marker-assisted selection in wheat

Chapter 1 – An overview of the issuesthey could be genetically complex quantitativetraits, involving many genes (i.e.so-called quantitative trait loci [QTL])and environmental effects. Most economicallyimportant agronomic traits tend tofall into this latter category. For example,using 280 molecular markers (comprising134 RFLPs, 131 AFLPs and 15 microsatellites)and recording populations of ricelines for various plant water stress indicators,phenology, plant biomass, yield andyield components under irrigated and waterstress conditions, Babu et al. (2003) detecteda number of putative QTL for droughtresistance traits.Having identified markers physicallylocated beside or even within genes ofinterest, in the next step it is now possibleto carry out MAS, i.e. to select identifiablemarker variants (alleles) in order to selectfor non-identifiable favourable variants ofthe genes of interest. For example, considera hypothetical situation where a molecularmarker M (with two alleles M1 and M2),identified using a DNA assay, is knownto be located on a chromosome close toa gene of interest Q (with a variant Q1that increases yield and a variant Q2 thatdecreases yield), that is, as yet, unknown.If a given individual in the population hasthe alleles M1 and Q1 on one chromosomeand M2 and Q2 on the other chromosome,then any of its progeny receiving the M1allele will have a high probability (how highdepends on how close M and Q are to eachother on the chromosome) of also carryingthe favourable Q1 allele, and thus wouldbe preferred for selection purposes. On theother hand, those that inherit the M2 allelewill tend to have inherited the unfavourableQ2 allele, and so would not be preferredfor selection. With conventional selectionwhich relies on phenotypic values, it is notpossible to use this kind of information.The success of MAS is influenced bythe relationship between the markersand the genes of interest. Dekkers (2004)distinguished three kinds of relationship:• The molecular marker is located withinthe gene of interest (i.e. within the geneQ, using the example above). In thissituation, one can refer to gene-assistedselection (GAS). This is the mostfavourable situation for MAS since, byfollowing inheritance of the M alleles,inheritance of the Q alleles is followeddirectly. On the other hand, these kindsof markers are the most uncommon andare thus the most difficult to find.• The marker is in linkage disequilibrium(LD) with Q throughout the wholepopulation. LD is the tendency of certaincombinations of alleles (e.g. M1 and Q1)to be inherited together. PopulationwideLD can be found when markersand genes of interest are physicallyvery close to each other and/or whenlines or breeds have been crossed inrecent generations. Selection using thesemarkers can be called LD-MAS.• The marker is not in linkage disequilibrium(i.e. it is in linkage equilibrium[LE]) with Q throughout the whole population.Selection using these markerscan be called LE-MAS. This is the mostdifficult situation for applying MAS.The universal nature of DNA, molecularmarkers and genes means that MAS can,in theory, be applied to any agriculturallyimportant species. Indeed, active researchprogrammes have been devoted to buildingmolecular marker maps and detecting QTLsfor potential use in MAS programmes in awhole range of crop, livestock, forest treeand fish species. In addition, MAS can beapplied to support existing conventionalbreeding programmes. These programmesuse strategies such as: recurrent selection (i.e.