marker-assisted selection in wheat - ictsd

36Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishpolymorphism (Chen, Cho and McCouch,2002). Thus, the use of stepwise SSRmutation models would be inappropriate forhighly diverged populations. Homoplasy isalso a problem in SSR markers because thehyper-variability leads to some shared allelesizes through parallelism, convergence andreversion (Doyle et al., 1998). Homoplasyfrom reversions can affect transposonbasedmarkers or any markers withpolymorphisms potentially derived fromClass II DNA transposable elements. Thisclass of TEs has a cut and paste mechanismof transposition, so a TE may insert onto alocus and later excise.In RAPDs, ISSRs and AFLPs, homoplasycan occur when two or more lociproduce PCR fragments of similar molecularweight. Although it is desirable to havehigh numbers of bands to maximize theamount of information per lane, this mustbe balanced against the increasing risk ofhomoplasy as more loci are represented.Special considerations formarker-assisted selectionQuality markers for use in MAS shouldbe reliable and easily shared amongresearchers. Co-dominant markers are preferredto avoid the need for progeny testing.Sometimes less desirable markers for MASsuch as RAPDs, ISSRs and AFLPs areuseful for finding markers linked to thedesired allele. Once such a marker is found,it is possible to extract and sequence thecorresponding band. This sequence canbe used to develop co-dominant markerssuch as cleaved amplified polymorphicsequences (CAPS) (Konieczny andAusubel, 1993) or to sequence characterizedpolymorphic regions (SCARs) (Paranand Michelmore, 1993). SCAR and CAPSmarkers are co-dominant and simplify thescreening of large numbers of individuals.When a genetic map exists, markers canbe positioned on the map and other linkedmarkers can be substituted. The additionalmarkers are useful for higher resolutionmapping to find markers more closelylinked to the desired allele or ultimately forpositional cloning of the underlying gene.Reproducibility of molecular markerdataFor orphan species, clearly there is a hugevalue to the anonymous primer approaches(AFLP, DArTs, ISSRs and RAPDs) thatdo not require sequence information ormuch up-front investment. However,the data can be difficult to score, andreproducibility requires a lot of technicalskill. Technologies that depend on thepresence or absence of PCR amplifiedbands are susceptible to changes in PCRconditions and the quality of sample DNA,and the data from separate experimentsmay differ. Further, in any method thatdepends on accurate measurement ofmolecular weight differences between bands(e.g. SSRs), the exact mole-cular weightsassigned to each allele may be differentin each analysis because of differencesin labelling of PCR products, roundingof allele molecular weight estimates andbinning of alleles. Without controls foreach allele encountered, it is difficult orimpossible to merge separate sets of data.Despite discrepancies in the exact dataderived from molecular markers, the resultsand conclusions should be consistent withinindependent experiments. For reliabilityin making inferences across independentdata-sets, SNP markers are preferred. SNPdata-sets can be easily integrated basedon sequence, and SNPs have properties(such as a low mutation rate) that areparticularly valuable for evolutionaryinference (Nielsen, 2000).