marker-assisted selection in wheat - ictsd

Chapter 10 – Strategies, limitations and opportunities for marker-assisted selection in livestock 171Figure 2Within-family marker-QTL LDWithin-family LD among progeny of a sireLinkage phase can differ between familiesSire 1 Sire 2 Sire 3 Sire 4M Q M q M Q M qmqmQhowever, only exists within this family;progeny from another sire, e.g. an Mq/mQsire, will also show LD, but the LD is inthe opposite direction because of the differentmarker-QTL linkage phase in thesire (Figure 2). On the other hand, MQ/mQ and Mq/mq sire families will not bein LD because the QTL does not segregatein these families. When pooled acrossfamilies these four types of LD will canceleach other out, resulting in linkage equilibriumacross the population. Nevertheless,the within-family LD can be used to detectQTL and for MAS provided the differencesin linkage phase are taken into account, aswill be demonstrated later.mQmqQTL detection and types ofmarkers for MASApplication of molecular genetics forgenetic improvement relies on the abilityto genotype individuals for specific geneticloci. For these purposes, three types ofobservable genetic loci can be distinguished,as described by Dekkers, 2004:• direct markers: loci for which the functionalpolymorphism can be genotyped;• LD-markers: loci in population-wide LDwith the functional mutation;• LE-markers: loci in population-widelinkage equilibrium with the functionalmutation but which can be used for QTLdetection and MAS based on withinfamilyLD.For these alternate types of markers, differentstrategies are appropriate to detectQTL in livestock populations. These aresummarized in Table 1 and will be describedin more detail. Strategies for QTL detectionin livestock differ from those used in plantsbecause of the lack of inbred lines.QTL detection using LD markers withincrossesCrossing two breeds that differ in allele and,therefore, haplotype frequencies, createsextensive LD in the crossbred population.This LD extends over large distancesTable 1Summary of strategies for QTL detection in livestockType of population Within crosses Outbred populationF2/BackcrossAdvancedintercrossHalf- or full-sibfamiliesExtendedpedigreeNon-pedigreed populationsampleType of markers LD markers LE markers LD markersGenome coverage Genome-wide Genome-wide Candidate gene Genome-wideregionsMarker density Sparse Denser Sparse More dense Few loci DenseType of LD used Population-wide LD Within-family LD Population-wide LDNumber of generations ofrecombination used formapping1 >1 1 >1 >>1Extent of LD around QTL Long Smaller Long Smaller SmallMap resolution Poor Better Poor Better High