marker-assisted selection in wheat - ictsd

180Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishbetween lines or breeds. Thus, marker-QTLassociations identified in the F 2 generationcan be selected for several generations, untilthe QTL or markers are fixed or the disequilibriumdisappears. Zhang and Smith(1992) evaluated the use of markers in sucha situation with selection on BLUP EBV.Although both studies considered the idealsituation of a cross with inbred lines, therewill be opportunities to utilize a limitednumber of markers to select for favourableQTL regions that are detected incrosses between breeds, thereby enhancingthe development of superior synthetics.Pyasatian, Fernando and Dekkers (2006)investigated use of the whole genomeapproach of Meuwissen, Hayes andGoddard (2001) for MAS in a cross byincluding all markers as random effectsin the model for genetic evaluation. Theyshowed that this resulted in substantiallygreater responses to selection than selectionon identified QTL regions only. Due to themuch greater LD, whole genome selectionin a cross can be accomplished with a muchsmaller number of markers compared withthe number required for whole genomeselection in an outbred population.Within-breed selectionThe procedures described previously forincorporating markers in genetic evaluationresult in estimates of breeding values associatedfor QTL, together with estimates ofpolygenic breeding values. Alternatively, ifmolecular data are not incorporated intogenetic evaluations, as will be the casefor more ad hoc approaches and for genetests for Mendelian characteristics, separateselection criteria will be available thatcapture the molecular information. The followingthree selection strategies can then bedistinguished (Dekkers, 2004):• select on the QTL information alone;• tandem selection, with selection on QTLfollowed by selection on polygenic EBV;• selection on the sum of the QTL andpolygenic EBV.Selection on QTL or marker informationalone ignores information that isavailable on all other genes (polygenes)that affect the trait and is expected to resultin the lowest response to selection unlessall genes that affect the trait are includedin the QTL EBV. This strategy does not,however, require additional phenotypesother than those that are needed to estimatemarker effects, and can be attractivewhen phenotype is difficult or expensiveto record (e.g. disease traits, meat quality,etc.). Selection on the sum of the QTL andpolygenic EBV is expected to result in maximumresponse in the short term, but maybe suboptimal in the longer term becauseof losses in polygenic response (Gibson,1994). Indexes of QTL and polygenic EBVcan be derived that maximize longer-termresponse (Dekkers and van Arendonk,1998) or a combination of short- and longertermresponses (Dekkers and Chakraborty,2001). However, if selection is on multipleQTL and emphasis is on maximizingshorter-term response, selection on the sumof QTL and polygenic EBV is expected tobe close to optimal. Optimizing selectionon a number of EBVs, indexes and genotypes,while also considering inbreedingrate and other practical considerations isnot a trivial task. Kinghorn, Meszaros andVagg (2002) have proposed a mate selectionapproach that could be used to handlesuch problems, and it can be expected thatwith more widespread use of genotypicinformation for a larger number of regions,specific knowledge about individual QTLbecomes less interesting and will simplycontribute to prediction of whole EBV orwhole genotype.