marker-assisted selection in wheat - ictsd

294Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishgenotyping techniques that have drasticallyreduced the cost of genotyping SNPs inassociation populations (www.illumina.com/products/prod_snp.ilmn). It is nowfeasible to genotype SNPs in hundreds ofgenes potentially associated with a trait.QTL mapping remains largely a researchtool to improve our understanding of thenumber, distribution and mode of action ofgenes controlling quantitative traits. QTLcan also play a role in GAS as a vehicle forvalidating significant SNP correlations identifiedin association populations (Thummaet al., 2005). In the near future, associationstudies promise to yield numerous SNPmarkers that could be used in breedingprogrammes for early selection of superioralleles associated with a wide range of traits.As the efficiency of techniques for microarrayanalysis, SNP discovery, genotypingand other molecular procedures improvefurther, the opportunities to incorporatemolecular technologies into breeding programmesfor forest trees will increase.use of MAS to enhance breedingprogrammes in developingcountriesThe adoption of molecular techniquesvaries widely, not only between developedand developing countries but also amongthe less developed economies (Chaix andMonteuuis, 2004). Countries such as China,India, Indonesia, Malaysia, Thailand andViet Nam have established molecular laboratoriesfor genotyping. Molecular markersare being used routinely to assess the levelof genetic diversity in breeding programmesand to monitor any changes following selection(Butcher, 2003; Marcucci Poltri et al.,2003). They are also being used to estimatelevels of contamination and inbreeding inopen-pollinated seed orchards (Chaix etal., 2003; Harwood et al., 2004), to validateintra- and interspecies crosses and todetermine error rates in clonal propagationor trial establishment (see, for example,Bell et al., 2004). This has identified relativelyhigh error rates in several breedingprogrammes, affecting calculations of heritability,breeding value and genetic gain.Genetic linkage maps have been publishedfor eucalypts in China (Gan et al., 2003)and Brazil is prominent in eucalypt mappingand genomics (Grattapaglia, Chapter14). EST libraries have been developed formangroves in India as a first step towardscharacterizing genes associated withsalinity tolerance (Mehta et al., 2005), whileDNA markers have been used for backwardselection to identify superior maleparents in eucalypt seed orchards in Brazil(Grattapaglia et al., 2004). This approachhas some potential for accelerating thebreeding cycle in open-pollinated breedingprogrammes, particularly with species thatare difficult to hand pollinate (Butcher,Moran and DeCroocq, 1998). The applicationof QTL-MAS in developing countriesremains limited, exceptions being selectionof coconut parents for breeding (FAO,2003) and identification of QTL for rubbertree improvement (Lespinasse et al., 2000).More widespread application may dependon economic considerations. Reports onthe financial viability of MAS differ, withJohnson, Wheeler and Strauss (2000) indicatingthat large areas would need to beplanted with MAS-improved germplasm tojustify initial investment, while Wilcox etal. (2001) suggest significant financial gainsare possible even when selection is basedon DNA markers linked to a few loci eachof relatively small effect. Association mappinghas the potential for more widespreadapplication in developing countries due,in part, to the ability to transfer markersamong individuals, regardless of pedigree