marker-assisted selection in wheat - ictsd

320Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishrate of 6.7 x 10 -4 when 13 464 gametes andmarker information from 12 loci werescreened in a turbot population. Mutationsand scoring error have the sameeffect on excluding potential parents, givingrise to incorrect assignments.• Unlinked loci and linkage equilibrium.Linkage and linkage disequilibriumbetween the loci will reduce the effectivenumber of loci used for the parentalassignment. Note that the power to assignparental pairs correctly can thereby differbetween different sets of microsatellites.Estoup et al. (1998) quantified the differencein the power of microsatellite markersets used to assign parents correctly inturbot (eight loci, eight alleles per loci)and rainbow trout (eight loci, four allelesper loci) populations by calculating thefrequency of good and unique parentassignments (f gu ). The more variable setof microsatellites resulted in higher f gu forlarger maximal mating schemes for turbotthan the less variable set of microsatellitesfor rainbow trout. In general, a set of lociwith an equal number of alleles has thehighest exclusion probability (Weir, 1996;Jamieson and Taylor, 1997).Walk-back selection schemesPractical breeding schemes using molecularmarker-based parental assignment havebeen reported. Doyle and Herbinger (1994)proposed carrying out parentage assignmentfor individuals using genetic markers,such that full-sib families would not have tobe kept separately until tagging but, rather,would be held in one large tank. Note thatindividuals that are genotyped also need tobe physically tagged, so that genotypingresults can be traced back to particularindividuals. At the time for selection, fishin the tank were first ranked on their phenotypicvalue, assuming that selection wasfor only one trait that could be measuredon the selection candidates (e.g. weight).Then the individual with the highest phenotypicvalue was selected and genotypedfor family identification. Thereafter, theindividual with the second highest phenotypicvalue was genotyped and selected if itwas not a full- or half-sib of other, alreadyselectedindividuals, such that within-familyselection was performed. This procedurecontinued until the desired number ofbrood stock was selected. This approachof progressing through the performanceranking, genotyping and selecting the bestperformingindividuals within families wastermed “walk-back” selection. Matingssubsequently would be made betweenfamilies, a strategy preferred because itwould keep the rate of inbreeding low(Falconer and Mackay, 1996). Herbingeret al. (1995) reported setting up a rainbowtrout breeding programme using the walkbackselection programme of Doyle andHerbinger (1994) and genetic markers toestimate full/half relationships among thecandidates using a likelihood ratio methodand thereafter performing within-familyselection.Using stochastic simulations, Sonesson(2005) studied a combination of optimumcontribution selection and walk-back selection.Optimum contribution is a selectionmethod that maximizes genetic gain witha restriction on the rate of inbreeding(see earlier in this chapter). Hence, thecombination of optimum contribution andwalk-back selection ensures that the rateof inbreeding is under control, while thegenetic gain is higher than in the withinfamilyselection schemes of Doyle andHerbinger (1994) because selection is bothwithin and between families. In the studyby Sonesson (2005), batches of candidateswere pre-selected from a single tank on