Introduction to on-farm Organic Plant Breeding

Introduction to On-farm Organic Plant Breeding www.seedalliance.org

Introduction to On-farmOrganic Plant Breeding

Organic Seed AllianceAdvancing the ethical development and stewardship of the genetic resources of agricultural seedPO Box 772, Port Townsend, WA 98368

This publication was made possible through a grant from Organic Farming Research Foundation and Seed Matters

Introduction to On-farm Organic Plant Breeding www.seedalliance.org2

Section I: Introduction...................................................................................................................................................3 Whyplantbreedingisimportant......................................................................................................................................3 Aphilosophyoforganicplantbreeding.........................................................................................................................4 Ourfarmingancestorsneverstoppedbreeding...........................................................................................4 Returningfarmerstotheirroleasseedstewards........................................................................................4

Section II: Plant breeding basics...............................................................................................................................5 Selectionintheoryandpractice........................................................................................................................................5 Howtoselect..............................................................................................................................................................................8 Acropsmatingsystemandhowitaffectsplantbreeding.....................................................................................8 Self-pollinatedcrops................................................................................................................................................9 Cross-pollinatedcrops............................................................................................................................................9 Breedingself-pollinatedcropsvs.breedingcross-pollinatedcrops..................................................................9

Section III: Developing a plant breeding plan.....................................................................................................12 Thinkingaboutyourtargetenvironment...................................................................................................................12 Determiningtraits.................................................................................................................................................................13 Prioritizingtraits...................................................................................................................................................................13 Howcanthetraitsbemeasured?.....................................................................................................................13 Howeasilycanthetraitsbeinherited?.........................................................................................................14 Choosingparents...................................................................................................................................................................13 Creatingabreedingtimeline............................................................................................................................................15

Section IV: Theories of field-based organic plant breeding...........................................................................21 Howgenestravelfromparentstooffspring..............................................................................................................21 Howgenesdeterminetheappearanceandperformanceofplants..................................................21 Howgenestraveltogetherduringreproduction......................................................................................22 Howgenesoperateinpopulations................................................................................................................................24 Howtoseethegeneticdifferencesbetweenplants...............................................................................................28 Understandtheeffectsoftheenvironment.................................................................................................28 Ensurethatplantsreceiveconsistenttreatment.......................................................................................29 Usesufficientpopulationandplotsizes.......................................................................................................29

Section V: Examples of farmers breeding for organic systems......................................................................30 AbundantBloomsdaleorganicspinachbreedingproject...................................................................................30 Whatwerethegoalsofthisproject?..............................................................................................................30 Breedingprocedure...............................................................................................................................................30 WinterSproutingBroccoli...............................................................................................................................................31 Whatwerethegoalsofthisproject?..............................................................................................................31 BreedingProcedure...............................................................................................................................................31

Glossary and index.......................................................................................................................................................33

References and resources..........................................................................................................................................36

Table of Contents


Why plant breeding is importantThehistoryofthedomesticationofourcropplantsisalsothehistoryofplantbreeding.Throughmanygenerationsoflaborioushumanselection,wildplantsbecameusableasagriculturalcrops.

Ourhunter-gathererancestorshadtohaveanintimaterelationshipwithplantstonoticethegeneticvariationthatexistedandcontinuallyaroseinordertomakemeaningfulprogressinthedo-mesticationprocess.Thisisoneofthefundamentalpreceptsofplantbreedingandgivestheseearlyinnovatorsfullstatusasplantbreeders.

Coupledwithearlyhumanselectionwasastrongelementofnatural selection.Alloftheancestorstoourmoderncropspeciesweregrownwithoutsup-plementalnutrition,fertility,orpestprotectants,andwereconstantlyexposedtothechallengesoftheenvironment.Thebestofthefarmer-breed-ersspedthisprocessalongbyselectingfromthemostdesirableplantsfortheirfoodandfibervalue,usingtheseastheparentalstocksforsubsequentgenerations.Thisbalancebetweenhumanandnaturalselectionpersisteduntilthebeginningoftheindustrialagriculturaleraofthe20thcentury.

Allagriculturalcropshavecontinuouslychangedwiththeselectionpressuresappliedfrombothfarmersandtheenvironmentsinwhichtheywerecultivated.Whenfarmersandtheenvironmentchanged,thecropchanged.Manyofourcropscon-tinuetochangeandadapttonewchallenges.

Thenumberofenvironmentsthatcropsarebredin,andthenumberofbreeders,havebothshrunkoverthepast100years.Thisisbecausefarmersinmostagriculturalregionsoftheglobedolittleornoplantbreedinganymore,andthenumberofre-gionalizedseedcompaniesdoingbreedinghasalsodrasticallyshrunkinthepast40to60years.

Withtheadventoftheindustrialagriculturalmodeltherehasbeenanarrowingofthesetoftraitsthatareconsideredcriticaltotheproductionofmostmoderncrops.Theindustrialmodelhasalsoled

toagradualspecializationshiftinwhereandhowmanyofthemosteconomicallyimportantcropsaregrown.Inthepre-industrialagriculturalera,almostallcropswerespreadacrossmanyenvironmentalandgeographicnichestosatisfythediversityofagriculturalsettlements.Thismeantthattheywereconstantlyadaptingtoadiversityofclimaticcondi-tionsandtheever-changingneedsofthehumanag-riculturalsocietiesthatwereusingthesecrops.Thefarmersineachregionwerethebreeders.Somefarmerswereundoubtedlybetterbreedersthanothers.Therehasalwaysbeensomespecializationinmanyaspectsofagriculturalsocieties,butinthispre-industrialera,everyagriculturalcommunitycertainlyhadtheseedneededbythatcommunity.Seedofeachofthesecommunityvarietiesweregeneticallyuniquefromasimilarvarietyofthesamecropinthenextcommunity.Thispatchworkofuniquevarietiesisthenmultipliedthousandsoftimesacrosstheuniqueenvironmentsofagricul-turalcommunitiesaroundtheglobe.

Cropgeneticdiversityinthepre-industrialerawasalsomuchgreaterthanwhatcurrentlyexistsinmodernagriculturebecausethediversitywithineachcommunityvarietywasfarricher.Farmersdidnotdemandthekindoftraituniformitythatisnowthenorminourmoderncrops.Thisallelic*di-versitywaspartofeverycroppopulationandwasreflectedbymanyuniquegenotypes(andpheno-types)ineachfield.

TherewasagreatblossomingofseedcompaniesinNorthAmericaandEuropeinthesecondhalfofthe19thcentury.Withtheadventofseedasacommercialcommodity,andtheemergenceofseedcompanies,therewasanincentivetoproduceseedofcropvarietiesthatweremuchmoreuniformandpredictable.Theseearlyseedcompanieswereregionalinnature.Theyreliedonacentralstoreinametropolitancenterandsupplementedwithmailordersformuchoftheirbusiness.

Theindustrializationofagricultureinthe20thcenturyledtoamuchhigherdegreeofspecializa-tion.Specificregionswithmoreidealclimatesforacertaincroptypeandprimeagriculturallandbe-camecentersoflarge-scaleproductionforcertaincrops.Inaddition,plantbreedingprogramsstarted

I. Introduction

*Definitionsfortechnicalwordsthatareitalicizedandboldedcanbefoundintheglossary


cateringtoindustrializedsystems,frommechanicalplanting,cultivation,andharvesting,totheneedsofthepackers,shippers,andretailershandlingthecroppost-harvest.

The philosophy of organic plant breedingAsorganicplantbreeders,wehaveanopportunitytoshapeorganicagricultureinfundamentalways.Bymakingnewvarietiesavailabletoorganicfarm-ers,weareabletogivethesefarmersnewoptions.

Buildingahealthy,sustainableagriculturefuturerequiresfarmer-centricseedsystemsatthere-gionallevel,wherefarmersandthecommunitiestheyserveconsciouslychoosewhichcropgeneticstheyuse,howtheyaremaintained,andhowthesegeneticsarecontrolled.

Donewell,organicplantbreedingcanhelpensurethatfarmerscontroltheseedtheyuse.Breedingworkcangivefarmersfreeaccesstogeneticre-sourcesandthefreedomtogrowwhattheyplease,whilesupplyingthemwiththeknowledgeandskillstobothgrowseedandimproveacropschar-acteristicstobestmeettheirneeds.

Overthepastseveraldecades,plantbreedinghasbecomeincreasinglyformalizedandcentral-ized.Breedingworkthatwasoncedonemainlyinfarmersfieldsisnowdonealmostexclusivelybylargeseedcompaniesandonstate-runagricul-turalexperimentstations.Mostbreedersworkingforlargeseedcompanies,aswellasmostpublicbreeders,focustheirattentionprimarilyonthelargestmarketsforseed,whicharetypicallylarge,conventionalfarmingsystemslocatedinprimeagriculturalregions.Thisfocusontheneedsoflarge-scale,conventionalagricultureleavesorganicfarmerswithoutvarietiesthatareadaptedtotheneedsoftheirsystems.Researchhasfoundthatthelackoforganicallyadaptedvarietiesleavesorganicfarmersatadisadvantage,resultingin,amongotherthings,loweryieldsthaniftheyhadvarietiesadaptedtotheirsystems.Organic,on-farmbreed-ingworkisdevotedtoservingtheneedsoftheseorganicfarmers.

Our farming ancestors never stopped breedingAllgoodfarmerswhosurvivedandflourishedwere,bynecessity,plantbreeders.Theyusedob-

servationalskillstodetermineandselectthebestadaptedplantseveryyear.Thismeantselectingthehighestyielding,besttasting,andmostdisease-re-sistantplants.Alloftheheirloomcropvarietiesweknowandenjoytodayweredevelopedoveralong,richperiodofourhistory,tellingthetaleofourplantbreedingancestorswhoweremakingselec-tionsandsavingseedfromthehealthiestandmostvigorousplantsyearafteryear.Thesefarmerswereconstantlystrivingtoimprovevarietiestobettersuittheirneeds,engaginginaconstantdanceofimprovementandco-evolutionwiththeirfood.

Theseancestorswereneverfullysatisfiedwiththecropstheyhad.Theywantedtoimprovetheirfarmer-bredvarieties(sometimescalledlandra-ces),sinceitcouldmeanthedifferencebetweenlifeanddeathfortheirfamiliesandcommuni-ties.Modernorganicfarmerswhoarechoosingtoproduceandselectcropvarietiestoflourishintheirregionalagro-ecosystemsarerubbingshoul-derswiththebestfarmer-breedersofthepastwhodomesticatedandcontinuallyimprovedourcropgeneticresources.

Therewillalwaysbeaneedtoadaptnewvariet-iestocurrentchallenges,suchasclimatechange.Classicalplantbreedingallowsustoselect,adapt,andcontinuallyco-evolvewithourfoodcrops.Thisformofplantbreedingisnottobeviewedasmessingwithnature,anditiscertainlynotgenet-icengineering.Theprinciplesofevolutionshowusthatthereisalwaysvariationinbiologicalpopula-tions,environmentalconditionsalwayschange,andnobiologicalentityeverstaysthesameinresponsetoitsenvironment.Inotherwords,noorganismiseverstaticinnature.Selectionpressureandchangeovertimeareinevitable.Weadvocateforanevolu-tionarybreedingmodelthatallowsthevarietiesweusetobepartofthesustainableagriculturalsys-temswearepioneering.

Returning farmers to their role as seed stewardsOurworkatOrganicSeedAlliance(OSA)isintend-edtoempowerfarmerstoagainbepartoftheseedsystemthatmostfarmershavebeendivorcedfromforalmost100years.Overthelastcentury,wehavenotonlylostvaluablegeneticdiversitythroughmodernagriculturalpractices,wehavealsolostmuchofthefarmerknowledgeneededtosteward


thegeneticresourcesthataremostimportanttothemandtheircommunities.Webelievethereisjustasmuchimportantworktobedoneintrainingfarmerstobreed,maintain,andgrowhigh-qualityseedcropsadaptedtotheneedsoflow-input,agro-ecosystemsasthereisforpreservingthegeneticresourcesofthepast.Thebestwayforvaluablegeneticresourcestobecomepartofmodernag-ricultureistogetthemintothehandsoffarmers.Asskilledstewards,thesefarmerswillcontinuetoadoptandfurtheradaptthegeneticstotheirneeds.Itisthereforecriticalthatfarmersfirsthaveaccesstothesegeneticresources.

Ourbreedingworkisdoneonagro-ecologicalfarmsbyapplyingsoundclassicalplantbreedingmethodology.Weemphasizebuildinggeneticresil-ienceanddiversityintoeverycroppopulation.Ourplantbreedingworkstrivestoestablishadiversi-fiedandecologically-basedagriculture,tofosterthemanagementofcropsgeneticsattheregionallevel,andtostrengthenaregionseconomy.OSApromotesthestewardshipofseedinamannerthatencouragestheadaptationofplantgeneticstotheecologicalandmarketneedsoffarmersandthecommunitiestheyfeed.Thisincludeshelpingfarmersperformon-farmplantbreedinginthesamemannerasourmostinnovativeancestors.Tonotencouragesuchimprovementswouldbeadisservicetofarmers,eaters,theplanet,andfuturegenerations.

Thissectioncoversthebasicsofhowtocreateandimprovevarietiesforyourorganicfarm.Firstwedescribethebasicstepsofplantbreeding.Thenwedescribesomebasicgeneticprinciplesandhowtheyapplytoplantbreeding.

Initsessence,plantbreedingcanbeboileddowntothefollowing:

Select plants with superior genes from a genetically variable population of plants.

Howyoudothiswilldependonyourgoals,thecropsyouareworkingon,andthetimeandre-

sourcesyouwanttoinvest.

Selection in theory and practiceSelectioninplantbreedingreferstotheprocessofchoosingwhichplantsproducethenextgenerationofapopulation.

Therearetwomajortypesofselectionappropriateforon-farmbreeding:massselectionandfamilyselection.Therearebenefitsanddrawbackstoeachtypeofselection.Whetheryouuseoneortheother,oracombinationofboth,willdependonthecropyouareimprovingaswellasyourtimeframe,resources,andultimategoals.

Withmass selection,youmakeselectionsbasedonhowindividualplantswithinapopulationperform.Massselectionisthemoststraightforwardbreed-ingmethod.Assuch,itrequiresminimumtime,labor,andrecordkeeping.Becauseofthesimplicity,itcanmakeworkingwithlargepopulationsmorepracticalduringthebreedingprocess.However,itdoeshaveafewdrawbackswhencomparedtofamilyselection.First,becauseyourselectionsarebasedsolelyontheplantsphenotype(itsoutwardappearance),youaremorelikelytochooseaplantbasedonenvironmentalinfluenceratherthanonsuperiorgenetics.Forexample,thesoilwherethatplantisgrowingmaybemorefertileincomparisontoaneighboringspotinthefield.Theseconddraw-backwithusingmassselectionisthepotentialthatundesirablerecessive genesmaybecarriedbytheplantsyouselectinahiddenheterozygousstate.

Griddedselectionisonetechniquethatcanbeusedwhendoingmassselectiontohelpaccountfortheinfluenceoffieldvariationonplantpheno-types.Whenusinggriddedselection,imaginethefieldthatisplantedwithyourbreedingpopulationdividedintoagridofsmallersections.Forexample,thefieldcouldbedividedintoquarters.Whense-lecting,attempttoselectanequalnumberofplantsfromeachsection.Evenif,forexample,theplantsinthenorthwestcornerofthefieldlookinferioringeneraltotheotherquarters,selectthebestplantsfromthatsection.

Incontrasttomassselection,withfamilyselec-tionyouarelookingattheoverallperformanceofagroupofrelatedplants(afamily)andusingthe

II. Plant Breeding Basics


Figure 2. This diagram exhibits the steps to execute family selection in three successive steps.

familysoverallperformancetomakeselections.Infamilyselection,youplantaseriesofrowsofplants,whereeachrowcomesfromseedsavedfromasingleselectedplantfromthepreviousgeneration.Theadvantagesoffamilyselectionaretwo-fold.First,becauseyouaremakingselectionsbasedonawholerowofplantsthatarecloselyre-lated(siblingsorsibs),ormorethanonerowforeachfamilyifyouareusingreplication(seemore

Key: Each star represents a selected plant

Gridded Selection

Figure 1. Gridded selection is one technique that can be used when doing mass selection to help account for the influ-ence of field variation on plant phenotypes.

aboutthisconceptbelowinthetheorysection),itbecomeslesslikelythatyoumightselectplantsbasedontheinfluencesofverylocalizedenviron-mentaleffects.Second,becauseyouareabletoseemanycloselyrelatedplantsnexttoeachother,youaremorelikelytospotsomeplantsexhibitingdeleteriousrecessivetraitsthatmaybecarriedinagivenfamily.


Figure2exhibitsthestepstoexecutefamilyselec-tioninthreesuccessivesteps.Instep1,eachoftherowsisafamilyinacornbreedingprogram,withthesamerowrepresentedlefttorightsequentiallyacrossthethreeselectionsteps.Step1involvesevaluatingeachfamilyasawholebasedontheper-formanceoftheentirerow.Step2istoeliminateanyfamiliesthatdonothaveahighproportionofsuperiorplants.Althoughtherearenohardandfastrulesinplantbreeding,whendecidingwhichfamiliestoselect,atOSAweeliminateafamilyunlessithasatleast60to70%acceptableplants.Onceyouhavedeterminedwhichfamiliestokeep,step3istoeliminatethepoorest30to40%oftheplantswithinthesefamilies.Step4showsthefinalfieldarrangement,withonlytheselectedplantsintheselectedfamiliesremaining.

Thefamiliesthatareusedinfamilyselectioncancomeinvariousforms.Threeofthemostcommonformsarehalf-sibfamilies,full-sibfamilies,andS1families.Half-sib(HS)familiesarefamilieswherealloftheplantsshareacommonmotherbutmayhavedifferentfathers.Youwouldproduceahalf-sibfamilybysavingseedfromaplantthathasbeenallowedtoopenlypollinatewithmanyotherplants.Alloftheseedyousavefromthatplantsharesamother,buteachseedwaspotentiallycreatedbyfertilizationwithpollenfromdifferentfathers.Plantsinafull-sib(FS)familysharebothamotherandfather.Youwouldproduceafull-sibfamilybyconductingacontrolledpollinationbetweentwoplants.PlantsinanS1familyallcomefromaself-pollination.Inotherwords,theyallsharethesamesingleparent,whichactedasbothmotherandfather.Allthreeofthesefamilieshavetheiruses.Ingeneral,asyougofromfamilieswithlessrelat-ednesstofamilieswithmorerelatedness(HStoFStoS1),thefamiliesbecomemoreuniform.Thisuniformityallowsyoutobetterpredicthowtheir offspringwillperform.Inaddition,withS1familiesinparticular,youarebetterabletoseethetraitscontrolledbyrecessivegenesinthatfamily.How-ever,FSandS1familiesoftentakemoretimeandeffecttoproduce,andtheycreateagreaterriskforinbreedingincross-pollinatingspecies.

Selectioncan,andshould,bedoneatmanypointsthroughouttheseason.Selectionfortraitssuchasgermination,vigor,plantstature,leafshape,color,

andweedcompetitivenesscanoccurearlyintheseason.Byplantingatahighinitialdensity,someofthesetraitscanbeselectedforduringthethinningprocess.Manyvegetablecrops,suchascarrots,let-tuce,cabbage,onions,andkaleproduceaharvest-ablecropbeforepollination.Ontheotherhand,theharvestablecropofsomecroptypes,suchascorn,wintersquash,tomatoes,andmelons,canonlybeevaluatedafterpollinationoccurs.Itisdesirabletodoasmuchselectionaspossiblebeforepollina-tionoccurstoincreasetherateofprogressofyourbreedingwork.Anyselectiondoneafterpollinationislesseffectivethanselectiondonebeforepollina-tion.Thisisbecauseinthelatterscenariothepol-lenfrominferiorplantsisallowedtofertilizethesuperiorplants,thuspassingtheirgenesontothenextgeneration.

Thefinalconcepttounderstandinselectionistheselection intensity.Inessence,theselectioninten-sityisbasedonthefractionofplants,orfamilies,youselectfromthestartingpopulation.Forexam-ple,youwouldbepracticingagreaterintensityofselectionifyouselectedonly50plantsoutof500tosaveseedfromthanifyouselected300plantsoutof500.Asyouincreasetheselectionintensity,youwillmakemoreprogressinyourbreeding.However,especiallyincross-pollinatedcrops,youneedtoavoidendingwithtoosmallofapopula-tion,whichcanincreasetheriskofinbreedingdepressionorlosingvaluablegeneticdiversitythatyoumayneedinthefuture.Ageneralguideontheminimumnumberofplantstokeepinyourpopu-lationcanbefoundinOSAsSeed Saving Guide for Gardeners and Farmers.Becauseitisimportanttoavoidgoingbelowtheseminimumpopulationsizerecommendations,thebestwaytoincreaseyourbreedingefficiencythroughincreasingtheselec-tionintensityistostartwithmoreplants.

Therearetwobroadtermsthatconveytheinten-sityofselection.Thetermpositive selectionisusedwhenasubstantialfractionoftheplantsinapopulationarebeingremoved.Negative selection,alsoknownasroguing,referstotheremovalofonlyasmallfractionofthepopulation,usually10to20%orless,duringaseason.Manytimes,suchaswhenmaintainingavariety,negativeselectionmaybeallthatisneeded.Evenifyouareunsureofwhichplantsarebestinyourpopulation,youwill


probablybeabletospotandremovethepoorestperformingplantsandtheplantsthatareobviousoff-types.Thisconceptisbestexpressedintheoldplantbreedingaxiom:IdontalwaysknowwhatIlike,butIalwaysknowwhatIdontlike!

How to selectHowdoyouactuallypracticeselectioninthefield?Thereareanumberofmethodsforchoosingwhichplantswillproducethenextgenerationofthebreedingpopulation.Afewofthesemethodsaredescribedbelow.

Eliminate inferior plants or entire families as you identify them.Thismethodcanbeeasilyusedwhenselectingfortraitsduringthinning,asmentionedabove,orwhenpracticingnegativeselection.Thismethodhastheadvantageofbeingverysimpleanddirect:cutdown,hoeout,orpullupanyplantsthatdonotmeetyourselectioncriteria.Themethodhasafewlimitations,however.First,ifyourbreed-ingpopulationhasrelativelyfewgoodplantsandrequiresahighselectionintensity,itcanbemoretime-consumingtoidentifytheinferiorplantsinsteadofidentifyingthefewsuperiorplants.Sec-ond,ifyouarelookingformultipletraitsatonce,andyoudontexpecttofindplantsthatperfectlyexhibitthesetraits,youmayneedamorerobustwayofselectingplantsbasedontheiroverallper-formanceacrossmultipletraits.

Select superior plants or families as you see them. Thismethodistheconverseoftheonejustde-scribed.Typicallyyouwalkyourbreedingfieldonanumberofoccasionsthroughouttheseason,evalu-atingforoneormoretraitsatappropriatetimes.Toselectaplantorfamily,placeaflagorstakenexttotheplantorfamily.Youcanusedifferentcoloredflagsduringevaluationsfordifferenttraits,oryoucanmakenotesonastakeorinanotebooktodescribewhyyouareselectingcertainplantsorfamilies.Thismethodisusefulwhenfindingasmallpercentageofsuperiorplantsorfamiliesoutofalargerpopulation.Thismethodcanalsocutdownonextensiverecordkeepingwhenthechoicesofwhichplantsorfamiliestoselectareobvious.

Select superior plants of families based on data. Thismethodinvolvesrecordingmeasurementsorscoresforeachplantorfamilyforthetraitsof

interest.Thedataisthenusedtomakeselections.Thismethodisthemosttimeandlaborintensiveofthethreeandonlybecomespracticalwhendealingwithsmallernumbersofplantsorfamilies(lessthanafewhundred).However,thereareanumberofreasonstousethismethod.First,thismethodisusefulforidentifyingasmallnumberoffamiliesthatperformedbestbasedonarangeoftraitsthataremeasuredovertheseason.Forexample,sayyouwanttopickoutthebestkalefamiliesbasedonearlyvigor,leafcolor,resistancetoearlyaphidpressure,andlengthofharvestseason.Inthiscase,youmayneedtomakeyourselectionattheendoftheseason,butyouwillneeddetailedinformationabouteachfamilysperformancethroughoutthewholeseason.Second,thismethodhelpsincaseswherethetraitsarenotimmediatelyvisiblebutyouneedsomemeasurementstoevaluate.Thesemeasurementsmightincludeweighingyieldsormeasuringplantheights.Third,thismethodworkswellwhenyouhaveplantedyourfamiliesinmulti-plereplicationsandwanttofindtheaverageper-formanceofafamilyacrossallreplications.

Whenrecordingdatatoguideselections,atraitcaneitherbemeasuredorscored.Tomeasureatrait,toolssuchasscalesoryardsticksareusedtogetavalue.Toscoreatrait,youassignavaluetoaplantorfamilybasedonaratingsystem.Forexample,youmightscoreleafsizeonascalefrom1to9,where1representsatinyleafand9representsalargeone.Whenscoringtraits,beginbywalkingtheentirefieldtoassesstherangeofexpressionwithinthepopulationforthetraitofinterest.Theplantsorfamilieswiththeworstorleastdesirableexpressionofthetraitwillbethe1onyourscaleandtheplantsorfamilieswiththemostdesir-ableexpressionwillbeyour9.Thenproceedtoscoreallplantsorfamiliesbasedonthatrange,attemptingtousethewholerangeofscoresfrom1to9.MoreinformationonhowtoconducttheseevaluationscanbefoundinOSAsOn-farm Variety Trials: A Guide for Organic Vegetable, Herb, and Flower Producers.Boththisguideanddatasheetsforevaluatingandselectingplantsareavailableforfreedownloadatwww.seedalliance.org.

A crops mating system and how it affects plant breedingThewayaplantmatescanbedescribedasfalling


alongaspectrumbetweenstrongly self-pollinating andstrongly cross-pollinating.Whereacropfallsonthisspectrumhasseveralimplicationsforwhichbreedingmethodwillbemosteffective.Thisideawillbediscussedindetailbelow.

Self-pollinated cropsInplants,self-pollinationoccurswhenthespermofanindividualplantfertilizesanovuleofthesameplant.Essentially,theplantmateswithitself.Theplantsinbredoffspringreceivealloftheirgenesfromthisoneandonlyparent.Thus,theoffspringareverygeneticallysimilartothisparent.Allpre-dominatelyself-pollinatingplantshaveperfectorbisexualflowers,whereboththemaleandfemalesexualstructuresareborneineachflower.Self-pol-linatingplantsalsohaveflowersthatexcludecross-pollinationasdescribedbelow.

Therearetwoimportantadvantagesofself-pol-lination.First,inplantsthathaveevolvedtobe-comeextremelywelladaptedtotheirenvironment,self-pollinationoffersawaytoensurethataplantsoffspringwillbejustaswelladaptedasitsparents.Inotherwords,self-pollinationisawayofreplicat-ingsuccess.Second,self-pollinationhelpstoensurereproductivesuccessunderavarietyofenviron-mentalcircumstances,asitdoesnotrequirethepresenceofwind,insects,oranimalstotransferpollenfromoneplanttoanother.

Theplantsthatwecallstrongly self-pollinatingrelyalmostcompletelyonself-fertilizationtoreproduce.Theperfectflowersoftheseplantshaveevolvedwaysofexcludingpollenfromotherflowerstopreventcross-pollination.Forexam-ple,theflowersofmostmoderntomatovarietieshaveanthersthatformaconearoundthepistil,effectivelysealingofftheflowersstigmafromanypollenotherthanitsown.Inpeas,thepet-alsofthefloweraretypicallyclosedwhenthestigmafirstbecomesreceptivetopollen,givingpollenfromitsownanthersexclusiveaccesstothestigma.Whenthepeafloweropens,itisnearlyalwaysalreadyfertilized.Otherexamplesofstronglyself-pollinatingplantsincludecom-monbeans,wheat,andoats.

However,evenastronglyself-pollinatingplantwilloccasionallycrosswithanotherplantofthe

samespecies.Forexample,beescaneatthroughortearopenflowersanddepositpollenfromadifferentplantofthatspecies.Anumberofplantbreedersandseedgrowershavealsonotedthatwiththeincreaseofinsectactivitythatusuallyoccursinorganicallymanagedsystems,thereisoftenanincreaseinthepercentageofcrossesthatoccurinstronglyself-pollinatingplantspecies.Also,undercertainclimaticconditions,theflow-ersofsomeself-pollinatingplantswillopenearli-erthannormalandthestigmawillbereceptivetoreceivingpollenfromanotherplantbeforeithasachancetoself-fertilize.Andofcoursehumanscanperformcontrolledcrossesbetweenself-pol-linatingplantsbyintentionallytransferringpollenfromoneplanttoanother.

Cross-pollinated cropsOntheotherendofthebiologicalspectrumarecross-pollinatedplants.Cross-pollinationoccurswhenthespermofoneplantfertilizesaneggofadifferentplantofthesamespecies.Inotherwords,aplantmateswithanotherplantofthesamespe-cies.Whentwoplantscross-pollinate,theyproduceoffspringthataregeneticallydifferentfromeitherparent.Ingeneral,allplantshavethepotentialtocross-pollinate,becauseeveryplantcanbefertil-izedbyanotherplantofthesamespecies.

Thecentraladvantageofcross-pollinationisthatitfacilitatesaplantspeciesabilitytoadapttochang-ingenvironments.Plantspeciesthatconstantlymixtheirgenesintonewcombinationsincreasethelikelihoodthatatleastafewindividualswithinthespecieswillhavetherightcombinationofgenestowithstandnewenvironmentalchallenges.

Breeding self-pollinated crops vs. breed-ing cross-pollinated cropsThematingsystemofthecropaffectsbreedingstrategiesinsomefundamentalways.Self-polli-natedcropsneedlessisolationdistancefromeachotherandothercompatiblespeciesthancross-pol-linatedcropstoavoidunintendedcross-pollination.Theneedforlessisolationmakesiteasiertoman-ageseveralsimultaneousbreedingprojectsofthesamespeciesinalimitedspace,andwillallowyoutogrowyourbreedingprojectnearacommercialcropwithoutthreatofcross-contamination.Itisgenerallyhardertomakecrossesbetweenself-pol-


linatedplantsthancross-pollinatedones.Inordertoovercomeaself-pollinatedplantstendencytoonlyself-pollinate,somehandlaborisoftenre-quired,suchasremovingthemalepartsofoneplant(knownasemasculation)andcollectingandbringinginpollenfromanotherplant.Foron-farmbreedingprojects,cross-pollinatedcropscanbehandledwithsimpletechniqueslikestraincross-ing,explainedbelow.

Thechallengeofcross-pollinationinself-pollinatedcropshasanimportantadditionaleffect.Popula-tionsofcross-pollinatedcropscaneasilycross-pollinateandrecombinetheirgenes.Ontheotherhand,afteraninitialcrossismadeinaself-polli-natedcrop,eachsubsequentgenerationofself-pol-linationrapidlyfixesgroupsofgenes.Seebelowforanillustrationofthisphenomenon.

Doingbreedingworkwithself-pollinatedcropsallowsyoutoeasilycreateuniformvarietiesfromcrosses.Oncethesevarietiesaredeveloped,theyaremucheasiertomaintaincomparedtocross-pollinatedvarieties.

Finally,self-pollinatedcropssufferlessfromin-breedingdepression.Thisallowsyoutoworkwithfewerplantsinaself-pollinatedbreedingprogramcomparedtoacross-pollinatedbreedingprogramandstillproduceavigorousvariety.

Asfigure3shows,ifwefollowthegenerationsofplantsafteracrossismadeineitheraself-pol-

Comparison of Attributes of Self- and Cross-pollinated Crops

Self-pollinated crops Cross-pollinated crops

Isolation Less More

Crossing Harder Easier

Self-pollinating Easier Harder

Inbreeding depression Less More

linatedspeciesorinacross-pollinatedspecies,fundamentaldifferencesariseinthestructureofthepopulations.Inacross-pollinatedspecies,theplantsineachgenerationareabletointermate.Intermatingcreatesaunifiedgene poolandallowsnewcombinationsbetweenplantstobemadeeachyear.Incontrast,unlesshumansintervenetomakeadditionalcrosses,self-pollinatedplantswillself-pollinateineachgenerationaftertheinitialcross.Self-pollinatingineachgenerationleadstoeachplantderivingseparatefamiliesorlines.Ineachgeneration,theplantsineachfamilywillbecomemoreuniformwithinthefamily,whilestrongerdifferenceswillarisebetweenfamilies.Thegeno-typesofeachfamilybecomefixed,andnewgeneticcombinationsbetweenfamiliesonlyoccurthroughhand-pollinationorthroughrarenaturalcross-pollination.Theconsequenceforbreedersisthat,whendealingwithself-pollinatedcrops,asufficientnumberoflinesmustbecreatedandmaintainedtofindalinethathasallofthetraitsofinterestfrombothparents.Incontrast,thegenepoolofcross-pollinatedcropscanbegraduallyimprovedbyeliminatingtheworstplantsorfamilies,andallow-ingthebesttocross-pollinatetocreatenewcom-binationsthatmaycontainthedesiredtraitsfrombothparents.

Inbreeding depressionisalossofvigorduetoself-pollinationorthecrossingofgeneticallysimi-larplants.Essentially,inbreedingdepressionisthereverseofheterosis(hybridvigor).Inbreedingdepressionresultsfromtheaccumulationofho-


mozygouspairsofrareanddetrimental recessive alleles.Tosimplifytheidea,figure4servesasanexamplewherethereisararemutantrecessiveallele,a,inapopulation.Ifaplanthastwocop-iesofthisallele(aa),theplantcannoteffectivelyproducechlorophyll.Theplantappearsverylightgreenandgrowspoorly.Aslongasaplanthasonecopyofthefunctioningallele,A,itwillbeabletoproducechlorophyll.Inotherwords,plantswiththegenotypeAAorAaarehealthy.Asmallfractionofthepopulationcarriesthisalleleasaheterozy-gote(Aa).WhentheseAaplantscross-pollinate(ontheright-sideoffigure4),almostallofthepollentheyreceivewillcarrythedominantAallele,andtheiroffspringwillbehealthy,evenifhalfoftheoffspringarecarryingthedeleteriousrecessiveaallele.However,iftheseheterozygousAaplantsself-pollinate,oriftheypollinatewithcloserela-

tives,thesituationchanges.Asyoucanseeontheleftinfigure4,whenoneoftheseplantsself-pol-linates,25%oftheiroffspringwillbehomozygousaaandwillshowthedetrimentaleffectsfromhav-ingtwocopiesofthisallele.Mostcross-pollinatingplantscarrymanydeleteriousrecessivealleles.Theseplantsrelyoncross-pollinationamonglargepopulationstoavoidinbreeding.Withself-pollinat-ingplants,ontheotherhand,selectionhasactedovermanygenerationstoweedouttheplantswithdeleteriousalleles.

Figure 3. This diagram show how populations of self-pollinated and cross-pollinated crops differ in their genetic structures.


Thinking about your target environmentInaperfectworld,plantbreederscoulddevelopva-rietiesthatthrivedinanysituationandanywhereontheplanet.Infact,mostlargeseedcompaniesstrivetoproducevarietiesthatcanbegrownacrosswidegeographicregionsinmanyagriculturalsitua-tions.Thisconceptisknownasbroad adaptation.However,varietiesthatarebroadlyadaptedmaynotbethebestvarietyforanygivenarea,andtheymayrequirehighlevelsofinputstorecreatethegrowingenvironmentunderwhichtheywerebred.Creatingbroadlyadaptedvarietiesmayalsore-quireextensivetestingthatmostsmallerbreedingprogramsdonothavetheresourcestoundertake.Incontrasttobreedingbroadlyadaptedvarieties,specifically adaptedvarietiesarebredtoexcelinspecificenvironments.Thesevarietiesarenotex-pectedtodowelleverywhere,justinthetargeten-vironment.Theconceptoftherelativeperformance

ofavarietychangingbasedontheenvironmentitisgrowinginiscalledthegenotype by environ-ment interaction(GxE).

Oneofthefirststepsinplanningabreedingproj-ectistoidentifythetargetenvironment.Theenvi-ronmentcanbeasbroadornarrowasyouchoose,keepinginmindthatadditionalresourceswillberequiredasthebreadthoftheprojectincreases.Developingabroadlyadaptedvarietywillrequiremoretimeandresourcesthandevelopingavari-etyspecificallyadaptedtoyourlocalconditionsandchallenges.

Whendetailingthetargetenvironmentwhereyouwantyourvarietytoexcel,thereareseveralimpor-tantfactorstoconsider.Someoftheseare:

Geographicregion(daylengthandfrost-freeperiod)Temperatureregime(highs,lows,fluctuations,andcumulativeheatunits)Rainfall(amountandtiming)

Figure 4. Inbreeding depression results from the accumulation of homozygous pairs of rare and detrimental recessive alleles. This diagram serves as an example where there is a rare mutant recessive allele, a, in a population.

III. Developing a Plant Breeding Plan


SoiltypeDiseasepressuresWeedpressures

Youshouldalsoconsiderculturalfactorsinyourtargetenvironment,suchas:

Croppingsystem(directseedingvs.transplanting)Irrigationsystem(overhead,drip,orflood/furrow)Fertilization(typeandfrequency)Cultivationtechniques(frequencyofplowing,mechanicalvs.handtechniques)

Finally,considerthemarketandsocialfactorsthatareintegraltoyourtargetenvironment,includingexpectationsfor:

ColorStoragepropertiesFlavorCulinaryusesQualityofproductTransportationability

Determining traitsKnowingwhatyouwantiscriticaltogettingwhatyouwant.Themostsuccessfulbreedingprojectshaveclearlydefinedtraitsthatarebeingselectedfororagainst.Priortostartingthebreedingeffort,itisimportanttotakethebroadlydefinedgoalsforthevarietyanddigdowntodefineexactlywhatyouwillbelookingforinthefield.Itmaybeveryeasytocomeupwithalistofthetraitsthroughbrain-storming.Anotherwaytounderstandwhichtraitsareimportantisbydiscussingthebestcurrentlyavailablevarieties.Whatarethetraitsthatmakecertainvarietiessogreat?Whataretheylacking?Ausefulconceptisthatofan ideotype.Anideotypeisessentiallyanidealizedcropvarietythatisper-fectlysuitedtoaparticularsetofproductionandmarketcriteria.Whatwouldthisidealvarietylooklike?Howwoulditperform?Whattraitswoulditneedtohavetobesuccessful?Whatarethetraitsthatareimportanttothefarmerandmarketplace?

Someexamplesoftraitsthatyoumaywanttose-lectforinclude:

PlantheightPlantstature

DaystomaturityHarvestableyieldColorFlavorTextureStoragelifeSeedlingvigorPestResistanceDiseaseResistance

Prioritizing traitsOnceyouhavecompiledalistoftraits,thenextstepistoprioritizethem.Ingeneral,abreedingprojectshouldnotattempttoactivelyselectformorethanfiveorsixtraitsatanygiventime.Theremaybemorethanfivetraitsthatareimportant,butitsnotfeasibletoworkoneverythingallatonce.Alsoconsiderthatsometraitsmaybeeasilyfixed,orlockedin,bychoosingparentsthatsharethesetraits.Inthiscase,effectiveselectionmaybeachievedsimplybythrowingoutacoupleofoff-typeplantshereandthere.

Toprioritizethetraitsandlimitthelisttofive,twoquestionstoconsiderare:

Isthetraiteasilymeasurable?Howheritableisthetrait?

How can the traits be measured?Plantbreedingisanexerciseinbalancingwhatwewantwiththeresourceswehavetodothework.Mostplantbreedingprojectshavelimitedresources,soitmakessensetoavoidbreedingfortraitsthatrequireexcessivelabor.Itmightbewonderfultode-velopalettucevarietythatsupportsadiversefloraofmicroorganismsarounditsroots,butunlessyourprogramhastheresourcestodeterminetheidentityofawidevarietyofspeciesofsoilmicrobesinhabit-inghundredsoflettucelines,youwillneedtoworkwithtraitsthatareeasiertomeasureandselect.Intheprocessofprioritizingselectioncriteria,consid-erwhenandhowthetrait(s)willbemeasured.Thisplandoesntneedtobefleshedout,butitshouldbesufficientlydetailedsothatyouhaveanideaofhowmuchworkwillberequired.Willyoubeabletovisuallyratethetraitona1to9scale?Willyoubeabletoquicklymeasurethetraitwithayardstickorascale?Howmanytimesthroughouttheseasonwillthetraitneedtobemeasured?


How easily can the traits be inherited? Theseconditemtoconsiderwhendeterminingwhichtraitstoprioritizeinyourbreedingproj-ectistheheritability ofthetraits.Simplystated,heritabilityexpressesthelikelihoodthatatraityouseeinaplantthisyearwillshowupintheplantsoffspring.Putanotherway,heritabilityexpresseswhatfractionoftheappearanceofatraitcomesfromtheplantsgeneticsasopposedtotheenvironment.Althougheachcropandsituationisdifferent,traitsthatarehighlyheritableoftenincludesuchqualitiesascolor,shape,andspinesversusspinelessness.Themorehighlyheritableatraitis,theeasieritistoselectandseerapidprog-ressfromonegenerationtothenext.Traitswithlowheritabilitytypicallyincludeyieldandvariousformsofstresstolerance(i.e.,drought,salinity,andheattolerance).Thesetraitsrequiremorebreedingexpertise,aswellasamorefinelytunedexperi-mentalfieldmodeltoteaseoutsubtledifferencesinthesetraitstomakeimprovementsacrosscyclesofselection.Werecommendthatyouchooseonlyacoupleoftraitswithlowheritabilitytoselectforinyourbreedingproject,especiallyatthebeginning.Manytraits,suchasflavor,plantheight,anddiseaseresistance,maybeeitherhighlyheritableorlessheritable,dependingonthepopulation.Gettingadvicefromaformallytrainedbreederwhohasexperiencewithyourcropofinterestcanhelpyoudefinewhichtraitsaremoreorlessheritable.

Choosing parentsGermplasmisageneraltermthatreferstothecollectionofgeneticresourcesforaplantspecies.Varieties,landraces,collections,breedinglines,andunimprovedmaterialarealltypesofgerm-plasm.Essentiallygermplasmisanyformoflivingtissue(e.g.,seeds,cuttings,roots,andtubers)fromwhichplantscanbegrown.Germplasmistheparentalmaterialusedtobeginyourbreed-ingwork.Sourcingqualitygermplasmdetermineshoweasilyandrapidlyyouwillbeabletodevelopyourdesiredvariety.

Therearetwomainfactorstoconsiderwhenchoosinggermplasm:

Quality:thegermplasmshouldincludeelementsoftheideotypeyouarestrivingtoproduce

Variability:thegermplasmshouldhavevaria-tionforthetrait(s)youwanttoimprove

Considervarietiesthat:

PerformwellinyourtargetenvironmentAreconsideredtobecommercialstandardsContainuniquetraitsthatyouwanttoincorpo-rateintoyourproject

Manyvaluablevarietiesforbreedingworkcanbefoundinthecatalogsofdomesticandinternationalseedcompanies.However,beawareoflegalpro-tectionsonsomevarietiesthatrestricttheiruseforbreedingorlimitwhatyoucandowiththeminotherways.Theseprotectionsincludeplantpat-ents,utilitypatents,plantvarietyprotectioncertifi-cates,andlicenses.YoucanfindmoreinformationabouttheseprotectionsoneOrganicsintellectualpropertyprotectionpageathttp://www.extension.org/pages/18449.Alwaysinvestigateyourgerm-plasmsourcestoensuretherearenolegalrestric-tionsonbreeding.

Besidesseedcompanies,youcanalsosourcegermplasmfrom:

FarmersSeedexchangesGermplasmResourceInformationNetwork:http://www.ars-grin.gov/

Unlessyouarealreadyfamiliarwiththegermplasmyouwanttouseinyourproject,itiswisetocon-ductvarietytrialstoevaluatetheavailablesourcesofgermplasm.MoreinformationonhowtoconductvarietytrialscanbefoundinOSAsOn-farm Vari-ety Trials: A Guide for Organic Vegetable, Herb, and Flower Producers.

Herearefourcategoriesofgermplasmthatareusefultoevaluateandconsiderforuseinorganicplantbreeding:

1) Heirloom varieties:Thiscategoryincludesfamilyorcommunity-basedheirloomsaswellasnon-hybridcommercialcropvarietiesthatwereinexistencebeforeWorldWarII.Heirloomsareopen-pollinated(OP)varietiesthatwereselected,adapted,andmaintainedovergenerationswithin


familiesoragriculturalcommunities.Theywereoftenuniquelyadaptedtothechallengesofthesoil,climate,andendemicdiseasesofparticularregions.Inmanycases,thecommercialvarietiesreleasedduringthisperiodbyregionalseedcompanieswereimprovedorrefinedheirloomvarietiesal-readyimportanttothatparticularregion.ThesecommercialOPvarietieswereeitherdevelopedbyoneofthemanyregionalseedcompaniesthatflourishedduringtheearly20thcenturyorbyplantbreedersatoneofthelandgrantuniversities.Thesevarietieswerethenmadewidelyavailabletofarmersandgardenersacrosstheregion.

2) Early modern varieties:Thisisatermforcropvarietiesdevelopedbybothregionalseedcompa-niesandlandgrantuniversitiesfromtheendofWorldWarIIuntilabout1980.Mostofthesevari-etiesarenotF1hybridsbutopen-pollinatedvariet-iesincross-pollinatedcropsandpurelinevariet-iesinself-pollinatedcrops.Earlymodernvarietieswerebredfortheconditionsofspecificregions.Thebreedingofvegetablesandotherminorcropswasntusuallydoneunderoptimumfertilityorheavysprays.Manyofthesevarietiesthatarestillusedtodayhaveproventheirworthasworkhorsevarieties,andanumberoffarmer-breedershavechosenvarietiesoutofthiscategorytoserveasgermplasmfortheirbreedingprojects.

3) F1 hybrid varieties:Hybridvarietieswerefirstextensivelydevelopedincornduringthe1920sandbegantorepresentalargepartofthevarietyofferingsofmanycross-pollinatedcropsafterWorldWarII.Hybridsbecamepopularfor

anumberofreasons.Theyareaneffectivewaytocreategeneticallyuniform,vigorousvariet-ies.Inaddition,theyrepresentaformofbiologi-calintellectualpropertyprotectionfortheseedcompaniesthatdevelopthembecausetheoff-springofhybridsdonotgrowtrue-to-type(duetotheirhighlyheterozygousnature).BecausemanybreedingeffortssinceWorldWarIIhavefocusedondevelopinghybridvarieties,alotofthemostelitecropvarietiescurrentlyarehybrids.Hybridsareoftengeneticallydiverseandcanrepresentgoodgermplasmformanybreedingprojects.

4) Modern open-pollinated varieties (non-hybrids):Variousseedcompaniesarebreedinggoodopen-pollinatedvarieties(generallysmall-tomedium-sizedregionalcompanies)asaresomepublicbreedersatlandgrantuniversities.Thebestmodernopen-pollinatedvarietiesprovideexcellentgermplasmforbreedingprograms.

Beforebeginningabreedingproject,itisagoodideatoscreencropvarietiesfromawideswathofgerm-plasmsources,includingsomefromeachofthefourcategoriesabove.Thisprocesswillhelpyouidentifythehighestqualitygermplasmcurrentlyavailable.Thepotentialforincreasingyoursuccessandde-creasingyourfrustrationisgreatestwhenyoubeginaprojectwiththebestpossiblegermplasm.

Creating a breeding timelineFigure5onthefollowingpageisasummaryofageneralbreedingtimeline.Afterthesummary,wewillgothroughthestepsinmoredetail.


Step 1.Conductvarietytrialstoidentifythebestpotentialparentalgermplasm.

Step 2. Ifnecessary,makecrossesbetweenparents.Ifadequatevariationexistsinafavorableexistingvariety,thennocrossesarenecessary.

Step 3.Ifyouareworkingwithacross-pollinatingcropandyoumadecrosses,allowtheoffspringtorandomlymateforatleasttwoorthreegenera-tionswhileremovingobviousundesirableplants.Inthecaseofself-pollinatedcrops,allowtheplantstonaturallyself-pollinateforatleasttwoorthreegenerationsafterthecross,removingonlytrulydysfunctionalplants.

At this point, you can conduct a breeding program purely based on mass selection by proceeding to step 8. To conduct family selection, first go through steps 4 through 7.

Step 4.Growalargepopulationandsaveseedseparatelyfromindividualplants.Theseedfromindividualplantsbecomefamilies.

Step 5. Thefollowinggeneration,growfamiliesoutinrows.Planteachrowfromseedharvestedfromanindividualplant.Evaluateandselectthebestperformingfamiliesandplants.

Step 6. Harvestseedfromtheselectedplantswith-intheselectedfamilies.Dependingonwhatyouseeandyourgoals,eitherkeepseedfromindividualplantsseparateorcombinewithinfamilies.

Step 7. Repeattheprocessofgrowingandselectingfamilyrowsuntilyouaresatisfiedwiththeperfor-manceofallfamilies.

Step 8.Oncetheselectedfamiliesareallaccept-able,combinetheseedofthesefamiliesintoabulkpopulation.

Step 9.Growthebulkedpopulationagainandre-movetheleastdesirableplants.Repeatasnecessary.

Step 10.Oncethepopulationisuniformlyaccept-able,increaseseedforrelease.

Figure 5. This diagram shows a summary of a general breeding timeline.


Herearefurtherdetailsoneachstep:

Step 1. Conduct variety trials to identify the best potential parental germplasm.

Beforecommittingtoalong-termbreedingproj-ect,carefullyevaluatepotentialparentalgerm-plasm.Thisevaluationtypicallytakestheformofavarietytrial.Avarietytrialisasystematicwaytoevaluateasetofvarietiesusinggoodtrialdesign.Thepurposeofatrialdesignistohelpminimizetheenvironmentalvariationtoensurethatthedif-ferencesobservedrepresentgeneticdifferencesbetweenplants.Moreinformationonhowtocon-ductvarietytrialscanbefoundinOSAsOn-farm Variety Trials: A Guide for Organic Vegetable, Herb, and Flower Producers.

Step 2. If necessary, make crosses between parents. If adequate variation is present in a favorable existing variety, then no crosses are necessary.

Toimproveyourpopulation,somedegreeofvaria-tionforimportanttraitsisnecessary.SeeSectionIV. Theories of field-based organic breedingbelowformoreinformationabouthowvariationworks.Tohaveavariablepopulation,youneedtoeitherstartwithgermplasmthatisvariableforthetraitsyouintendtoimprove,oryouneedtocreatevariationbycrossingtwoormorevarietiestogeth-er.Thesecrossescanbemadeinanumberofways,dependingonyourgoalsandresources.

Types of Crosses

Controlled pollinations:Plantbreedingmightevokeanimageofbreedersmakingcontrolledcrosses,perhapswithtweezers,magnifyingglasses,andsmallpaintbrushes.Thegeneralstrategywilldependonwhetherthespeciesyouworkwithhasperfectflowersornot.Per-fectflowershavebothmalestamenandfemalepistilsonthesameflower.Iftheplanthasper-fectflowers,youwillgenerallyneedtoemas-culatethefemaleparentbyremovingthemalestamenandthentransferpollenfromthemaleparent.Iftheplanthasonlyunisexualflow-ersflowersthatcontaineitherallmaleorall

femalepartsthereisnoneedtoemasculate.Youjusttransferpollenfromamaleflowertoafemaleflower.Afterpollinating,somesortofcoverisoftenusedtoexcludeotherpollenfromcontaminatingthecross.

Open pollinations:Thesecrossesarealsoknowasstrain crossesorblindcrosses,andaredonebyallowingoneplantorasetofplantstocrosswithanotherplantorsetofplantswithoutmakinganattempttoensurethatpollenisonlytransferredbetweencertainplants.Thisisaccomplishedbybringingalloftheplantstogetherandallowingthemtofreelycross-pollinate.Outsidepollenisexcludedeitherbyisolationdistanceorbycagingtheplantsinsideastructurethatpreventsinsectsandpollenfromentering.

Hybrids:Thesevarietiescanbeusedaspre-madecrosses,savingastepinthebreedingpro-cess.Keepinmind,however,thatmosthybridsaremadebycrossingtwonarrowlyselectedin-bredparentsandthereforeapopulationformedfromasinglehybridwillhavecomparativelylittlegeneticdiversityrelativetoonecreatedfromastrainorblindcrossbetweenopen-pol-linatedvarieties.

Step 3. If you are working with a cross-pol-linating crop and you made crosses, allow the offspring to randomly mate for at least two or three generations while removing obvious un-desirable plants. In the case of self-pollinated crops, allow the plants to naturally self-polli-nate for at least two or three generations after the cross while removing undesirable plants.

Priortoselection,growyournewbreedingpopula-tionforafewgenerations,allowingtheplantstoflowerandfreelycross-pollinate.Duringthistime,youmaypracticenegativemass selectiontorogueouttheworstperformingplants.

Itistemptingtobeginintensiveselectioninthegenerationafteryourcrossesaremade,asplantbreedingcanbesuchalongprocess.However,werecommendthatyoudonotskipthisstep.Incross-pollinatedcrops,allowingafewgenerationsofran-


dommatingbreaksupthelinkagebetweengenes.Simplystated,linkagereferstohowgenesinaplantwilltendtotraveltogether.Forexample,ifyoucrossatallplantwithdarkleaveswithashortplantwithlightleaves,youremorelikelytogeteitheratalldarkplantorashortlightplantthanyouaretogetatall,lightplantorshort,darkplant.Randommatingforacouplegenerationsallowsthegenestoshuffleandmakesitmorelikelythatyouwillseenewcom-binationsofgenesinthepopulation.

Forself-pollinatedcrops,itisalsovaluabletowaitforatleasttwoorthreegenerationsbeforemak-inganysignificantselections.Thereasonforthisisdifferentthanforcross-pollinatedcrops.Asde-scribedinthepreviousdiscussionofdifferencesingeneticstructuresbetweencross-andself-pol-linatedcrops,randommatingandthebreakingoflinkagesdoesnotoccurinself-pollinatedcrops.Instead,eachplantderivedfromtheoffspringofacrosshasthepotentialtobecomeaseparate,independentfamilylinewithuniquecombina-tionsoffixedpairsofgenes.Aseachoftheselinescontinuestoself-pollinateoverthecourseofafewgenerations,eachlinewillbecomemoreuniformandthedifferencesbetweenlineswillbecomemoreobvious.Itwillbeeasiertomakedistinctionsbetweenfamiliesifsufficienttimehaspassedtoallowthefamiliestoessentiallybecomefixedanddistinctfromoneanother.

Additionally,themoregenerationsyouspendimprovingthepopulationbythisgradualprocess(massselection),thebetterthegeneticsofthepopulationwillbe,andthemorelikelyyouwillbesuccessfulinthelaterphasesofbreeding.

Thesegenerationswillalsogiveyouachancetogettoknowthepopulation,toseewhatkindsofvaria-tionexistinit,andtoevaluatewhatitsstrengthsandflawsare.Usetheseyearstorefineyourgoals,traitsofinterest,andevaluationtechniques.Re-member,whenpracticingselection,makesurethefieldlocationrepresentsthelocationyouwanttoselectforandisrelativelyuniformthroughout.

Step 4. Grow a large population and save seed separately from individual plants. The seed from individual plants become families.

Duringthisgenerationyouwillbeselectingyourbestplantstoserveasparentsforfamilies.Evalu-ateyourplantsmultipletimesthroughouttheseason,consideringthegoalsandtraitsyouhaveprioritized.Sincetheremaybesomevariationinthesoilquality,weedpressures,andotherfactorsinyourfield,selectthebestplantsfromallpartsofthefieldequally.Ifalloftheplantsinonecor-nerofyourfieldlookworseoffthantherest,stilltrytopicksomeofthebestlookingplantsinthatpatchthoseareplantsthatcansurviveundersomeenvironmentalstressorpotentiallysub-op-timalconditions.

Ifyourcropiscross-pollinatingandisacropwhereyouhaveanopportunitytoevaluateandselectthebestplantsbeforepollinationoccurs,youwillmakefasterprogressbyremovingallinferiorplantsfromthefieldbeforepollinationoccurs.Inthisway,anycross-pollinationthatoccurswillonlybebetweentheselectedplants.

Whenyouharvestseedfromselectedplants,putseedfromeachplantintoaseparatebag.Theseedineachbagrepresentsafamily.Labeleachfamilywithauniquenumber.Alongwiththenumberoneachlabel,youmaywanttomakenotesaboutwhyyouselectedthatplant.Theseplantswillrepresentfamiliesforthenextgenerationsroundofselec-tion.Inthecaseofcross-pollinatedcrops,trytosaveseedfromatleast20to50individualplants.Inthecaseofself-pollinatingcrops,saveseedfromatleast30to100plants.

Step 5. The following generation, grow family plots by planting each separate plot with seed harvested from an individual plant. Evaluate and select the best performing families.

Thisgenerationyouwillbelookingattheprog-enyofyourselectedplantsasfamilies.Inbreed-ingterms,thisistheprocessoffamily selection.Thismeansyouwillplantseedfromeachplantthatyouselectedinseparateplotsorrows,justasifyouwereconductingatrial,followingthebestpracticesoftrialdesignasoutlinedinOSAsOn-farm Variety Trials: A Guide for Organic Vegetable, Herb, and Flower Producers.

Examineeachplotasawhole.Howdoesthisfamily


ofrelatedplantslook?Onaverage,whichfamilieslookbestgivenyourgoalsandtraits?Selectthebestfamiliesbasedontheiroverallquality,andeliminatetheotherfamilies,preferablybeforetheyhaveachancetocross-pollinatewiththeselectedfamilies.Lookforfamilieswhereatleast60to80%oftheplantsareacceptable.

Next,selectthebestplantswithinthebestfami-lies.Aimtoeliminate30to40%oftheplantswithinafamily,keepinginmindtheminimumpopulationsizeyouwanttomaintaintokeepthepopulationhealthy(seebox,Whymaintainlargepopulationsizes?).

Step 6. Harvest seed from the best plants within the best families.

Atthispoint,savetheseedfromeachfamily.Inotherwords,combinetheseedfromallofthese-lectedplantswithineachfamilysothatyouendupwithaseparatebagforeachfamily.

Why maintain large population sizes?

Whatistheadvantageofmaintaininglargenumbersofplantsinyourbreedingpopula-tions?Afterall,ifyouhaveafewexcellentlook-ingplantsinthefield,whysaveseedfromanyplantsthatdontlookasnice?Therearetwomainreasonstomaintainlargepopulations.

Inthecaseofcross-pollinatingcrops,largepopulationshelpavoidinbreedingdepression.

Inbreedingdepressionisalossofvigorduetothecrossingofgeneticallysimilarplants.Plantssufferingfrominbreedingdepressiongerminatepoorly,yieldpoorly,andsuccumbmorequicklytoenvironmentalstress.Ingen-eral,plantsthatarestronglycross-pollinatingaremostsusceptibletoinbreedingdepression,whilethosethatarestronglyself-pollinatingareleastsusceptible.

Thesecondreasontomaintainlargepopula-tionsizesistoavoidlosingimportantgenesthroughgenetic drift.Geneticdriftistherandomchangeinthefrequencyofgenesinthepopulationasitreproduces.Evenintheabsenceofselection,thepopulationthatgrowsfromonegenerationtothenextmayhaveaslightlydifferentpercentageofgenesjustbychance.If,bychance,noneoftheplantsinagivengenerationcarryacertaingene,itwillbelosttothepopulation.Thisismuchmorelikelytohappeninsmallpopulationsthaninlargeones.Thethreechartsbelowshowasimula-tionofthechangeingenefrequencyafter25generationsforsomehypotheticalgenesthatarefoundinbetween20to80%oftheplantsinapopulationtostartwith.Whenthepopula-tionsizeiskeptat200plants,allofthegenesarestillpresentinthepopulationattheendof25generations.Withonly30plants,one-fifthofthegenesarefixedorlostwithin25genera-tions.Whenseedissavedfromonly10plantseverygeneration,themajorityofgenesarefixedorlostwithin25generations.


Step 7. Repeat the process of growing and se-lecting family plots until you are satisfied with the performance of all selected families.

Thefollowinggeneration,continuetoplanttheselectedfamiliesinseparateplotsandevaluatethemagainthroughouttheseason.If,duringthesecondroundofevaluations,someofthefamiliesnolongerseemacceptable,discardthosefami-lies.Alsoeliminateallinferiorplantswithintheselectedfamiliesthatyoudecidetocarryontothenextgeneration.

Step 8. Once the selected families are all accept-able, combine the seed of these families togeth-er into a bulk population.

Forthesepastfewgenerations,youhavebeenmaintainingthepopulationasasetofseparatefamilies.Oncealloftheremainingfamiliesmeet

yourgoals,youcancombinethemtogethertore-formthepopulation.

Step 9. Grow the population again and remove the least desirable plants. Repeat as necessary.

Oncethefamilieshavebeenreformedintoasinglepopulation,youcanmaintainthispopulationinsubsequentgenerationsthroughmassselection(i.e.,selectingthebestindividualplantstorepro-duceeachgeneration).Ifatanypointyoubelievethevarietyneedstobemoreintensivelyselected,youcancompleteanothercycleoffamilyselectionbysavingseedseparatelyfromindividualplantsandplantingtheminindividualplotsthefollowinggeneration,aspreviouslydescribed.

Step 10. Once the population is uniformly ac-ceptable, increase seed for release.


Asyouincreasetheseed,continuetorogueoutanyundesirableplantsastheyarise.

Lookingatbroccoliseedandkaleseed,youmaynotbeabletotellthemapart.Theyarebothsmall,brownish-greyseeds,essentiallyindistinguishablefromoneanother.Butplanttheseedintheground,andastheygerminateandgrowintomatureplants,thedifferencesbecomegreater.Thekaleseedpro-duceskaleplantswithbroad,curlygreenleaves,whilethebroccoliseedproducesbroccoliplantswithlarge,tightflowerheads.Whatexactlyiscontainedinthatseedthatcausesbroccoliseedtogrowintobroccoliandkaleseedtogrowintokale?Genes,madeupofDNA,programthewayplants(andalllivingthings)grow,thewaytheylook,andthewaytheytaste,amongmanyothercharacteris-tics.Genesarehowaplantsprogrammingpassesdownfromonegenerationtothenext.Asplantbreeders,ourjobistopicktheplantswiththebestgenesandmakesurethosegenesgetpasseddown.

Thissectionwillintroduceyoutothebasicsofgeneticsbyexplaininghowgenesarepassedfromonegenerationtothenextandhowthosegenesde-terminetheappearanceandperformanceofplants.

How genes travel from parents to offspringJustasitisinhumans,DNAisbundledtogetherintopackagescalledchromosomesinplants.Plantsalsohavemultiplechromosomes,eachofwhichcontainsmanygenes.Mostcropspeciesarediploid,meaningtheyhavetwosetsofchromosomes:onesetfromtheirmotherandonefromtheirfather.Forexample,tomatoes,ingeneral,have12pairsofchromosomes,withtwo#1chromosomes,two#2chromosomes,etc.,foratotalof24chromosomes.However,someplantsarepolyploidy,meaningtheyhavemorethantwosetsofchromosomes.Forexample,commonwheatisahexaploid,meaningithassixsetsofchro-mosomes.Althoughpolyploidyisfoundinanumberofimportantcropplants,forthesakeofsimplicity,wewillfocusonlyondiploidspeciesforthefollow-ingexplanationsandexamples.

Toreproduce,plantsproducespermandeggs.Spermandeggshaveonlyonesetofchromosomesratherthantwo.Again,lookingattomatoes,whiletherestoftheplanthas24chromosomes,thespermandeggsonlyhave12.Wheneachspermoreggiscreated,itreceives,atrandom,eitherachromosomefromtheplantsmotherorachromosomefromtheplantsfather.Thismakeseachspermandeggunique.Later,whenthespermiscarriedonthepollenandfertilizesanegg,auniquenewplantwillbecreated.Becauseofthis,plantscreatedfromthesamecrossbetweentwoplantscanalllookdifferent.Theexceptiontothisisiftheparentplantsarehighlygeneticallyuniform,whichcanoccureitherthroughinbreedingacross-pollinatedspeciesortheuseofpurelineself-pollinat-ingvarieties.Inthiscasetheoffspringfromthecrosswillalllooknearlyidentical.

How genes determine the appearance and per-formance of plantsAswelearnmoreaboutthecomplexityoflife,weseemoredeviationsandexceptionstohowweoriginallyunderstoodgenestofunction.Neverthe-less,althoughthefollowingdescriptionsaresimpli-fiedversionsofhighlycomplexsystems,theyarestillrelevantandusefulforplantbreedingwork.

Genesareinstructionsforourcells,writteninthelanguageofthenucleicacidsthatmakeupDNA.Cellsreadtheseinstructionsandmakeproteins.Typi-cally,onegenemakesoneprotein.Eachchromosomecontainshundredsorthousandsofgenesmostoftheinstructionsnecessarytocreateaplant.

Asmentioned,halfofthosegeneswillcomefromthemother(maternal)andhalffromthefather(paternal).Foranygiventraitthatiscontrolledbyonegene,suchasgrowthhabitintomatoes,aplantwillhaveamaternalgeneandapaternalgene.Whatifthematernalandpaternalgenesdif-fer?Forexample,whatifthegenereceivedfromthemotherproducesproteinsthatmakeashorter,determinantplant,whilethegenefromthefathermakesalarger,indeterminateplant?Formanytraitstherearegenesthatresultinproperlyfunc-tioningproteinsandgenesthatresultindefective,non-functioningproteins.Also,formanytraits,oneproperlyfunctioninggeneisenoughtocreatesuf-ficientproteintomeettheplantsneeds.Inthesecases,ifaplanthasjustonecopyofagenethat

IV. Theories of Field-based Organic Plant Breeding


Tomato 1Sp Sp

Tomato 2Sp sp

Tomato 3sp sp

encodesforfunctioningproteins,itwilllookandfunctionthesameasifithadtwoofthosegenes.Onlywhentherearenocopiesofthatgenepresenttoencodeforthefunctioningproteindoweseeadifferenceinappearance.Toillustrate,letuslookatdeterminantversusindeterminategrowthhabitintomatoes.Figure6illustratestomatoesthathave:(1)twofunctionalcopiesoftheself-pruninggene(Sp),(2)onecopyofSpandonenon-functionalself-pruninggene(sp),and(3)twonon-function-alself-pruninggenes.

Noticethattomatoes1and2lookthesame.ThatisbecauseonlyonecopyofSpwasrequiredtopro-ducetheproteinsthatallowedthetomatotogrowcontinuously.Onlywhenbothcopieswerenon-functional,asintomato3,doesthetomatoendupshortanddeterminate.Inthiscase,wewouldcallsparecessivegeneandSpadominantgene.Inthecaseofdominantandrecessivegenes,thefunda-mentalconcepttounderstandisthatrecessivegenesareonlyvisibleinthephenotypeofaplant(whataplantlookslike)whentwocopiesofthegenearepresent,whereasasinglecopyofadomi-nantgenewillresultinthedominantphenotype.

How genes travel together during reproductionUltimately,whenweengageinplantbreedingweareparticipatinginthesexualreproductionofplants.Inthissexualprocess,someoftheparentalcellsundergomeiosis,splittingtheirchromosomepairsintogametes:eitherspermoreggs.Thesegametesthencombinewithacomplementarygam-eteandformazygote,whichisthebeginningofanewplant.Oneofthewaysinwhichthisprocessprofoundlyaffectsplantbreedingisthroughthephenomenonoflinkage.

Linkagereferstothefactthatsomegenesresideonthesamechromosomeandarethusphysicallylinkedtogether.Inbreeding,weoftenrepresentlinkedgeneswithtwolines,eachlineconnectingoneofthelinkedpairsofgenes:

AbaB

InthisexampleAandbarelinkedtogetherononehalfofachromosomepair,whileaandBarelinkedontheotherhalf.Linkagecausessomeoutcomesthatwewouldnotanticipateifthegeneswere

Figure 6. This figure illustrates determinant versus indeterminate growth habit in tomatoes.


notlinked.Forexample,ifweself-pollinatedtheaboveplant,wewouldgetthefollowingoffspring:AAbb,aaBB,andAaBb.WewouldnotseeanyAABBoraaBB,becauseAbandaBarelinkedpairsthattraveltogetherthroughtheprocessofmeiosis.Thisiswhathappensduringreproduction:

AbGametes:AbaBaB

Zygotes:AbAbaB AbaBaB

ButwhatifthemostdesirablegenotypeisAABB?Unfortunately,linkagepreventsthisgenotypefromoccurring.Whenlinkagecausesanabundanceorlackofgenotypesthatisdisproportionatetowhatwewouldexpectbasedonthegenesthatareinthepopulation,wecallitlinkage disequilibrium.Fortunately,naturehasawaytoreducetheeffectsoflinkagebycrossing overchromosomes.

Duringmeiosis,pairsofchromosomesconnecttogether.Whentheycomeapartagain,partsofonechromosomecanendupswappedwithpartsoftheotherchromosomethatitpairedwith.Thisswappingofchromosomepiecesbreaksuplinkedgenes.Dependingonhowclosetwogenesaretoeachother,thelinkagesbetweenthemmaybreakupmoreorlessquicklyandeasily.Tightlylinkedgenes,orthosethatareveryclosetogether,aremoredifficulttobreakapartthanthosethatarelooselylinkedorfartherapartfromeachother.Itispossibleforgenestobesotightlylinkedthatbreakingthemapartisvirtuallyimpossible.Hereisanillustrationofhowcrossingoveractstobreakapartlinkedgenes:

Ab Ab ABaB aB ab

Whyarelinkageandlinkagedisequilibriumimpor-tantforusasbreeders?Therearemanyreasons,buttwoofthemostimportantaretheneedforcautionwhenselectinginearlygenerationsandlinkagesrelationtoheterosis.

Aftermakingacrossorcrossestogenerateanewpopulation,youneedtobecarefulaboutselectingjustafewofthebestplantsforthefirstfewgenera-

tions.Toillustrate,letscontinuewiththetomatoexamplewherethelinkedgenesthatcomefromoneparentareA b,andthegenesfromtheotherparentarea B.IfwewanttofindplantsthathavetheA Bgenotypethenweneedtowaituntilthepopulationhasgonethroughenoughgenerationstoallowtimeforthoseparticularchromosomestohavecrossedoverbetweenthoseparticulargenes.OnlythencanweendupwithAandBonthesamechromosome.Ifselectionsaremadetooearlyontheycanreducethepotentialforcertaingenecombinationstooccur,ultimatelylimitingwhatyouhavetoworkwith.

Heterosisisthetermusedwhentheoffspringofacrossaresuperiortotheirparents.Heterosisisalsocalledhybridvigor.Therehavebeenmanyargu-mentsovertheyearsaboutwhatcausesheterosis.Recently,mostscientistsagreethattheprimarycauseofheterosisinvolvestwoprincipleswehavealreadydiscussed:dominanceandlinkage.Tounderstandheterosis,letslookatthecrossoftwocornplants.

Parent1

Parent2

Offspring

Figure 7. This diagram illustrating heterosis shows the cross of two corn plants that creates an offspring superior to its parents.

Whyistheoffspringsomuchtaller?Inthesecornplants,therearetwoloci(locationofagene)thatdetermineplantheight:AandB.PlantswithAaretallerthanplantswitha,andplantswithBaretallerthanplantswithb.BothAandBarecom-pletelydominantgenes,soaslongastheplanthasonecopyofthedominantgene,itisastallasifithadtwocopies.Inthisexampleparent1isAAbbandparent2isaaBB.

Sowhathappenswhenwecrossthem?Theoff-springgetAbfromparent1andaBfromparent2,


sotheirgenotypeisAaBb.BecausebothAandBaredominant,theyaffectplantheightinthesamewayregardlessofwhetherthegenotypeisAABBorAaBb.Thechartbelowshowsthatwhenparents1and2arecrossed,theiroffspringgetsaboosttoheightfromparent1sdominantAgene(shownasa+)andaboosttoheightfromparent2sdomi-nantBgene.Thisresultsinthehybridoffspringbeingtallerthaneitherparent.

Parent 1

Parent 2

Offspring

Genes AAbb aaBB AaBb

Effect of A + +

Effect of B + +

Overall height

+ + ++

Inthiscase,theparentseachhadcomplementarygenes.Whentheycrossed,eachparentcontributedallelesthat,throughtheirdominanteffects,maskedtheinferiorrecessiveallelesoftheotherparent.

Heterosisisquitecommoninmanycropplants.Why,then,betweennaturalselectionandtheef-fortsofplantbreeders,havewenotbeenabletocombineallofthebestgenesintooneplant/vari-ety?Whydowehavetomakehybridstohidethepoorgenesoftheparents?Thisiswherelinkagecomesintoplay.LetsassumethelociforAandBarerightnexttoeachotheronthechromosomeandaretightlylinked.Inparent1scase,A bwilltraveltogetheruntilthechromosomecrossesoverintotheregionbetweenthegenes.Likewise,inparent2scase,aBwilltraveltogether.Untilacrossoveroccurstobreakthislinkageapart,thebestwecandoiskeepremakingthehybrid.Mosttraits,suchasplantheight,aredeterminedbymul-tiplegenes,notjustone.Manyofthesegenes,bothdesirableanddeleterious/undesirable,arelinkedtogether.Sinceitisunlikelywewillevercreateorcomeacrossaplantwiththeperfectcombinationofgenesforeverytraitwefinddesirable,wemustcontinuetoexploittheeffectofdominantgenestoproducesuperioroffspringbyfindingparents

whosegenecombinationscomplementeachother.

How genes operate in populations Upuntilnowwehavebeenfocusingonhowgenespassfromonegenerationtothenextandhowtheyaffecttheappearanceoftheplantswegrow.Tokeepourdiscussionsimple,wehavepresentedexampleswherejustoneortwogenescontrolatraitlikeplantheight.Now,letustakeastepclosertoreality.Manyofthetraitsthatwecareaboutplantheight,vigor,flavor,stresstolerancearecontrolledbymultiplegenes.Ratherthanplantsappearingeitherbigorsmall,theirheightmightex-istalongaspectrum.Inthisspectrum,afewoftheplantswillbeverysmall,afewwillbeverylarge,andmostwillbesomewhereinthemiddle.Ifyoumeasuredalltheplantheightsandgraphedhowcommonthevariousheightswere,youmightseethemappearasabellcurve,asshowninfigure8.

When,asbreeders,weworkwiththesepoly-genic(multiple-gene)traits,ourgoalistoselecttheplantswiththetraitswewantandslowlyshiftthewholepopulationinthedesireddirec-tion.Figure9showstheslightimprovementyoumightexpectfromonegenerationtothenextthankstoyourselection.

Tobesuccessfulasplantbreeders,wewanttoimproveplantpopulationsforthetraitsweareinterestedin.Fundamentally,thewaytoimproveapopulationistofindplantsthatwillproducesupe-rioroffspring.Howdowefindtheseplants?Letslookatfigure10toseeanexampleofafieldplant-edwithapopulationofcornthatweareinterestedinimprovingforheight.

Thereisobviousvariationinthephenotypesoftheseplants.Ifthetaskistopickoutthetallestplants,itwouldbesimple:plants2,4,5,6,and12arethetallest.However,whatwereallywanttoknowiswhichoftheseplantswillproducethetallestoffspring.Thefirststepinfindingtheseplantsistounderstandthatthephenotype(P)isinfluencedbytwoprimaryfactors:thegenetics,orgenotype(G),oftheplantandtheenvironment(E).Inbreedingterms:P=G+E.Thegenotypeisthesumofallthegeneticinformationwithintheplant,althoughwegenerallyusethetermtorefertothegenesintheDNA.Theenvironmentencompasses


Frequency of plants

Plant height

Figure 8. Rather than plants appearing either big or small, their height might exist along a spectrum. In this spectrum, a few of the plants will be very small, a few will be very large, and most will be somewhere in the middle as shown in this bell curve.

Frequency of plants

Plant height

Generation 1 Generation 2

Figure 9. This graph illustrating how polygenic traits operate in populations shows the slight improvement you might expect from one generation to the next thanks to your selection.

Figure 10. This figure represents a field planted with a population of corn that we are interested in improving for height.


allofthenon-geneticinfluencesonthephenotype.Examplesofenvironmentalfactorsaffectingplantgrowthincludefertility,temperatures,water,weedcompetition,plantingdensity,andpestanddis-easepressure.Sayweareabletogrowthesesametwelveplantswithverylittlewaterandtheyallgrow10inchesshorterthanbeforeasseeninthebelowfigure:

Clearly,theenvironmentaffectedtheplantpheno-types,butdiditaffecttheminawaythatchangesourabilitytopickthebestparents?Inthiscase,no.Wewouldstillpick2,4,5,6,and12asourfavor-ites.Ifalleffectsfromenvironmentalstresseswereuniformlikethisexample,itwouldbesimpleforustopickthebestparentsbasedontheirpheno-types.Unfortunately,lifeisnotsosimple.Thereareenvironmentaleffectsthatmakeitmorechalleng-ing.Theseeffectsarebasicallyclassifiedintotwotypes:errorandgenotypebyenvironmentinterac-tion(GxE).Errorisacatch-alltermforeffectsthatwecannot,ordidnot,measureoraccountfor.Forexample,imaginethatadditionalfertilizerwasac-cidentallyappliedtothesoilunderplant4,provid-ingafertilityboostthatnoneoftheotherplants

experienced.Thisfertilityboostwouldbeaneffectthatwasnotreplicable,andwouldinfluenceourselectioninanunpredictableandprobablyunhelp-fulway.Thisiserror.Someerrorwecanreducethroughgoodexperimentaldesign,especiallytheuseofreplicationandrandomization.Toillustrate,letstakeanotherlookatthecornplants.Whatifplants7through12aresmalleroverallbecausethe

fieldisdrierontheright?Totestthiswecouldsplitthefieldintotwosectionsandreplicatetheexperi-mentbyplantingeachcornrandomlyoneachsideofthefieldasshowninfigure11.

Byreplicatingourtrial,weseetheplantsontherightareconsistentlysmallerthanthoseontheleft.Replicationallowsustomeasurethiseffectandcorrectforit.Unlikeanyoftheothereffectsonplantphenotype,weareabletoaccountforandremoveeffectsthatarecapturedbyreplication.

ThesecondeffectthatconfoundsourabilitytopickthebestparentsistheGxEinteraction.GxEisastatisticaltermthataccountsforthefactthatdif-ferentgenotypessometimesresponddifferentlyto

Figure 11. Here is the above field split into two sections and the experiment replicated by planting each corn randomly on each side of the field.


Original environment

Dry environment

thesameenvironment.Tocontinuewithourcornexample,saythatwegrewourcornbothintheenvironmentandinamuchdrierenvironmentasshownbelow.

Inthisexample,theheightofmostplantswasre-ducedinthedryenvironmentrelativetotheorigi-nalenvironment.However,theplantheightswerenotuniformlyreduced.Number4ismuchsmaller

thanintheoriginalenvironment,andnumber12isthesameheightinbothenvironments.Thisunequalresponsefromdifferentgenotypestodif-ferentenvironmentsiscapturedbytheconceptofGxE.Asbreeders,wehavetwochoicesofwhattodowiththisinformation.Wecanfocusourbreed-ingeffortstowardacertainenvironmentinthiscasetoselectforadryenvironment.Thismethodiscalledselectingforspecificadaptation.Alternately,wecanselectforthegenotypesthat,onaverage,performbestinallenvironments.Thismethodiscalledselectingforgeneral adaptation.Inreal-ity,breedingoftenmixesthesetwoapproachesbybreedingforadaptationwithinacertainspecifiedtarget population of environments(TPE).

Asplantbreeders,weareinterestedintheplantsthataremostlikelytoproducethebestoffspring,notsimplyperformthebestthemselves.Hereisanotherkeytoplantbreeding:Theplantswiththebestgenotypesmaynotproducethebestoffspring.

Thisisbecause,unlesstheyareclonallyreproduced,plantspassongenes,notgenotypes.Thenextsec-tionwillexplainwhy,includingtheimplications.

Dominanceeffectsconfoundoureffortstofindthebestparentsbecausetheyaregeneticeffectsthatarenottransferablefromparenttooffspring.Tounderstanddominanceeffects,wewillreturntoourtomatoes(seenextpage).

Again,givenidenticalenvironments,tomatoes1and2havethesameappearance,becausetheybothhaveatleastonecopyofthedominantSpallele.However,whiletomato1willonlyproduceindeter-minateoffspring,tomato2hasachanceofproduc-ingdeterminantoffspring.

Sincetomato1(Sp Sp)andtomato2(Sp sp)areindistinguishablefromeachother,youareequallyaslikelytochoosethemasparents.Thisisprob-lematicbecauseyoumaypreferoneortheotherforyourbreedingwork.ThedominanceeffectthatallowsSp spplantstoappearthesameastheSp Spplantsisagenotypiceffectthatisnotreliablytransferabletoitsoffspring.Thebottomlineisthatgenotypiceffectsduetodominancearenottransferabletooffspring.

Insummary,geneticeffectsandenvironmentaleffectsinfluenceplantphenotypes.Ifproperex-perimentaldesignsareusedwecanaccountfor


environmentaleffects.Theseexperimentaldesignsallowustoachieveoneofourprimarygoalsasplantbreeders,whichistominimizeandaccountforthevariabilitycausedbynon-geneticeffects.

Onemoreimportantplantbreedingtermisherita-bility.Heritabilitydescribeshowpredictablyatraitispassedonfromparenttooffspring.Plantbreed-ersoftentalkabouttheheritabilityofatraitandhowtoincreaseit.Sometraitsarenaturallyhighinheritability.Oftenthesetraitsarerelativelyunaf-fectedbyenvironment,likeseedcolororflowershape.Wecanincreasetheheritabilityinalltraitsbyusingmatingdesignsthatincreaseormaintainadditivegeneticvariance,andbyusingexperimen-taldesignsthatreducethevarianceofothereffects.

How to see the genetic differences between plantsEarlierwetalkedabouttheimportanceofreduc-ingenvironmentalerror.Webrieflymentionedreplicationasonetooltohelpreducethiserror.Nextwellgointomoredepthabouthowtousereplicationandothertoolsofexperimental de-signtohelpmakemoreeffectiveselectionsinourbreedingwork.

Experimentaldesignreferstohowtheexperimentissetuporarrangedinthefield.Oneofthemore

commondesignsforbreedingiscalledrandom-izedcompleteblockdesign,orRCBD.ARCBDisreplicatedusingmultipleblocks,witheachblockcontainingthecompletesetofbreedinglineswithinit.TocreateaRCBD,assigneachbreedinglinetoaplotineachblockandarrangetheplotsinarandomizedorderwithineachblock.Thebreed-ingtrialshouldideallybelocatedwherethereisaslittlevariabilityaspossible.Wherevariabilityexists,trytoorienttheblockssothevariabilityisbetweenblocksratherthanwithinthem,becausebreedinglinesarecomparedtoeachotherwithineachblock.Replication,randomization,andblock-ingaretheessentialelementsoftheexperimentaldesignthathelpstoseparateoutthegenotypicef-fectsfromtheenvironmentaleffects.

Understand the effects of the environmentEnvironmentaleffectsrefertotheinfluencethatvariablefieldconditionshaveontheperformanceofplants.Forexample,ifthefieldisonaslopeandthesoilisricheronthedownhillside,thenplantsonthedownhillsidemaygrowlargerbecauseofbettersoilconditions,notbecausetheyhavesupe-riorgenetics.Likewise,plantsgrownonthesouth-westsideofafieldmaygrowlargerbecausetheyreceivemoreafternoonsun,orsmalleriftheyaresun-sensitiveandtheirrootsareeasilydriedoutbyafternoonsun.Naturalvariabilityoftenexistsinthefieldthataffectscropgrowth,includingvariations

Tomato 1Sp Sp

Tomato 2Sp sp

Tomato 3sp sp


insoilquality,soiltexture,soilpH,soilfertility,drainage,pestpressures(insect,weed,disease,andanimals),sunexposure,irrigation,andtemperature(bothwarmandcoldpockets).Somesourcesofenvironmentalvariationarerelativelystable,likesoiltypeandproductionpractices,whileothersvaryfromyear-to-year,likeweatherandclimate.Pests(diseases,insects,andweeds)maybestableorvariabledependingontheorganism.Forex-ample,thesoilinsectsknownassymphylansareusuallyfoundinthesamespotyearafteryearandwouldberegardedasstable,whereasaphidsblownintotheplotsfromanotherregionwouldbemorevariable.Stablesourcesofvariabilitycanbecom-pensatedforbytheuseofrandomizationwhereasseasonallyvariablesourcesofvariabilityrequiretestingovermultiplelocationsand/orseasons.Seasons,asusedhere,maybedifferenttimesofyearordifferentyears.Theobjectiveistoobtaindatainanumberofdifferentgrowingenviron-ments.Thegoaloftheexperimentaldesignistominimizetheeffectsofenvironmentalvariabilityontrialresultsbyblockingreplicationssofieldvariationisminimizedwithinblocks.Inessence,replicationinthebreedingtrialaccountsforstableeffectsandrepeatingtheexperimentovertimecompensatesforvariableeffects.

Ensure that plants receive consistent treatmentManagementpracticesshouldbeconsistentacrossallbreedingplots,includingirrigation,soilfertil-ization,pestmanagement,staking,cultivationandweeding,oranyotherhorticulturalaspectofcropproduction.Ifpracticesarenotconsistent,differ-encesinperformancemaybetheresultofunequaltreatmentsasopposedtogeneticdifferencesinvarieties.Forexample,ifhalfthefieldwasculti-vatedandtheotherhalfleftuncultivated,theplotsintheuncultivatedsectionwouldhaveanunfair

disadvantage,astheywouldlikelybesubjectedtogreaterweedcompetition.

Randomize the plotsRandomizingplotswithineachblockhelpstoincreasetheconfidencethattheevaluationresultsareduetogeneticdifferencebetweenvarietiesratherthanvariationintheenvironment.Themorereplicationsusedthegreatertheassurancethatmeasurementswillreflectdifferencesinthevariet-iesratherthanvariationinthefield.Randomizingisalsoimportanttominimizetheinfluencethatvarietieshaveononeanother.Forexample,ifeachbreedinglinewasplantedinthesameorderineachblockratherthanifonelineisplantednexttoanotherverytall,vigorousline,itmightbeunfairlyaffectedbythecompetitionforlightandnutrients.

Theorderofplotsmayberandomizedusinganyba-sicrandomizationtool,asbasicasdrawingnumbersfromahat.Aneasymethodistomarkalloftheplantstakesforeachblockandthenmixthemup,walkingtheblockandinsertingwhicheverstakecomestohandfirsttomarkthefirstplot.Continuedowntherowmarkingplotsinthismanner.

Use sufficient population and plot sizesThesizeofplotsinthetrialshouldbelargeenoughthattheresultingnumberofplantsprovidesagoodrepresentationofthewholefamilyorpopulation.Thegreatertheplotsize,themorerepresentativeitwillbeofthepopulation.However,thelargertheplotthemoredifficultitmaybetomanage,especiallyifyouaredealingwithalargenumberofvarietiesandthreeormorereplications.Ingeneral,whenevaluatingopen-pollinatedvarietiesofself-pollinatedcrops,fewerplantsarenecessarytogetarepresentativesamplingthanincross-pollinatedcrops.Thisisduetothegenerallygreaterinherent

Example of RCBD, where all varieties would be in each block or rep


geneticvariabilityincross-pollinatedpopulations.

Ideallyplotsshouldbelargeenoughthatyoucantreatthemthesameastherestofyourfarmandmaintainthemwithyournormalfarmingpractices.Forexample,ifyouusuallyplantyourcabbageon36-inchcentersandfieldcultivatewithatractor,youwilllikelygetdifferentresultsthensomeonewithasmallgardentrialon24-inchspacingus-inghandhoeing.Similarly,ifyouusuallyapplydripirrigation,thenoverheadirrigationmayskewresults.Forbestresults,locateyourbreedingtrialwithinyourproductionfieldofthesamecropsothatallproductionpracticesarethesameasforcommercialproduction.Plotsizemaybedictatedbyyournormalplantingandmanagementprac-tices.Forexample,aminimumamountofseedmayberequiredtoplantwithaseeddrillorvacuumplanter,andtheplantingequipmentmayneedtorunacertaindistancetofunctionproperly.Me-chanicalharvestingequipmentmayalsorequireacertainminimumscaletooperateappropriately.

Anothervariabletoconsiderwhendeterminingplotsizeisthenumberofrowstoincludeperplot.Singlerowplotsallowyoutoplacemorelinesorfamiliesinyourtrial,butmaygivemorevariableresultsbecauseoffewerplantsperplotandpoten-tialcompetitionbetweenvarietiesinadjacentplots.Withthreeorfourrowplots,thecenteroneortworowscanbeevaluatedwithoutconcernofcompeti-tioneffectswithneighboringplots.Whilethisap-proachtakesmorespace,itdoesminimizeinter-plotcompetitionandproducesmoreaccuratedata.Aswithplotlength,aminimumnumberofrowsmaybedeterminedbyequipment.Forexample,youmaybelimitedbythesetupofyourplantingequipment.Borderrowsaroundyourexperimentalplotswillminimizewhatisknownastheedgeeffect,where-byplotsontheedgeexperienceslightlydifferentgrowingconditionsrelativetotherestofthetrial.Withoutborders,plotsontheedgemaybemoreproductivebecausetheylackcompetingplantsaroundthemorlessproductivebecausetheyarenexttoamorecompetitivecropordamagedbyfieldoperationsoccurringinadjacentcrops.Assuch,datafromun-borderedplotsaroundtheout-sideofthetrialwillbebiasedrelativetothecenterofthefield.Borderrowsshouldbeplantedatthefrontandbackofatrialaswellasalongthesides.

Abundant Bloomsdale organic spinach breeding projectWhat were the goals of this project?Thereisastrongdemandformoreopen-pollinatedsavoyspinachvarieties,whichareimportanttodiversifiedorganicfarms.ThegoaloftheAbundantBloomsdaleprojectwastodevelopadarkgreen,open-pollinatedsavoyspinachvarietywithhighnutritionalcontent,goodflavor,andsuperiorboltresistance.Thevarietyneededtohaveanuprightplanthabitandbeusefulatallstagesfrombabyleaftofullymaturebunchingtypes.

ThePacificNorthwestisaprimespinachseedproducingregion,yetthereislittleorganicspin-achseedproducedthere,asmostseedcompanieshaveignoredtheorganicspinachseedmarket.Anendresultofthisbreedingprojectwillbetohelpbothorganicfarmersandsmallorganicseedcompaniesbysupplyingthemwithanalternativetothespinachhybridsthatarelargelybredforconventionalsystems.

Breeding procedureTheprojectbeganwithacrossofWinterBlooms-daleandEvergreen.WinterBloomsdaleisacoldhardy,open-pollinatedspinachvarietywithdarkgreenleaves,deepcurl,andgoodflavor.ThevarietywasoriginallybredforwinterandearlyspringharvestincoastalVirginia.ItisthelastoftheoldfullysavoyspinachvarietiesthatisstillwidelygrowninNorthAmerica.Evergreenisasemi-savoyspinachvarietydevelopedbyDr.TeddyMorelockoftheUniversityofArkansasforwinterproductioninArkansasandTexas.Thevarietyhasstronghorizontalresistancetomanyofthemajordiseasesofspinach.

Inthefirstyearofbreeding,OSAbreederJohnNa-vaziomadeastraincross,whereapproximately20plantsofbothparentalvarietieswereplantedside-by-sideandallowedtocrossthroughopen-pollina-tion.Bymakingthecrossinthismanner,ratherthanpollinatingbyhand,morecrossesbetweenthevarietiescouldoccurandmoreofthegeneticvari-abilityofthetwoparentsisretained.

V. Examples of Farmers Breeding for Organic Systems


Afterthatinitialcross,theresultingpopulationwasgrownforfivegenerationsonvariousfarmsinWesternWashington.Thisintermatingprocessbrokeupsomeofthegeneticlinkages(seelinkagedescriptioninprevioussection)andallowedthegenesofthetwoparentstothoroughlymix.Duringthisprocess,alowintensityofmassselectionwasappliedforappropriateleafshapeandvigor.

Inthesixthseason,afterfivegenerationsofin-termating,NavazioandlocalfarmerMarkoColbyplanteda2,000plantspaceplantnursery,whereeachplantwasspacedfarenoughfromallotherssotheycouldbeevaluatedindividually.Fromthese2,000plantstheyselectedintenselyforthetraitsalreadymentioned,andendedupwith130spin-achplants.Theseselectedplantswereallowedtoopenlypollinate.

Asspinachisdioecious,withplantscontainingeithermaleflowersorfemaleflowers,onlyabouthalfoftheselectedplantswereseedbearing.Ulti-mately,seedfrom67femaleplantswereharvestedintoseparatebagsthatwerenumberedsequential-lyfrom1to67.Sevenfamiliesweresubsequentlydroppedbecauseoftheirpoorseedqualityoryield.Inthefollowingyear(yearseven),seedoftheremaining60familieswereplantedinfamilyrowsandevaluatedatseveralstagesofgrowthbetweenthebabyleafandmaturebunchingstages.Ofthese60families,onlyfiveprovedtobesuperiorthroughallgrowthstages.Theother55undesirablefami-lieswereeliminatedandtheremainingfivese-lectedfamilieswereallowedtointermatethroughopen-pollination.Theresultingseedofeachofthefivefamilieswereharvestedseparatelyintofivefamilybags.

Inyeareight,NavazioandColbyplantedseedfromthesefivefamiliesasfamilyrows,withthegoalofidentifyingthebestoftheseselectedfamiliestocomprisethefinalpopulationthatwouldbere-leasedasAbundantBloomsdale.Thefivefamilieswereagainevaluatedatallstagesofgrowthbe-tweenthebabyleafandmatureleafstage.Inthisfinalevaluation,onlyoneofthefivefamilieswasuniforminallofthetraitsthatsatisfiedthebreed-inggoals.Thisfamilyhaddarkgreen,fullysavoyedleavesonaveryupright,vigorousplant,andarich,

sweetflavorandsuperiorcoldhardiness.Theotherfourfamilieswereeliminatedandthechosenfam-ilywasroguedforofftypes.TheremainingplantswereallowedtointermateandproducethestockseedofAbundantBloomsdale.

Winter sprouting broccoliWhat were the goals of this project?Thisbreedingprojectisongoing,andthegoalsaretodevelopapurplesproutingbroccolivarietythatreliablyoverwintersinthePacificNorthwestandproducesgoodyieldsoftender,flavorful,6to8inchshootswithpurpleflorets.Thepurplewintersproutingbroccolivarietiesthatar

Documents

Introduction to on-farm Organic Plant Breeding