marker-assisted selection in wheat - ictsd

Chapter 10 – Strategies, limitations and opportunities for marker-assisted selection in livestock 173Thus, in those populations, only markersthat are tightly linked to QTL may show anassociation with phenotype (Figure 1), andeven then there is no guarantee because ofthe chance effects of random sampling.There are two strategies to find markersthat are in population-wide LD with QTL(see Table 1):• evaluating markers that are in, or closeto, genes that are thought to be associatedwith the trait of interest (candidategenes);• a genome scan using a high-densitymarker map, with a marker every 0.5 to2 cM.The success of both approaches obviouslydepends on the extent of LD in thepopulation. Studies in human populationshave generally found that LD extends overless than 1 cM. Thus, many markers areneeded to obtain sufficient marker coveragein human populations to enable detectionof QTL based on population-wide LD.Opportunities to utilize population-wideLD to detect QTL in livestock populationsmay be considerably greater because of theeffects of selection and inbreeding. Indeed,Farnir et al. (2000) identified substantialLD in the Dutch Holstein population,which extended over 5 cM. Similar resultshave been observed in other livestock species(e.g. in poultry, Heifetz et al., 2005).The presence of extensive LD in livestockpopulations is advantageous for QTLdetection, but disadvantageous for identifyingthe causative mutations of theseQTL; with extensive LD, markers that aresome distance from the causative mutationcan show an association with phenotype.The candidate gene approach utilizesknowledge from species that are rich ingenome information (e.g. human, mouse),effects of mutations in other species, previouslyidentified QTL regions, and/orknowledge of the physiological basis oftraits, to identify genes that are thoughtto play a role in the physiology of thetrait. Following mapping and identificationof polymorphisms within the gene,associations of genotype at the candidategene with phenotype can be estimated(Rothschild and Plastow, 1999).Whereas the candidate gene approachfocuses on LD within chosen regions of thegenome, recent advances in genome technologyhave enabled sequencing of entiregenomes, including of several livestock species;the genomes of the chicken and cattlehave been sequenced and public sequencingof the genome of the pig is under way.In addition, sequencing has been usedto identify large numbers of positions inthe genome that include SNPs, i.e. DNAbase positions that show variation. Forexample, in the chicken, over 2.8 millionSNPs were identified by comparing thesequence of the Red Jungle Fowl with thatof three domesticated breeds (InternationalChicken Polymorphism Map Consortium,2004). This, combined with reducing costsof genotyping, now enables detection ofQTL using LD-mapping with high-densitymarker maps.QTL detection using combined LDand linkage analysis in outbredpopulationsAs markers may not be in complete LDwith the QTL, both population-wideassociations of markers with QTL and cosegregationof markers and QTL withinfamilies can be used to detect QTL. Usingthese combined properties of being bothLD and LE markers, methods have beendeveloped to combine LD and linkageinformation. These methods are furtherexplored under genetic evaluation modelsin what follows.