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Preview Application of biotechnology in breeding lentil for resistance to biotic and abiotic stress

Euphytica(2006)147:149–165 DOI:10.1007/s10681-006-7108-0 (cid:2)C Springer2006 Application of biotechnology in breeding lentil for resistance to biotic and abiotic stress FrederickJ.Muehlbauer1,∗,SeunghoCho3,AshutoshSarker4,KevinE.McPhee1, ClariceJ.Coyne2,P.N.Rajesh1 &RebeccaFord5 1U.S.DepartmentofAgriculture,AgriculturalResearchService,303JohnsonHall,WashingtonStateUniversity, Pullman, WA 99164-6434, U.S.A.; 2U.S. Department of Agriculture, Agricultural Research Service, 59 Johnson Hall,WashingtonStateUniversity,Pullman,WA99164-6402,U.S.A.;3DepartmentofAgronomyandPlantGenetics, UniversityofMinnesota,St.Paul,MN,U.S.A.;4GermplasmProgram,InternationalCenterforAgriculturalResearch intheDryAreas,Aleppo,Syria;5SchoolofAgriculturalandFoodSystems,theUniversityofMelbourne,Melbourne, Victoria,Australia(∗authorforcorrespondence:e-mail:[email protected]) Received31December2004;accepted31January2006 Keywords:geneticmapping,genomics,Lensculinaris,marker-assisted-selection,synteny Summary Lentilisaself-pollinatingdiploid(2n =14chromosomes)annualcoolseasonlegumecropthatisproducedthrough- outtheworldandishighlyvaluedasahighproteinfood.Severalabioticstressesareimportanttolentilyieldsworld wideandincludedrought,heat,saltsusceptibilityandirondeficiency.Thebioticstressesarenumerousandinclude: susceptibilitytoAscochytablight,causedbyAscochytalentis;Anthracnose,causedbyColletotrichumtruncatum; Fusariumwilt,causedbyFusariumoxysporum;Sclerotiniawhitemold,causedbySclerotiniasclerotiorum;rust, caused by Uromyces fabae; and numerous aphid transmitted viruses. Lentil is also highly susceptible to several speciesofOrabancheprevalentintheMediterraneanregion,forwhichtheredoesnotappeartobemuchresistance in the germplasm. Plant breeders and geneticists have addressed these stresses by identifying resistant/tolerant germplasm, determining the genetics involved and the genetic map positions of the resistant genes. To this end progresshasbeenmadeinmappingthelentilgenomeandseveralgeneticmapsareavailablethateventuallywill leadtothedevelopmentofaconsensusmapforlentil.Markerdensityhasbeenlimitedinthepublishedgeneticmaps andthereisadistinctlackofco-dominantmarkersthatwouldfacilitatecomparisonsoftheavailablegeneticmaps andefficientidentificationofmarkerscloselylinkedtogenesofinterest.Molecularbreedingoflentilfordisease resistancegenesusingmarkerassistedselection,particularlyforresistancetoAscochytablightandAnthracnose,is underwayinAustraliaandCanadaandpromisingresultshavebeenobtained.Comparativegenomicsandsynteny analyseswithcloselyrelatedlegumespromisestofurtheradvancetheknowledgeofthelentilgenomeandprovide lentil breeders with additional genes and selectable markers for use in marker assisted selection. Genomic tools suchasmacroandmicroarrays,reversegeneticsandgenetictransformationareemergingtechnologiesthatmay eventuallybeavailableforuseinlentilcropimprovement. Introduction othercoolseasonpulsesintheNearEastarcabout8000 years ago (Cubero, 1981; Ladizinsky, 1979). World Lentil(LensculinarisMedik.)isahighlyvaluedannual Production of lentil is estimated at 3.3 million met- foodlegumecropthatcoevolvedwithwheat,barleyand ric tons from an estimated 3.8 million hectares with 150 anaverageyieldof850kg/haFAOSTAT,2005).These Molecular markers and gene “tagging” has pro- yieldsseemsmall,butgenerallylentilisproducedon videdplantbreederswithameanstoacceleratebreed- marginal lands that are relatively dry and without the ingprogramsandanefficienttoolforindirectselection benefitoffertilizerinputsorirrigation.Attemptstoim- for traits that would otherwise be difficult to se- proveyieldsthroughbreedingareunderwaythrough- lect for using standard procedures. Biotechnological outtheworldandespeciallyattheInternationalCenter techniques such as Microarrays, TILLING, Genetic forAgriculturalResearchintheDryAreas(ICARDA), transformation and others hold promise for improv- USA,Canada,Australia,Turkey,SouthAsiaandmany ing our knowledge of the lentil genome and acceler- countries of the West Asia-North Africa (WANA) re- ating progress through breeding. Our objectives were gion. Major producing countries are India, Turkey, toreviewthestatusofavailableandemergingbiotech- Canada, Australia, Ethiopia, Morocco, Spain, Chile nologiesandtheircurrentandpotentialapplicationfor andArgentina.Ofthese,themajorexportingcountries overcoming major biotic and abiotic stresses of lentil areCanada,AustraliaandtheU.S.Thecountriesofthe crops. MiddleEastandNorthAfricaaremajorconsumers. The genus Lens comprises seven taxa in four species (Ferguson & Erskine, 2001; Ferguson et al., Constraintstoproductionoflentil 2000). Lens orientalis is the presumed progenitor of cultivated L. culinaris and the two species are fully Abioticstresses crossable and produce fully fertile progenies. How- ever, except for L. odemensis, there is difficulty in The major abiotic stresses affecting cool season food crossing the other wild species to the cultigen. From legumes were the subject of a comprehensive review thestandpointofcrossabilityforuseinbreeding,the (Singh&Saxena,1993).Stressesthataffectlentilwere Lensspeciescanbedividedintotwogroups(Ladizin- listedascold,drought,heat,salinity,nutrientdeficiency sky,1999):L.culinaris–L.odemensisandL.ervoides– andnutrienttoxicity.Ofthesestresses,droughtandheat L. nigricans that for convenience can be assigned to areconsideredthemostimportantworldwide(Turner primary and secondary gene pools. Crosses between etal.,2001).Coldstresswasconsideredimportantin membersofdifferentgroupsfailbecauseofhybridem- the West Asia-North Africa (WANA) region. Salinity bryoabortion;however,embryorescuehasbeenused isanimportantstressfactorintheIndiansub-continent successfully to obtain viable hybrids between groups andtosomeextentinWANA.Nutrientdeficiencyand (Ladizinskyetal.,1985). nutrient toxicity is of lesser importance world wide Several abiotic stresses such as cold, drought, but important in localized regions. For breeding ap- heat, salinity, nutrient deficiency and nutrient tox- proachesforcropimprovementinstressenvironments icity adversely affect lentil yields world wide seethereviewbyBuddenhagenandRichards(1998). (Monti et al., 1994; Saxena, 1993; Slindard et al., Susceptibilitytocoldtemperatureshaslimitedpro- 1994). Numerous biotic stresses that adversely af- duction of lentil in cold highland areas of the world. fect lentil include: susceptibility to Ascochyta blight, However,germplasmisavailablethathasusefuldegree caused by Ascochyta lentis; Anthracnose, caused by oftolerancetocoldtemperatureswhichmakesitpos- Colletotrichum truncatum; Fusarium wilt, caused by sibletobreedwinterhardycultivarsthatcanbeplanted Fusarium oxysporum; root rots caused by Fusarium in the fall with a reasonable expectation of surviving solani, Aphanomyces eutieches, Pythium ultimum, thewinter(Erskineetal.,1981;Spaeth&Muehlbauer, Rhizoctoniasolaniandpossiblyotherpathogens;Scle- 1991). Kahraman et al. (2004a) reported that winter rotiniawhitemold,causedbySclerotiniasclerotiorum; hardiness in lentil is conferred by several genes. In a rust,causedbyUromycesfabae;andnumerousaphid genetic analysis of winter hardiness, Kahraman et al. transmittedviruses.Lentilisalsohighlysusceptibleto (2004b) showed that the combined effects of several severalspeciesofOrabancheprevalentintheMediter- quantitativetraitlociaccountedfor42%ofthevaria- ranean region, for which there does not appear to be tion in winter survival. Molecular markers associated muchresistanceinthegermplasm.Resistancetosome withthoseQTLhavepotentialuseinamarkerassisted ofthesestresseshasbeenfoundingermplasmcollec- selection program for winter hardiness, but first must tions.SeeErskineetal.(1994b)forareviewofstrate- undergovalidation. giesforbreedinglentilforresistancetobioticandabi- Lentilisabletoproducesomethingofvalueinmany oticstresses. of the semi-arid regions primarily through drought 151 avoidance (Erskine & Saxena, 1993; Turner et al., subcontinentandEthiopiaandhasbeenshowntohavea 2001). Early senescence and crop maturity forced by geneticbasis(Erskine,1997;Erskineetal.,1993).The drought conditions that are often more severe due to acute yellowing symptomatic of iron deficiency can theusuallyassociatedhightemperatures.Rainfallac- bealleviatedbygermplasmefficientintheutilization counted for 41% and 55% of the variation in yields of iron (Erskine, 1997; Erskine et al., 1993). Boron of two lentil cultivars, respectively, in Syria. Various toxicityhasalsobeenproblematicandthereappearsto procedures have been attempted for screening lentil besometolerantgermplasm(Yau&Erskine,2000). germplasm and breeding material for drought toler- ance. Field screening using line source irrigation to Bioticstresses develop a moisture gradient has been attempted at ICARDA. Also, covering field plot areas to restrict Foliardiseasesarethemostseriousbioticstressesaf- moisture to form moisture differential areas, the use fecting lentil crops. Ascochyta blight caused by A. of late planting to increase exposure of the plants to lentis is problematic to various degrees in all lentil higher temperatures and greater moisture stress have growing regions of the world, but especially dam- allbeenattemptedwithinconclusiveresults.Increased aging in Canada (Ahmed & Morrall, 1996; Ahmed rootingdepthasameansofdroughtavoidancehasbeen et al., 1996), Australia and Middle Eastern countries suggested;however,thatapproachmaybeatconsider- (Johansenetal.,1994).SymptomsofAscochytablight able expense to succeeding crops, most likely wheat. includelesionsonallabovegroundpartsoftheplant, Molecularapproachessuchasmarkerassistedselection stemgirdling,podandseedlesionsandresistancehas mayhavemerit;however,considerableworkisneeded been found in the germplasm (Andrahennadi et al., toidentifytheimportantregionsofthegenome,most 1996).OthermajorbioticstressesoflentilincludeAn- likelythroughaQTLanalysis,andvalidationofasso- thracnosecausedbyC.truncatum,Botrytisgreymold ciatedmolecularmarkers. causedbyBotrytisfabaeandB.cinerea,Stemphylium Heatstressoftenaccompaniesdroughtcausingdif- blight caused by Stemphylium botryosum, lentil rust ficultiesinseparatingthetwostressesandtheireffects causedbyU.fabaeandSclerotiniawhitemoldcaused onlentilgrowthandyield.Thereisgeneralagreement by S. sclerotiorum. See Tivoli et al. this volume for that heat affects the distribution of dry matter to re- a description of Ascochyta blight, Anthracnose and productivegrowthandthathightemperatureshavean Botrytisgreymold. adverse effect on lentil yields. Research is needed to Stemphylium blight is a major threat to lentil critically define the effects of heat on the reproduc- in South Asia and North America (ICARDA, 2004; tive stages of lentil and the effects on yield. Evalua- Vandenberg:Personalcommunication).Thepathogen tion of the world collection of lentil germplasm has causes a leaf blight, plant defoliation and death. The indicated useful genetic variation is available for im- disease is poorly understood but apparently there is provingadaptationtoenvironmentalextremes(Erskine someresistanceavailableinthegermplasm;however, etal.,1990,1994b). thegeneticsofresistanceisstilltobedetermined. Salinity problems with lentil are not wide spread Lentil rust caused by U. fabae is widespread in but can be acute in certain regions of South Asia, South Asia, Morocco and Ethiopia and is character- the Nile delta of Egypt and in some areas of Turkey. izedbylesionsonthestemsandleaves,leafdropand Canadaalsohassomedifficultyinhighsalinityareasof prematureplantdeath(Ahmed&Morral,1996;Ahmed Saskatchewan.Ofthelegumes,lentilismoresaltsensi- etal.,1996).Lossesfromthedisease,estimatedatup tivewhencomparedtofababeanandsoybean(Katerji to70%,havebeenreported(ErskineandSarker,1997; etal.,2001,2003).Saltstresscanadverselyaffectnodu- Negussie et al., 1998). Resistance to the disease has lationandN fixation(Rai&Singh,1999;Raietal., beenidentifiedingermplasmlineILL5588andiscur- 2 1985)presumablybyrestrictinggrowthoftheroothairs rentlybeingusedasasourceofresistanceinbreeding andthepotentialsitesofinfectionbyRhizobium.Some programsandinstudiestodeterminetheinheritanceof germplasmwithtolerancetosaltstresshasbeenidenti- resistanceandtomaptheimportantgenes(Ahmed& fied(Ashraf&Waheed,1993;Ashrafetal.,1990;Jana Morral,1996;Ahmedetal.,1996). &Slinkard,1979). Sclerotinia white mold caused by S. sclerotiorum Nutrientdeficienciesandtoxicitiesareimportantin has been responsible for extensive damage to lentil specificsituations.Irondeficiencysymptomsappearin crops in areas that are relatively moist and humid. germplasm introduced to other areas from the Indian Dense crop canopies also contribute to the severity 152 ofthedisease.Thepathogenaffects148knownplant ular markers aim to improve pre-emptive breeding generaandthereislittleresistancetothedisease.Re- strategiesandovercomethedifficultiesassociatedwith searchisunderwaybytheUSDA-ARSGrainLegume screeningindistantlocalities. BreedingprogramatPullmantodeterminethegenet- The implementation of markers for routine use icsofresistance/tolerancefoundinlentilcultivarsand in lentil breeding programs is currently very limited, germplasm. Research is currently underway towards sometimesbecausethetraitstobeselectedcanalready conductingaQuantitativeTraitLocianalysisusingre- be phenotyped relatively cost effectively. The key to combinant inbred lines from crosses of presumed re- bothresearchandimplementationofmarkersforlentil sistantcultivarswithhighlysusceptiblecultivars. liesintheintegrationofthemarkerswithinthebreeding Root rots and wilts usually attack lentil plants in programtoensurethatcosteffectiveutilizationofthe the seedling stage and cause seed rot, damping off, technology is achieved. Globally, trait selection that wilt,destructionoftherootsystemandrottingoflower would greatly benefit from the availability of robust stems. These disease problems have been extensively and accurate markers includes; drought, frost, boron reviewed(Khare,1981;Kraftetal.,1988,1994).Fusar- (Hobsonetal.,2003;Yau&Erskine,2000)andsalinity ium wilt caused by F. oxysporum is considered to be tolerance,andresistancestoAscochytablight,Botry- themostdamagingsoilbornediseaseproblemfacing tisgraymold,Anthracnose,rust,FusariumandStem- lentilworldwide(Khare,1981)andseveralracesofthe phyliumblight. pathogencancausethedisease.Hamwiehetal.(2005) developedageneticmapoflentilthatcomprisesover Molecularmarkersandgenomemapping 300molecularmarkersandusedthemaptodetermine thelocationofthegeneforresistancetoFusariumwilt Morphologicalandisozymemarkerswereusedtoiden- (Figure1). tifythefirstgeneticlinkagesinlentil(Muehlbaueretal., 1989; Tadmor et al., 1987; Vaillancourt & Slinkard, 1993; Zamir & Ladizinsky, 1984). Soon thereafter Molecularmarkersandmarkerassistedselection manytypesofDNA-basedmolecularmarkers,arising frompointmutations,insertionsordeletionsorerrors Thecurrentstateofmolecularbreedinginlentil inreplicationsoftandem-repeatedDNA,wereidenti- fiedandusedformappingthelentilgenome.Restric- Lentil is a relatively small crop compared to wheat, tion fragment length polymorphism (RFLP) markers, rice,maizeandsoybeanandranksthirdamongthecool developedfromcuttinggenomicDNAwithrestriction season food legumes in area harvested (4.08 million enzymesandseparatingtheresultingDNAfragments hectares)annually(http://apps.fao.org/faostat),andbe- with electrophoresis, were the first type of molecular hind pea and chickpea. Much of the crop is grown in markerusedintheconstructionofalentilgeneticlink- economically poor countries where research funding agemap(Havey&Muehlbauer,1989).Subsequently, andexpertiseinnovelmolecularbreedingapproaches arbitrarilyproducedpolymerasechainreaction(PCR)- islimited.Consequently,molecularbreedingresearch basedmarkers,suchasrandomamplifiedpolymorphic has often been directed to address major production DNA(RAPD)wereusedtostudydiversity,phylogeny limitationsthatarerelevanttodevelopedcountriesand and taxonomy of Lens (Ford et al., 1997; Ferguson where resources for equipment and consumables are etal., 2000; Sharma et al., 1996), to develop linkage available.However,evenwiththeserestrictions,some maps(Eujayletal.,1997,1998a;Rubeenaetal.,2003), substantial advances have been made towards under- totaggenesofinterest(Chowdhuryetal.,2001;Eujayl standing the lentil genome and the development and et al., 1998b, 1999; Ford et al., 1999; Tullu et al., applicationofmolecularmarkerstoadvancebreeding 2003) and to determine pathogen population struc- strategies. ture (Ford et al., 2000). Arbitrarily produced ampli- Muchofthefocushasbeenondevelopingmolec- fied fragment length polymorphism (AFLP) markers ular markers for selecting resistance to a few major havealsobeenusedinlentillinkagemapping(Dura´n diseases, such as Ascochyta blight, especially where etal.,2004;Eujayletal.,1998a;Hamwiehetal.,2005; research is complementary between countries and re- Kahraman et al., 2004) and to study genetic diversity search groups. In the near future, the potential exists (Sharmaetal.,1996),differentiatecultivars(Za´vodna´ todevelopmarkersformanyotherhighlysoughttraits et al., 2000) and identify markers linked to specific that are difficult to breed for conventionally. Molec- traits (Tullu et al., 2003). Comparisons of the lentil 153 7_GL 651RSS6832m71p*7.317703m71p*.43b60gPO*4.1k34m401p6.1a80vPO*.131832m71p*8.10173m71p*2.1a51lPO*9.21113m43p*3.1888m61p*1.16703m71p*.07133m43p*0.13703m71p*1.1c80vPO*b41qPO*1.1b80vPO*2.1d31gPO*9.1a02iPO*4.1514m22p*6.7414m22p*8.0 spuorgegaknil srekram3 Mc057na 41_GL3 232m71p*81cPO*3832m71p*52.1a10sPO*A332RSS 6_G 01703m71p*wf*B-295RSSd80vPO*f34m401pc81mPO*51kPO*a81gPO*b30pPO*b91nPO*a21jPO*91RSS*5832m71p2131m43p*f41qPO*h34m101p324m61p*A2-95RSSi34m401p614m22p*e81mPO*b60oPO*164m81p*h34m401pb31gPO*d40sPO*688m61p*c34m401pb34m014p7POc*POa30p*212RSS664m81p*b34m101pa34m101p 41 82 pS 1_GL2 644m71p*5.3b34m11p.42 L 1 6094351706424271370758190439487601 _ .3.8.3.0.1.3.0.1.2.3.4.3.1.1.0.4.0.0.4.5.0.4.2.0.2.3.1.1.8.1.04..0.2 G 1 L 5.3 5). 99R b6 200 4_G a40xPO*c34m11pd34m401pc02kPO*d81mPO*544m71p*0gPO*c65cPO*d59m61p114m22p*g34m001p231m43p*3cPO*4cPO*B332SSRa70gPO*364m81p*d10sPO*8ePO*PO*1e5703m71p*B203RSS4ePO*j34m401p2ePO*a91nPO*388m61p*Sa60oPO*Sa81mPO*6ePO*1qPe4O*244m71p*51D4RSSm81*1164p430131mp*624m61p*41sPO*0164m81*pd10uP*Oa10uPO*924m61p*70wP*OA41RSS5763m41p* 11_GL 1sPO*5.8*fRRf amweihetal., 3L 3.316.10.23.23.27.1673m71p*0.233RSS16.84RSS0.1b61wPO*9.3873m71p*7.4a50sPO*2.1c40xPO*3.0488m61p*5.50188m61p*1.0a4pamPO*6.113124m6p*34.e34m401p0.41124m61p*30.c59m02p7.05b9m02p19.d41qPO*0.1431m3p*413.14m22p*79.16cPO*9.1a34m492p5.0a34m001p6.1b34m492p2.0b34m001p4.070sPO*5.0B512RSS5.0tPO10*2.1a31gPO*.17c41qPO*.191mPO*b85.16dPO*7.1mpg34m401pe34115.0B991RSS.192aPO*5.0sPO01*0.23mph4118.6*W.14pcs*11.m61p*5134264*m81p64*7m81p 01_GL e59m11pd59m11p431.0124m61p* neticmapoflentil(fromH _ e GL 1.610.57.15.417.013.015.514.53.12.26.11.44.47.18.26.32.13.18.55.05.04.03.14.16.37.3.212.43.19.58.06.03.41.27.3.103.31.79.41 9_ a8P1iO* C332RSS c4101p3m ure1.Ag 2_GL j34m001p5.5kP*8b02O.12.1934m61p*m41*41463p.0.3334m61p*6.00134m61p*134m61*42m61p*134p.3c30pPO*0.3d02oPO*5.1a20uPO*0.1b10uPO*7.271181m1p*4.22.0c40sPO*701RSS3.070m61*.788pPc51lO*1.0l34m001p3.0712344mp*.0314m22*3.0p5eP*4O.0c70gPO*3.0b40rP*1O.0A52RSS1.011.0481RSS31oPO*031RSS1.0c81gPO*9.0863m41p*a61sPO*1.0vP*3020O.b02iPO*4.04832m71p*5.080oP*4O.021m22*7.04p5kP.0a02O*831m43*2.4psP*1e40O.1c11oPO*4.4m61*62124p.0342c34m001pcm492p.6i*01p.e34m492p1.6d34m492p4.5Pb21jO*531m43*p GL8_ c10uPO*373m71p*10s*bPO4.61911RSS312RSS311RSS1.01b81iPO*S69RS*d30pPO D33RS2S Fig G f34 L m 942 1.61.670.1.19.13.467.8.3 1 434m61p*f34m01p0a59m61pa59m02pB31RSSi34m101pRSS08a34m11pa34m401p80nPO*563m41p*1b1oPO*e30pPO*A203RSSpk34m001p2b0oPO*0P*b7gO*2181m71p1gPO*b84SS02Rb40xPO*2-9RSS039ePO*d34m101pa91hPO*731m43p*631m43p*ARSS31633RSS914m22p*a*40rPO1oP*d1O)2(7S13RS)1(713RSS0*a6gPOA991RSSb*51lPO*b40sPOb80*sPO1c9hPO*C9RSS91*744m71ph34m001p7SS61Rg34m11p1*a4qPOg34m101p44*8m71pa80sPO* 1 _ G L 037242969238577223241477720825782526474603255962 .72..31..1.00..0.1.0.1.1.2.0.7.3.4.6.3.2.43..1.1.0.0.4.0.0.0.0.0.0.0.0.01..0.0.1.1.1.2.3.00..08. 154 linkagemapwiththatofchickpeaandpeaindicatein- ThemajordrawbackinusingF populationsisthat 2 terestingsimilarities(Simon&Muehlbauer,1995). theyareephemeralanddeterminate,unlikeRILpopu- Morerecently,simplesequencerepeat(SSR)ormi- lationsderivedinF orlatergenerationsandhomozy- 6 crosatellite markers, which consist of tandem repeats gousatmostoftheloci(Tahir&Muehlbauer,1994). of two to five nucleotide DNA core sequences that RIL populations can have multiple uses for mapping are spread throughout the genome, were used to con- and can easily be maintained for future genomic re- structlentillinkagemaps(Dura´netal.,2004;Hamwieh search.Itisalsonotedthatthesizeofamappingpop- etal.,2005).TheDNAsequencesflankingmicrosatel- ulationcangreatlyimpacttheultimateresolutionofa literepeatsaregenerallyconservedwithinindividuals map(Young,1994). ofagivenspecies,allowingthedesignofhighlyspe- Segregation distortion due to irregular chromo- cific and robust PCR primers that amplify the inter- somepairingisalsothoughttocausebiasedestimates vening SSR. Two sets of microsatellite markers were of marker distances in wide interspecific populations developedfromlentilbyZa´vodna´ etal.(2000)andat (Collardetal.,2003;Lorieuxetal.,1995;Tadmoretal., ICARDAbyHamwiehetal.(2005).TheICARDASSR 1987). Also, maps based on distantly related parents librarywasdevelopedfromthegenomeoftheNorth- arelessusefulinbreedingapplicationsbecausepoly- fieldcultivar(ILL5588)andwasfoundtohave(CA) as morphicmarkerslinkedtotraitsofinterestmaynotbe n themostabundantrepeattype(Hamwiehetal.,2004). present within the cultivated gene pool. To overcome Othermarkertypessuchasinter-simplesequence thisproblem,intraspecificcrosseswithincultivatedL. repeat (ISSR) markers, amplified with SSR-anchored culinaris have been used to construct genome maps primers,andresistancegeneanalogue(RGA)markers, using PCR-based markers (Kahraman et al., 2004b; amplifiedwithdegenerateprimersdesignedfromcon- Rubeenaetal.,2003). served regions of cloned plant resistance genes were Doubled haploid (DH) populations, produced by alsousedinlentilgenomemapping(Dura´netal.,2004; regenerating plants from single pollen grains and in- Rubeenaetal.,2003).PositionalcloningofRGAmark- ducingchromosomedoubling,mayrepresentafarbet- ers will be potentially aid in the localization of dis- tersolutionforreproducibleandmultipleenvironment easeresistancegenesviathecandidate-geneapproach lentiltraitmapping.Where,afterrecombination,each (Kanazinetal.,1996;Leisteretal.,1996). locusisfixedandself-pollinationcancreateaninfinite amount of genetically identical individuals in a rela- Lensmappingpopulations tivelyshortperiodoftime.However,theproductionof alentilDHpopulationisdependentonamenabilityto The choice of parents for use in constructing a map- anthercultureandingeneral,grainlegumesaremore ping population is crucial. Parents that are homozy- recalcitrant to in vitro manipulation than many other gous but highly variable from each other in the traits species(reviewedbyChristou,1997). tobemappedarepreferable.Duetolimitedpolymor- phism, mapping in inbreeding species often requires Lentilgeneticlinkagemaps theselectionofparentsthataredistantlyrelatedorbe- longtodifferentsubspeciesorevenspecies.Theinitial ThefirstlinkagemapoflentilusingDNA-basedmark- mappingpopulationsusedinlentilwereF progenies ers(RFLP)wasconstructedbyHaveyandMuehlbauer 2 fromcrossesbetweenwildspeciesandcultivars(Havey (1989). PCR based markers were used to construct a & Muehlbauer, 1989; Muehlbauer et al., 1989; Tahir more extensive linkage map comprising 177 mark- et al., 1993; Vaillancourt & Slinkard, 1993; Weeden ers (RAPD, AFLP, RFLP and morphological mark- et al., 1992). However, it is known that the use of ers)andwasbasedonaRILpopulationcreatedfrom such divergent parents often results in lower recom- an inter-subspecific cross (Eujayl et al., 1998a). The bination rates and smaller map sizes (Tadmor et al., firstintraspecificlinkagemapoflentilwasconstructed 1987).Indeed,thefirstlentilmapscomprisedrelatively with 114 RAPD, ISSR and RGA markers (Rubeena small marker numbers and spanned relatively small et al., 2003). Recently, two more extensive molecu- segments of the genome (Eujayl et al., 1997; Havey larlinkagemapswerereported,oneusinganintraspe- & Muehlbauer, 1989; Weeden et al., 1992). More re- cificpopulation(Kahramanetal.,2004)andtheother cently, linkage maps have been based on populations basedonaninter-subspecificpopulation(Dura´netal., ofrecombinantinbredlines(RILs)(Eujayletal.,1997, 2004).Thelentillinkagemap,producedbyDura´netal. 1998a;Hamwiehetal.,2005;Kahramanetal.,2004). (2004) contained 62 RAPD, 29 ISSR, 65 AFLP, four 155 morphological markers and one SSR, and spanned a lishedlinkagemaps.TherecentlyreportedSSRmark- distance of 2172cM within 10 linkage groups. The ers placed on the lentil genetic map should facilitate lentilspecificSSRmarkerwasthefirstofitstypetobe thedevelopmentofaconsensusmap. mapped in lentil. The map of Kahraman et al. (2004) covered1192cMwithinninelinkagegroupsandcom- Alensconsensusmap prisedatotalof130arbitrarilyproduced(RAPD,ISSR, and AFLP) markers. Most recently a comprehensive The existing maps have not been well linked to each inter-subspecificlentilmapwasdevelopedbyenrich- other due to the lack of common markers. However, ingthepreviousmapofEujayletal.(1998a)with39 morphological markers and the recently developed new lentil-specific SSRs and 50 new AFLP markers lentilSSRmarkers(Hamwiehetal.,2005)shouldprove (Hamwiehetal.,2005).Themap(Figure1)comprises useful in assigning common linkage groups. Of the atotalof283markersspanning751cMwithin14link- sevenmorphologicalmarkersalreadymapped,cotyle- agegroups(eightofthelinkagegroupshadmorethan doncolor(orangeversusyellow;Yc),presenceorab- threemarkers). senceofanthocyanininthestem(Gs),seedcoatpattern To date, all lentil genetic maps have had more or spotting (Scp), pod dehiscence-indehiscence (Pi), linkage groups than the species haploid chromosome groundcolor(brownversustan)oftheseedcoat(Ggc), number(n=7).Theestimatedamountofthegenome erectorprostrategrowthhabit(Gh)andpresenceorab- mappedcurrentlyvariesfrom751to2172cMwithan senceofanthocyanininthepod(Pdp),fourhavebeen averagemarkerdensityof2.7–15.9cM.Theexpected placedonmultiplemaps(Yc,Gs,ScpandPi). fullgenomelengthisasyetunknown.However,given Other markers that may be useful for consensus theclosephylogenyamongthespecies,perhapstheex- mapping include the repetitive DNA sequences that pectedlengthwouldbeclosetothatoffieldpea,which have been localized by fluorescent in-situ hybridiza- is 700–800cM as determined by cytological studies tion(FISH)andusedtoassigngeneticlinkagegroups (Halletal.,1997a,b). tospecificchromosomesandforintegratinginforma- Otherimportantcharacteristicsofthecurrentmaps tion from both physical and genetic maps (Galasso includetheclusteringofmarkersatvariousregionsand etal.,2001;Patiletal.,1995)andothergene-specific theinclusionofdistortedmarkers.Clusteringmaybe markerssuchasexpressedsequencetag(EST)mark- indicativeofcentromericandtelomericregions,which ers.Also,gene-specificmarkerstransferablefromre- experienceupto10-foldlessrecombinationthanother lated model legume crop species such as Medicago areasofthegenome(Tanksleyetal.,1992).Thiswas truncatulaandLotusjaponicusandconvertedtosingle alsoobservedinPisumandCicermaps(Laucouetal., nucleotidepolymorphism(SNP)orcleavedamplified 1998; Winter et al., 2000, respectively). Segregation polymorphism(CAP)typemarkers.Suchmarkerswill distortionistheconsequenceofunequalinheritanceof alsobeusefulforcomparativemappingacrossspecies. partsofchromosomesandmayaffecttheorderingof markerswithinalinkagegroup(Lorieuxetal.,1995). Traitmapping Factors that contribute to marker distortion include recessive alleles, structural rearrangements or differ- Manysimplyinheritedtraitshavebeenplacedonlentil ences in DNA content, abortion of male and female geneticmaps.Byknowingthemappositionofagene, gametesandtheselectivefertilizationofaparticularga- thepresenceofthegenecanbediagnosedusingflank- meticgenotype(Barzenetal.,1995;Berryetal.,1995; ing DNA markers without waiting for the gene ef- Jenczewski et al., 1997; Quillet et al., 1995; Tadmor fect to be present in the phenotype (Paterson et al., etal.,1987;Xuetal.,1997). 1991). Until recently, a major limitation to lentil map- Bulked segregant analysis (BSA), first described pinghasbeentheunavailabilityoflocus-specificPCR byMichelmoreetal.(1991),isamethodusedtoiden- based and co-dominant markers such as expressed tifymolecularmarkerslinkedtophenotypictraitscon- sequence tags (EST), cleaved amplified polymorphic trolled by single major genes. This method relies on sequences (CAPS), single nucleotide polymorphism theavailabilityofbulkedDNAsamplescollectedfrom (SNP)orsimplesequencerepeat(SSR)microsatellite individuals that segregate for the two extreme diver- markers, which are more robust and informative than gentphenotypeswithinasinglepopulation.Onebulk arbitraryDNAmarkers.Thelackofsuchmarkershas containstheDNAofthetraitbeingtargeted,whilethe largely hampered the ability to compare various pub- othercontainsDNAfromindividualslackingthetrait. 156 DNApolymorphismsbetweenthebulksaretherefore, repulsionphasetoLCt-2;however,thenearestmarker likely to be linked to genes that govern the trait. In was 21.5cM away. Tar’an et al. (2003) have demon- lentil, this method has been used to identify markers stratedtheusefulnessofOPE06 inmarkerassistant 1250 thataretightlylinkedtogenesforresistancetoFusar- selection to pyramid genes for Ascochyta blight and ium vascular wilt and Ascochyta blight (Chowdhury Anthracnose resistance. Fusarium wilt is reportedly etal.,2001;Eujayletal.,1998b;Fordetal.,1999). controlledbyasingledominantgene,Fw,andlinked Eujayletal.(1998b)usedanRILmappingpopu- to RAPD marker OPK-15 at distance of 10.8cM 900 lationtoidentifymolecularmarkerslinkedtothesin- (Eujayl et al., 1998b). More recently Hamwieh et al. gledominantgeneconditioningFusariumvascularwilt (2005),identifiedanSSRmarkerandanAFLPmarker resistance(Fw).TheyalsoidentifiedaRAPDmarker that flanked the Fusarium wilt resistance gene by 8.0 (OPS16 ) that was 9.1cM from the radiation-frost and3.5cM,respectively. 750 tolerance locus (Frt) (Eujayl et al., 1999). However, Successful winter cropping of lentil depends on mostprobablyduetoinsufficientgenomemapcover- seedlingsurvivalandanoptimumplantpopulationin age, the Frt locus and the linked RAPD marker were the early developmental stages. Eujayl et al. (1999) unabletobeplacedontheexistinglinkagemapdevel- observed that seedling frost tolerance was governed opedbyEujayletal.(1998a). byasingledominantgeneFrtinacrossbetweenILL Fordetal.(1999)identifiedRAPDmarkers,RV01 5588×L692-16-1(S)andthattheFrtlocuswaslinked and RB18, approximately 6 and 14cM, respectively, toRAPDmarkerOPS-16 at9.1cM. 750 from and flanking the foliar Ascochyta blight resis- tancelocusRal1(AbR )inILL5588.Theseweresub- Marker-assistedselectionandtraitpyramiding 1 sequentlyconvertedtolocus-specificsequencecharac- terizedamplifiedregion(SCAR)markersandscreened Markerassistedselection(MAS)istheabilitytoselect forapplicabilityacrossparentallinesintheAustralian forandbreedforadesirabletraitwithamarker,orsuite breedingprogram.Althoughthelinkagewasnotmain- of markers, from within a plant genotype without the tainedacrossallparentalgenotypes,greatpotentialex- need to express the associated phenotype. Therefore, istsforthetargeteduseofthesemarkersinbreedingand MASoffersgreatopportunityforimprovedefficiency thepyramidingofresistancegenesinILL5588-derived and effectiveness in the selection of plant genotypes geneticbackgrounds.Subsequently,twoRAPDmark- withadesiredcombinationoftraits.Thisapproachre- ers, UBC227 and OPD-10 , were identified that liesupontheestablishmentofatightlinkagebetweena 1290 870 flanked and were linked in repulsion phase to the re- molecularmarkerandthechromosomallocationofthe sistancegeneral2inthecultivarIndianheadat12and gene(s)governingthetraittobeselectedinaparticu- 16cM, respectively (Chowdhury et al., 2001). Most larenvironment.Oncethishasbeenachieved,selection recently,molecularmarkersweredevelopedthatwere canbeconductedinthelaboratoryanddoesnotrequire linkedtothecomplementarydominantresistancegenes theexpressionoftheassociatedphenotype.Forexam- in ILL7537 (Rubeena, pers. comm.). The resistance ple,usingMAS,diseaseresistancecanbeevaluatedin sourceswithinthesegenotypeswereshowntobenovel theabsenceofthediseaseandinearlystagesofplant using pathogenicity tests (Nguyen et al., 2001). Thus development. there is potential for using markers to pyramid As- Sequencetaggedsites(STS)areidealmarkersfor cochytablightresistancegenestodevelopdurablyre- MAS. STS markers are mapped loci for which all or sistantvarieties. partofthecorrespondingDNAsequencehasbeende- Molecular markers for resistance to Anthracnose termined.Thesequenceinformationisusedtodesign andFusariumwilthavealsobeendevelopedforscreen- PCRprimersforamplificationofallorpartoftheorig- ing breeding material. In the case of anthracnose re- inalsequence.Theyaremorerobustandreproducible sistance, bulk segregant analysis of 147 F -derived than the arbitrary sequences they are designed from, 5 F RILsfromthecrossofresistantPI320937andsus- such as RAPD markers, as they are developed from 6 ceptible cultivar Eston was used to identify markers the known sequences and produce an amplicon from linkedtoresistance(Tulluetal.,2003).RAPDmark- longer primers. Differences in the lengths of ampli- ersOPE06 andUBC704 werelinkedat6.4cM fiedfragmentsserveasgeneticmarkersforthelocus. 1250 700 (inrepulsion)and10.5cM(incoupling),respectively, If no length polymorphism is detected, the amplified to the resistance locus, LCt-2, (Tullu et al., 2003). fragments can be cleaved with restriction enzymes to ThreeAFLPmarkerswerealsoidentifiedaslinkedin observesubsequentlengthdifferences.Thistechnique 157 is often referred to as cleaved amplified polymorphic developed from an inter-sub specific population (L. sequencesorCAPS(Jarvisetal.,1994). c. ssp. culinaris×L. c. ssp. orientalis). A total of 22 Theuseofconvertedlocus-specificPCRmarkersis QTL were placed upon the map including five for alsoreferredtoasaspecificpolymorphiclocusamplifi- height of the first ramification, three for plant height, cationtest(SPLAT),aswellassequencecharacterized five for flowering, seven for pod dehiscence, one for amplified region (SCAR) markers and allele specific shoot number and one for F seed diameter (Dura´n 3 associated primer (ASAP) markers. SPLAT markers etal.,2002).QTLgoverningwinterhardinesswerere- aredesignedfromsequencingtheinsertofapolymor- centlymappedusinganF derivedpopulationof106 6 phicRFLPmarker(Gale&Witcombe,1992),whereas RILs from a cross between WA8649090 and Precoz SCARandASAPmarkersaredevelopedfromsequenc- (Kahramanetal.,2004).Thatpopulationwasusedto ingspecificRAPDmarkers(Guetal.,1995;Fordetal., constructaframeworkmapofninelinkagegroupscom- 1999;Paran&Michelmore,1993).Theconversionof prisingatotalof130markersandspanning1192cM. moretechnically-demandingRFLPmarkersintoPCR Wintersurvivalandwinterinjurydatawerecollected basedmarkers(e.g.SPLAT)mayprovideamorerapid, attwolocationsin1997(Pullman,USAandHaymana, cost-effectiveandefficienttoolinlentilbreeding. Turkey)andthreelocationsin1998and1999(Pullman, Nguyen et al. (2001) first converted an arbi- USA,HaymanaandSivas,Turkey).Fiveindependent trarily produced lentil sequence to a SCAR marker QTLweredetectedtoaccountforsurvivalwithaLOD (SCARW19) for selecting resistance to Ascochyta score>2.0.OneQTLonLG4wascommonamonglo- blightfoundinlentilaccessionILL5588.Tar’anetal. cationsalthoughtheeffectandpositiondifferedsome- (2003)convertedtheRB18 RAPDmarker,formerly what.TheseQTLaccountedfor33.4%ofthevariation 680 alsoshowntobelinkedtotheAbR1gene(Fordetal., inthewintersurvivalscoresintheRILpopulation.One 1999),intoarobustSCARmarker.Theysubsequently ISSRmarker,ubc808-12,wasidentifiedaspotentially usedSCARmarkerslinkedtotheAbR1geneandthe usefulforpredictingwintersurvivalusingMAS.Over- ral2 gene (Chowdhury et al., 2001), together with a all,fourQTLaccountedfor42.7%ofthevariationin marker linked in repulsion to a gene for Anthracnose winterinjuryscoresattheUSAlocation. resistance(LCt2),topyramidthetraitsinaRILpopu- PreliminaryQTLanalysisoftheAscochytablight lation.Usingthelinkedmarkers,11of156RILwere resistance in ILL7537 was conducted using a pop- shown to retain all three resistance genes. Of these, ulation comprising 153 F individuals (ILL 7537 2 82%, that contained the markers linked to AbR1 and (R)×ILL6002(S))andalinkagemapcomprising72 ral2, were resistant to a highly virulent A. lentis iso- markersspanning412.5cManchoredtoapre-existing late.Furthermore,85%ofthelinesthatdidnotcontain map(Rubeenaetal.,2003).Thediseasereactionwas the marker linked to the LCt2 gene were resistant to scored using a 1–9 scale on each of the F individu- 2 thevirulent95B36isolateofColletotricumtruncatum. als at 14, 21 and 28 days after inoculation and three Thisisthefirstevidenceofvalidatingtheuseofmolec- QTLpeaks(twoonLGIandoneonLGII)wereob- ularmarkersformarker-assistedtraitselectioninlentil. servedusingcompositeintervalmapping(CIM).Two Pyramidingofmultipleresistancegenestofoliarfungal QTL (QTL-1 and QTL-2) were observed on LG I in pathogensshouldprovideabroaderandmoredurable closeproximity,sincethesewere>10cMapart,they resistance,assimilarlyshowninriceagainstbacterial wereconsideredtobeseparateQTL.Theyaccounted blight(Singhetal.,2001). forapproximately47%,whereasQTL-3onLGII,ac- countedforapproximately10%ofthevarianceofthe Quantitativetraitlocimappingandidentification trait.ThepositionoftheQTLchangedslightlyoverthe ofgenes differentscoringperiodsafterinoculation.TheAFLP markerC-TTA/M-AC wasfoundtobe3.4cMaway 285 Whenatraitisgovernedbymultipleandquantitative fromQTL-1and12cMawayfromQTL-2.TheRAPD traitloci(QTL)and/orco-dominantlyinheritedgenes, marker M20 was located at the same position as 700 amoreholisticgenomemappingapproachmaybeun- QTL-3. When multiple interval mapping (MIM) was dertakentoidentifygenomiclocations,interactionand performed,onlytwosignificantQTL(QTL-2andQTL- subsequentmolecularmarkersforaccuratetraitselec- 3)wereidentified.ThesetwoQTLmaypotentiallybe tion. themajoreffectsofthetwocodominantresistantgenes Few QTL studies have been reported thus far for previouslyidentifiedtogovernresistanceinILL7537 lentil. The first employed a genetic linkage map (Nguyen et al., 2001). However, the QTL identified 158 mustbevalidatedindifferentgeneticbackgroundsand conductedintwoenvironments(rainfedandirrigated) populations before incorporation into breeding pro- overtwoyears.Thegenotypesandphenotypeswillbe grams. availableatwww.ars-grin.gov. Recently, resistance gene analogues belonging to the nucleotide binding site (NBS) gene families were Advancedgenomictoolsapplicabletolentilgenomics isolatedfromthelentilgenotypeILL5588(Yaishetal., 2004).MappingofRGA,togetherwiththeAscochyta Remarkableadvancementofgenomictoolsenabledex- blight resistance trait, may be useful to validate the cavation of entire genome sequences in model plant location of genes that are functional in the resistance species such as Arabidopsis (Bevan et al., 2001) and mechanism, a step towards map-based cloning of the rice(Goffetal.,2002;Yuetal.,2002).However,the activeresistancegenes. sameapproachdoesnotseemtobeapplicabletomost ofthecropspeciesincludinglentilnotonlyduetolarge Associationmapping genome size compared to the model species but also duetolimitationinfinancialandhumanresources.To Association or linkage disequilibrium (LD) mapping avoid these issues, it is desirable to establish indirect was used successfully to discover genetic determi- butefficientwaystounderstandgenomestructureand nants to traits initially in humans is now being used toinvestigategenesinnarrowbutimportantgenomic inplants(Flint-Garciaetal.,2003;Thornsburyetal., regions. 2001).Usingassociationmapping,entiregenomescan By virtue of advances in genome scanning tech- bescannedformarkersassociatedwithqualitativeand niquessuchasmicroarray(Blanchard&Friend,1999; quantitativetraits.Theassociationmappingapproach Kuhn,2001),investigationofentiregenomesforgenes may allow plant breeders to break out of restrictive ofinteresthasbecomefeasible.However,becausenew F -derivedmappingpopulationsandemployanyplant 1 techniques can also allow substantial degree of false populationincludingthosefrombreedingprogramsor positivedetection,weneedtobecautiousintheappli- germplasmcollectionstoconductmarker-traitassoci- cationofhighthroughputtechniquesincurrentbreed- ationstudies(Flint-Garciaetal.,2003).Gebhardtetal. ingprograms.Tosuccessfullysurveyanentiregenome (2004) clearly summarized the four potential benefits to identify genes determining traits of interest, the oftheassociationmappingapproach:(1)itallowsas- properchoiceofgeneticmaterialsisessential.Geneti- sessmentofthegeneticpotentialofspecificgenotypes callydefinedplantmaterialssuchasnear-isogeniclines before phenotypic evaluation; (2) it allows the iden- oranyothertypesofgeneticstockshavingdeletionsor tification of superior trait alleles in germplasm; (3) it additionswithinnarrowregionsofthegenomearecon- canassistinhighresolutionQTLmapping;and(4)it sidered efficient for this purpose. However, there are canbeusedtovalidatecandidategenesresponsiblefor nosuchgeneticstocksavailableforgenomicstudiesin individualtraits(Gebhardtetal.,2004). lentil. Creation of suitable genetic stocks suitable for The important issues to consider in designing applicationofadvancedgenomictoolsneedstobecon- andimplementinganyassociationmappingstudiesin sideredaspartoftheoveralllentilbreedingapproach. plants are: (1) determination of the population struc- Breeding strategies will have a significant impact on ture (Pritchard et al., 2000); (2) estimation of nu- long-termapplicationofadvancedgenomictoolsand cleotide diversity (Zhu et al., 2003); (3) estimates of theresultscanbere-appliedtotraditionallentilbreed- haplotype frequencies and LD (nonrandom associa- ing programs. In this section, we discuss feasible ap- tion of alleles at different loci) (Flint-Garcia et al., proaches to generate new genetic stocks and the use 2003);and(4)preciseevaluationofphenotypes(Neale in high throughput techniques that may benefit lentil & Savolainen, 2004). For lentil, the information re- genomicsandbreeding. garding nucleotide diversity and LD may be inferred from the Medicago truncatula sequencing project (www.genome.ou.edu/medicago) in conjunction with Developmentofnewgeneticmaterials comparativemappingbetweenM.truncatulaandlentil. TheUSDA-ARSlentilgermplasmprojectproposesto (1) Alien gene transformants. One of the direct ap- determinethepopulationstructureofthelentilcorecol- proachestocreategeneticmaterialswithenhanced lection(Simon&Hannan,1995)using30mappedSSR trait values are transformation of foreign genes markers.Theevaluationofthecorecollectionwillbe of which functions were validated. Although this

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Application of biotechnology in breeding lentil for resistance to biotic and . Salinity is an important stress factor in the Indian sub-continent.
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