marker-assisted selection in wheat - ictsd

Chapter 14 – Marker-assisted selection in Eucalyptus 261breeding and production forestry. Thisapplication is nowadays routinely used byseveral forest companies in Australia, Brazil,Portugal, South Africa and Spain. Qualitycontrol and quality assurance of largescaleclonal plantation operations becomecrucial aspects in forestry, especially invertically integrated production systemswhere the pulp mill plans on the availabilityof clones with specific wood propertiesat specific times. Given the scale of suchoperations that frequently have to feedplantation programmes of several thousandhectares per year, (i.e. several millionseedlings), mislabellings can seriously affectthe expected production. Correct clonalidentity has also important implicationsin several breeding procedures such asseed orchard management or controlledpollination programmes affecting theexpected gains of breeding cycles.Several technologies are available todayto resolve questions of clonal identity inEucalyptus. Dominant markers such asrandom amplified polymorphic DNA(RAPD) or amplified fragment lengthpolymorphism (AFLP) have been used forclonal fingerprinting of eucalypts (Keil andGriffin, 1994; Nesbitt et al., 1997; Costae Silva and Grattapaglia, 1997). Dominantmarkers are, however, very limited intheir ability to establish conclusively theidentity of two redundant individual treesdue to artefact polymorphisms. Dominantmarkers can be used to establish thattwo individuals are not the same, but thestatement that two individuals are identicalis usually only approximate and no formaltest statistics can be attached to thisassertion. The high degree of multi-allelismand the very clear and simple co-dominantMendelian inheritance of microsatellitesprovide an extremely powerful system forthe unique identification of individualsfor fingerprinting purposes and parentagetesting particularly when the individuals areexpected to be related. Kirst et al. (2005a)demonstrated the high resolving powerof this class of markers in Eucalyptus. Abreeding population of 192 individuals of E.grandis was genotyped with a set of six highlypolymorphic microsatellites. The numberof alleles detected ranged from 6 to 33 withan average of 19.8±9.2 and the expectedheterozygosity averaged 0.86±0.11. Usingthree loci all 192 genotypes could be readilydiscriminated. The combined probabilityof identity (i.e. the probability of twoindividuals having the same multilocusgenotype) considering all six loci was less thanone in 2 000 million. Similarity coefficientsestimated from microsatellite data weremuch smaller, thus more discriminative,than those usually obtained in similarstudies with RAPD and AFLP markers.In common with human forensic DNAanalysis, the standard method for clonalidentification in eucalypts today is basedon multiplexed, multicolour fluorescentanalysis of microsatellite markers sized inan automatic sequencer. The identity ofsamples is declared based on a maximumlikelihood ratio where the likelihood ofobserving those genetic data conditionalon the hypothesis of the two samples beingderived from the same clone is comparedwith the alternative hypothesis, i.e. thatthe two samples are derived from differentclones. Furthermore, the repeatabilityand precision of multilocus genotypedetermination allows correct comparisonsacross laboratories and at different times.Varietal protectionFollowing publication of the varietalprotection law in Brazil, specific instructionsfor protecting Eucalyptus cloneswere published in 2002 by the Ministry