marker-assisted selection in wheat - ictsd

136Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishit could. Although this should not impactthe economic efficiency of MABC or forwardbreeding, it could affect the overallcost efficiency of MAS.Finally, the efficacy for MAS in relativelycomplex populations such as syntheticsand open-pollinated varieties (OPVs) hasnot been investigated. Compared with thebi-allelic populations used in the privatesector, such populations are likely to havemore than two alleles at a given locus. Also,unlike the simple bi-allelic populations,allele frequency should be an importantcomponent of predictions with such populations.Therefore, there should be moregenetic effects and interactions to considerwhen making predictions based on MASwith OPVs and synthetics.In the future, successful implementationof MAS in maize may lead to more frequentproblems related to limited genetic variation.The emphasis of aggressive private sectormaize breeding programmes on crossesbetween elite, related inbred lines to createsegregating source populations has led toconcerns about the depletion of geneticdiversity in such gene pools and the abilityto enhance such gene pools with highquality genetic variation (Niebur et al.,2004). Such concerns, which existed priorto the deployment of DNA markers andMAS in maize, are likely to increase asMAS becomes more prevalent. If MAS inforward breeding schemes is as effective asreported, then alleles and haplotypes mayapproach fixation more rapidly (Crosbieet al., 2006). At that point, breedingprogrammes will need to repeat theprocess of calibrating genotype-phenotyperelationships in a slightly different arrayof reference populations to start the nextmetacycle of MAS (Johnson, 2004).There is much anticipation for the futureof MAS as genic sequences become themarker loci, functional information is discoveredfor the many candidate genes andgene products are assessed for their potentialas useful sources of information inbreeding programmes (Varshney, Granerand Sorrels, 2005; Lee, 2006). Certainly,these huge sets of raw data will contributeto progress. Eventually, other sources ofgenetic variation unrelated to the primaryDNA sequence such as DNA methylationwill be evaluated for their influence on genotype-phenotyperelationships. Currently,epigenetic variation is mostly ignored fromthat assessment although it is well knownthat much of the maize genome may bemethylated (Kaeppler, 2004) and may bemore dynamic than predicted by currentgenetic models and mechanisms (Fu andDooner, 2002). Also, the influences of noncodingsequences such as small interferingRNA (siRNA), matrix attachment regionsand long-distance regulatory sequenceshave yet to be considered for their effectson genetic variation and estimates of geneticvalues used in MAS (Lee, 2006).Most of the early limitations of MAS,due to the availability or cost of genotypicdata, have been overcome. However,the availability or cost of high-qualityphenotypic information is becomingone of the major limitations of MAS.During the past 20 years, developmentof new technologies and automation andminiaturization of laboratory procedureshave contributed to reducing the cost ofmarker data points as well as the timeneeded to produce them. Large-scalemarker laboratories produce marker datapoints at less than a tenth of the cost of20 years ago. By contrast, neither cost northe time required to produce phenotypicdata has changed much, if at all, in thesame timeframe. As the establishment ofmarker-trait associations and ultimately