marker-assisted selection in wheat - ictsd

Chapter 4 – Marker-assisted selection in wheat: evolution, not revolution 57system (LIMS), laboratory automation anddata capture and analysis are generic forany MAS set-up, and these are well coveredelsewhere in this volume. The limitationsaffecting MAS deployment in wheat flowfrom the restricted revenue generated bybreeding a self-pollinated, homozygous,non-hybrid product. As a result, the volumeof capital investment affordable in maize isnot available to a wheat MAS programme.Financial constraints also affect the developmentof marker platforms. It is wellknown that the predictive ability of a linkedmarker will be disrupted by recombination,and therefore that “perfect” markers aremore desirable than linked ones. However,the development of genome-wide genebasedmarkers, pre-eminently SNPs, whichare particularly suited to high-throughputgenotyping on automated platforms, is stillsome way off. At present, an insufficientnumber of such assays has been established(grain hardness, semi-dwarfness and graintexture) to consider adjusting the presentmajor genotyping methodology, which isfounded on SSRs. Doubts have been raisedthat SNP frequency in exon sequence willbe high enough to generate informativeassays for many critical genes, but earlyexperience suggests that sequence polymorphismis more than adequate in introns andother untranslated regions of wheat genes.At present, the consensus is that there isplenty of mileage left in SSR technology,and wheat maps continue to be refined bythe addition of new SSR loci.ConclusionIn 1999, Young set out his “cautiouslyoptimistic vision” for MAS. Seven years on,the situation continues to crystallize. Thetechnology itself is no longer limiting. Withrespect to marker availability, SSRs remainuseful and SSR-based genetic maps arebecoming increasingly densely populated,while SNPs may eventually represent asource of plentiful perfect markers for genesof defined function. The “big biology”spawned by the genomics revolution hasbrought miniaturization and automation tobiological assays so that levels of throughputrelevant to the wheat breeding processare becoming attainable. The issue thatremains unresolved is the affordability oflarge-scale MAS. As wheat is a broad-acrecommodity product, its value is low, andthis impedes the ability of the industry toinvest in MAS infrastructure to the extentthat is possible for crops such as maizewhere the generation of F 1 hybrid seed is aviable proposition. However, as economiesof scale and improvements in technologycontinue to drive down assay price, thepenetration of MAS into commercial wheatbreeding will surely grow. This growthshould progressively allow a widening in therange of possible MAS targets, in particularextending to critical ones such as QTL foryield and its components (mean kernelsize, kernel number per ear and numberof fertile tillers per unit area). These arealready widely exploited in maize breedingand their definition and validation in wheatrepresent a significant research theme inboth the public and private sectors. In themeantime, much MAS use will be directedtowards specific purposes such as acceleratedselection of a few traits that are difficultto manage by conventional phenotyping,for the maintenance of recessive allelesin backcrossing programmes, for thepyramiding of disease resistance genes andfor guiding the choice of parents to be usedin crossing programmes.