization(FISH),whichestablishedbasicchromosomenumbersofx=8forS.spontaneum(D’Hontetal.1998;Haetal.1999)andx=10forS.robustum(D’Hontetal.1998).MoleculardiversityismuchgreaterinS.spontaneumthaninS.robustum.AllopatricpopulationsofS.spontaneumandS.robustumareclearlydifferentiatedattheDNAlevel.Indeed,S.spontaneumsamplesfromKalimantanandSumatraandS.robus-tumfromNewGuineaandHalmaheraarestronglydifferentiatedbytheirnuclearRFLP(Glaszmannetal.1990;Burnquistetal.1992;Luetal.1994a),cytoplasmicRFLP(D’Hontetal.1993),AFLP(Selvietal.2004)andrandomlyampli?edpoly-morphicDNA(RAPD)(Nairetal.1999).DataaddressingrelationshipsbetweensympatricpopulationsofS.spontaneumandS.robustumarestillsparse.InNewGuinea,allS.spontaneumindividualsobservedhavethesamecytotype,2n=80.D’Hontetal.(1998)showedthatthiscytotypeisdecaploid,withatypicalS.sponta-neumbasicchromosomenumberofx=8.However,?eldobservationshaveshownamorphologicalcontinuumbetweenextremetypes,andsomeindividualspresentingintermediatemorphologicalcharacteristicsbetweenS.spontaneumandS.robustumaredif?culttoclassify(Henty1969).Moreover,asmallsampleofS.spontaneumindividualscollectedinNewGuineaappearstobemorecloselyrelatedtoS.robus-tumthantoanyotherS.spontaneum,basedonRFLPwithnuclearlowcopyprobes(Besseetal.1997)andonthehybridizationsignalintensityofarepeatedsatellitesequence,SoCIR1(Alixetal.1998).ThissuggeststhatS.spontaneumpopulationsfromNewGuineaaregeneticallyclosertoS.robustumthanaretheS.spontaneumpopulationswestofSulawesi.
MultiplelinesofmolecularevidencesupportadirectdescentofS.of?cinarum,thedomesticatedsugarcanecharacterizedbythickstalks,richinsugar(alsocallNobleclones),fromthewildspeciesS.robustum.AsinglemitochondrialhaplotypewasdetectedamongaseriesofS.of?cinarumclones(D’Hontetal.1993).ThishaplotypeisthemostcommonhaplotypedetectedinacollectionofS.robustumclonesfromNewGuineaandNewBritain.Itisalsodifferentfromthesixhaplo-typesrevealedinacollectionofS.spontaneumindividualssampledoveralargegeographicarea.RFLPanalysisofnuclearsinglecopyDNAplacedS.of?cinarumcultivarsveryclosetoS.robustum.TheaveragesimilaritybetweenaS.of?cinarumcloneandaS.robustumcloneisaboutthesameastheaveragesimilaritybetweentwoS.robustumclones(Luetal.1994a).S.of?cinarumhasabasicchromosomenumberofx=10,asdoesS.robustum(D’Hontetal.1998),andisoctoploidlikethemostcommoncytotype(2n=80)intheS.robustumwildspecies.
S.barberiandS.sinensehavehybridorigins.RFLPwithlowcopynuclearDNA(Glaszmannetal.1990;Burnquistetal.1992;Luetal.1994a;Selvietal.2004)