marker-assisted selection in wheat - ictsd

Chapter 3 – Molecular markers for use in plant molecular breeding and germplasm evaluation 37Table 2Key features of common molecular marker technologiesMarkertypeUsesrestrictionenzymesPCRbasedPolymorphismAbundanceCodominantAutomationLoci per assaySpecialized equipmentRFLP no yes moderate moderate yes no 1 to few Radioactive isotopeRAPD yes no moderate moderate no yes many Agarose gelsAFLP yes no moderate moderate no yes many Polyacrylamide gels/capillaryISSR yes no moderate moderate no yes many Agarose/polyacrylamide gelsDArT yes yes moderate moderate no yes many MicroarrayCAPS yes yes variable moderate yes yes single Agarose gelsSCAR yes no low moderate yes yes single Agarose gelsSSR yes no low moderate yes yes 1 to about 20 Polyacrylamide gels/capillaryTE-Anchor yes no variable variable yes yes single Agarose gelsSNP yes no variable highest yes yes 1 to thousands VariableChoosing a molecular markertechnologyClearly there is no single best choice ofmolecular marker for all situations. Factorsinfluencing the decision may include theobjectives of the study, availability oforganism specific sequences, equipmentand technical resources, and biologicalfeatures of the species. Several importantadvantages/disadvantages for each type ofmolecular marker discussed are summarizedin Table 2 (see review by Powell etal., 1996).If available, microsatellite or SNPmarkers are often the best choice. The rateof adoption of SSR markers can be facilitated,and the costs reduced, by preparing“kits” of selected SSR markers for certainspecies to provide a reliable set of markerswith good amplification, reasonable polymorphismand good genome coverage.This was done in the early days of the riceSSR effort and SSR kits were distributed atvery low cost through Research Genetics(called Rice-Pairs; McCouch et al., 1997).Similarly, for SNPs, there is a need todevelop useful sets of markers that arewidely available and can be mass-produced(at reduced cost) for distribution to theinternational community. SNP kits wouldalso have a clear benefit for databasingand analysing datasets obtained from multiplelaboratories. In addition to kits ofmarkers, there is a need to distribute setsof “control genotypes” as samples, particularlyto address the problem surroundingthe difficulties in integrating SSR datasets.When SNPs or SSRs are not available, it issometimes possible to transfer molecularmarkers from closely related species (Guptaet al., 2003; La Rota et al., 2005; Zhang etal., 2005). When financial resources arerestricted, RAPDs, AFLPs and ISSRs canprovide large numbers of markers with alimited investment. AFLPs, SSRs and ISSRscan provide high throughput using an automatedsequencer, while RAPDs and ISSRscan be run on agarose gels with minimalinvestment in equipment. The effectivenessof each method may vary by species and byapplication. Therefore, it is reasonable totry to use more than one method, particularlyat the early stages of research.impact of the rice genomesequence: A case historyDNA sequence information greatlyaccelerates the development of molecularmarkers. This is evident in the historyof rice microsatellite marker proliferationcoinciding with the release of data fromrice genome sequencing projects. Figure 1