marker-assisted selection in wheat

346Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishFine mapping methods attempt to overcomethis problem by quantifying the gameticphase or linkage disequilibrium (LD)present in an outbred population, i.e. acrossfamilies. This method makes use of thenumber of generations as the appearanceof a mutation and can produce extremelyprecise estimates of the QTL position(Pérez-Enciso et al., 2003). The rationalebehind using LD for mapping QTL is thatwhen the population size is rather small,founders of the population would haveonly a limited number of haplotypes, andwith very tightly linked loci there may notbe sufficient time for recombination tobreak up the association between markersand the mutation affecting the quantitativetrait.LD mapping is carried out by calculatingthe probabilities that haplotypes shared byindividuals are identical by descent from acommon ancestor conditional on markerdata (assuming t generations as the commonancestor and a certain N e ; Meuwissen andGoddard, 2001). The LD in the populationdepends on a number of populationparameters such as the degree of admixtureor stratification in the population andthe actual level of association between thecausal mutation and the polymorphisms.The correct determination of phases andof genotypes at the QTL is required forfine mapping purposes (Meuwissen andGoddard, 2001; Pérez-Enciso, 2003). Forthese reasons, a pure LD analysis is likelyto result in a large number of false positives,i.e. falsely inferring association when thereis no linkage.Methods that incorporate the linkageinformation (within families) and LDjointly are preferred, because the likelihoodof spurious association (i.e. LD withoutlinkage) diminishes, making much betteruse of the whole data set (Meuwissen andGoddard, 2001, 2004; Pérez-Enciso, 2004).All of these methods, however, require agreat deal of genotyping of tightly linkedmarkers such as SNPs, which currently arenot widely available for fine mapping inaquaculture species.Using fine mapping techniques, the confidenceinterval for QTL position can bereduced considerably. However, to developa direct test for a favourable polymorphismrequires use of comparative mappingapproaches with model species, such aszebrafish or fugu, to select the candidategenes that most likely affect the trait ofinterest. Otherwise, enrichment of markersin a specific region of the genome (tonarrow further the most likely position ofthe polymorphism) following sequencingis needed to compare sequences betweenindividuals that show different phenotypesor alternative QTL alleles.Candidate gene analysisIt is tempting to invoke variation at geneswith a known role in the physiology underlyinga complex trait such as growth toexplain phenotypic variability for the trait.These genes can be searched for polymorphisms(e.g. SNPs) and the variants thentested to determine whether they are correlatedwith the expression of the quantitativetrait. This approach requires knowledgeof the biology of the species, biochemicalpathways and gene sequences in order totarget variation at those specific genes. Inaquaculture, most of this information is currentlylacking, but it is expected that moregenes will be incorporated in databases inthe near future. The possibility exists to utilizedata from highly studied model species,such as zebrafish or rainbow trout, in comparativebioinformatic approaches.To date, this strategy has not proven particularlysuccessful for explaining genetic