marker-assisted selection in wheat - ictsd

Chapter 8 – Marker-assisted selection in maize 125is being enriched through a variety ofprojects on functional genomics.In sharp contrast to the many methodsand software packages developed for QTLidentification and mapping, little has beenpublished for MAS. This paucity of informationon MAS tools most likely reflectsboth the low level of activity in the publicsector and the fully proprietary nature ofdevelopments in the private sector.In parallel with advancements in DNAtechnology and statistical methods, privatesector programmes have enhanced the capabilitiesand capacities of their continuousnurseries. Such nurseries have been usedfor decades by programmes in both the privateand public sectors. In order to conductMAS to its greatest advantage, continuousnurseries had to be managed, equipped andstaffed in new ways so that the plants completetheir life cycle as quickly as possibleand that the genotypic data (and sometimessome phenotypic data) needed for MASmay be collected at each sexual generation.Three to four sexual generations per yearmay be completed at such nurseries.These activities and the continuous collectionof both genotypic and phenotypicdata in the target environment and theirintegrated analyses create huge data setsthat must be analysed quickly and relatedto other large extant data sets. Data managementand bioinformatics for breedershave therefore become critical componentsof the infrastructure needed to use MAS.Prior to the advent of MAS, some largeprivate breeding programmes had establisheda group of dedicated data managersto assist with research and marketing, andwith the arrival of genomics and MASthe need for such dedicated specialists hasincreased greatly.Once the basic infrastructure had beenestablished to complement the activitiesof maize breeders, programmes wereready to implement several basic aspectsof MAS; many of which are derived fromwell established methods and principles ofmaize breeding.MAS-based breedingSelection occurs at various stages in maizebreeding programmes. The first opportunityfor selection is the choice of inbredlines to mate as parents of new populations.Prior to the advent of DNA markerdata, the selection of such parents wouldbe based on a combination of phenotypicassessments, pedigree information, breedingrecords and chance (Hallauer and Miranda,1981; Sprague and Dudley, 1988). In someprogrammes today, all such inbreds aregenotyped systematically at DNA markerloci. Depending on the resources andobjectives, the degree of genotyping mayrange from a low density of marker loci(e.g. SNPs in candidate genes) to higherdensity whole genome scans (Varshney,Graner and Sorrels, 2005). These genotypicdata, alone or integrated with phenotypicinformation, may reveal novel aspects ofmaize gene pools, heterotic groups, haplotypeevolution, gene content and parentsused in MAS for specific target environments(Fu and Dooner, 2002; Niebur et al.,2004; Crosbie et al., 2006). When properlyintegrated with phenotypic informationand functional genomics, genotypic dataof inbred lines should allow breeders tochoose parents that, when mated, shouldprovide populations or gene pools enrichedfor the more desirable combinations offavourable alleles. Such a starting point isa huge advantage in plant breeding becauseit increases the probability of selectingprogeny that are superior to the parentsand that approximate a predicted optimumgenotype.