marker-assisted selection in wheat - ictsd

192Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishsexes and/or have a low heritability (e.g.egg production, disease resistance, carcassquality and welfare traits).Limiting factors for application ofMAS (Muir, 2003) include biological factors(reproductive capacity) and manytheoretical considerations related to theeffectiveness of MAS (e.g. diverting selectionpressure from polygenes to a singlemarked gene), which are generally applicableto MAS in livestock (Dekkers, 2004;Chapter 10). One of the concerns of Muir(2003) is the expected lack of major QTLfor traits that have been under selectionfor many generations (following simulationresults). However, recent QTL studieswithin commercial lines of pigs (Evanset al., 2003; Nagamine et al., 2003) andpoultry (de Koning et al., 2003, 2004) havedemonstrated that many sizeable QTL arestill segregating in commercial populationsdespite decades of selection.There is strong academic interest inchicken genomics outside agriculture from,among others, developmental biologists andevolutionary geneticists, and this has contributedgreatly to the development of thecurrent functional genomics toolbox availablefor chicken. Among livestock species,chickens are best placed to pioneer newapproaches where QTL studies are complementedby gene expression studies (Liuet al., 2001a) or where they become fullyintegrated within “genetical genomics” (deKoning, Carlborg and Haley, 2005; deKoning and Haley, 2005).If poultry breeders decide to embraceMAS, one of the main questions iswhether they are prepared to re-structuretheir breeding programmes aroundMAS or implement these around theircurrent breeding strategies. Adopting theterminology of Dekkers (2004), there arethree levels of MAS: gene-assisted selection(GAS) where the functional mutation andits effects are known; linkage disequilibriumMAS (LD-MAS) where a marker (ormarker haplotypes) is in population-widedisequilibrium with a QTL; and linkageequilibrium MAS (LE-MAS) where markersare in Hardy-Weinberg equilibrium withthe QTL at the population level, but linkagedisequilibrium exists within families. Afourth type of MAS that was recentlyproposed is “genome-wide MAS” (GW-MAS), where dense markers (i.e. SNPs)across the genome are used to predictthe genetic merit of an individual withouttargeting any individual QTL or measuring(expensive) phenotypes on every generation(Meuwissen, Hayes, and Goddard, 2001).Integrating current evaluations with MASis most straightforward for GAS and LD-MAS because the QTL effect can be includedin routine evaluations as a fixed effect(Chapter 10). LE-MAS, on the other hand,requires extensive genotyping and fairlycomplicated statistical procedures (Wang,Fernando and Grossman, 1998), while GW-MAS reduces the genome to a “black-box”but does not require selection of QTLusing arbitrary thresholds. Furthermore,the dense marker information requiredfor GW-MAS may dispense with oftenfaulty pedigree records because all pedigreeinformation is encoded in the genome-widegenotypes.In terms of quantitative genetic theory,there are ongoing developments in thetools required to detect and evaluate QTLin arbitrary pedigrees, moving away fromstrictly additive-dominance models toepistasis and parent-of-origin effects (Liu,Jansen and Lin, 2002; Shete and Amos,2002). At the same time, the technology toanalyse more than 10 000 SNPs in a singleassay is available, and a cost of as little asUS$0.02 per genotype is likely for chicken