marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 339ular information to infer the genealogicalpedigree. A simulation was conducted toreconstruct the pedigree of 100 potentialcandidates from ten full-sib families (witha Poisson family size equal to ten using sixequally-frequent microsatellites, withoutparental genotypes (Martinez, 2006c). Theposterior probability of either full [P(FS)]or half-sib [P(HS)] groups was obtainedusing the Bayesian model of Emery, Boyleand Noble (2001). In the simulation results,there was a tendency to overestimate relationships,with posterior probabilities over0.5 when individuals were in fact unrelated.On the other hand, not all true full-sibswere assigned to the correct full-sib familywith the greatest probability, and some truefull-sib family members were reconstructedas half-sibs. On average (among ten replicates),the probability of mating relatedindividuals was significantly smaller wheninformation from molecular markers wasused, compared with what was expectedby chance (4.7 percent versus 18.1 percent,p = 0.002). The practical implication is thatinbreeding in the progeny generation wouldaverage 5 percent when random matingis used and 1 percent when optimizationusing molecular information is used.In practice, to perform mating in thebase population, the relatedness inferredfrom molecular information does not needto be perfectly accurate, but it does requirethat relatedness is not underestimatedgreatly. Among the technical issues thatarise when using marker data are that apair of individuals could be misclassifiedas related when they are in fact unrelated(Type I error) or a pair may be wronglyclassified as unrelated when the pair is infact related (Type II error). Type II erroris of greatest concern as this could result inrelated pairs being mated. This is becausemating of individuals (males and females)as unrelated when in fact they are fullsibs will increase true inbreeding in thepopulation, while misclassification leadingto unrelated individuals being assigned toa full-sib family would not increase theinbreeding in the progeny. The presence ofmutations, null alleles or genotyping errorswill underestimate the true relationships inthe population and eventually increase theprobability of mating true full-sibs (Butler etal., 2004). Recently, Wang (2004) suggesteda method for inferring relationships formarker data with a high error rate andmutation that can be used to address thisissue. It should also be noted that studiesdealing with estimation of heritability orprediction of breeding values with pedigreesreconstructed using molecular markersmay be very inefficient when pedigreesare reconstructed with an increased rate ofType I errors (Mosseau, Ritland and Heath,1998; Thomas, Pemberton and Hill, 2000).Detecting self-fertilization in scallopsIn scallops, a main drawback whenimplementing breeding programmes is theoccurrence of self-fertilization, even whengametes from later spawning pulses are usedfor obtaining family material (Martinezand di Giovanni, 2006), i.e. a mixtureof selfed and outcrossed individuals canbe present even at later stages within asingle family. Bias in estimating geneticparameters is expected due to this residualself-fertilization, which can occur withconsiderable frequency (average 20 percent)within particular families.A simulation study was used to investigateto what extent markers with differentinformation content can be used todiscriminate between selfed and outcrossedindividuals within a family (Figure 2). Theresults showed that microsatellites gavemean values of posterior probabilities greater