marker-assisted selection in wheat - ictsd

Chapter 14 – Marker-assisted selection in Eucalyptus 269Figure 5Classification of three different types of marker-trait associations relevant to Eucalyptus MAS(see text for details)QTLLE markers – Linkage equilibriumEx. microsatellite markers flanking a QTL mapped in a highLD pedigree - Centimorgan resolution, ~ 10 5 a 10 7 bpQTL or candidate geneResolutionLD markers – Linkage disequilibriumEx. SNPs strongly associated with the QTL or candidategene - Subcentimorgan resolution ~ 10 2 a 10 4 bpGene and exact polymorphism (QTN) identifiedDirect markersEx. causal SNPs ( QTNs ) of quantitative variationMaximum resolutionand identification of exact allelemore precise understanding of genetic architectureof quantitative traits; the absence ofsimply inherited traits that could be immediatelyand more easily targeted; and finallyto the very limited number of scientistsactually working on forest trees.If applying MAS in other intensivelystudied crops besides maize is already asignificant challenge; this challenge is evenmore difficult and complex for Eucalyptusand forest trees in general as it pre-supposes:(i) the manipulation of polygenic traits withvariable heritabilities in breeding populationswith a heterogeneous genetic baseand in linkage equilibrium; (ii) its incorporationin breeding schemes that involvealtering the frequencies of favourable allelesthrough recurrent selection in large populations;and (iii) dealing with age x agetrait correlations, and late expressing phenotypes(Grattapaglia, 2000). In applyingMAS for forest trees, more will likelybe learned from experiences in livestock(Dekkers, 2004; Chapter 10) than fromannual crop plants, with the added advantagethat gains can be quickly realized bylarge-scale cloning of selected individuals.In this context, the categorization of threedifferent levels of marker-trait associationdescribed by Dekkers (2004) are relevant totrees: (a) direct markers, i.e. loci that codefor the functional mutation; (b) linkage disequilibrium(LD) markers: loci that are inpopulation-wide LD with the functionalmutation; (c) linkage equilibrium (LE)markers: loci that are in population-wideLE with the functional mutation in outbredpopulations (Figure 5). In forest trees,besides the recent encouraging discoveryof an LD marker for MFA in Eucalyptus(Thumma et al., 2005), only LE markertraitassociations have been described. LEmarkers have been readily detected ona genome-wide basis by analysing largefull-sib families with sparse marker mapsallowing the detection of most QTL ofmoderate to large effects. For the othertwo types of marker-trait association, it isonly now that the first association mappingexperiments are being started to uncover