marker-assisted selection in wheat

Chapter 8 – Marker-assisted selection in maize 131of phenotypic selection in some referencepopulations. Marker-only recurrent selectionschemes have been implemented fora variety of traits including grain yield andgrain moisture (Eathington, 2005), or abioticstress tolerance (Ragot et al., 2000), andmultiple traits are being targeted simultaneously.Selection indices were apparentlybased on 10 to probably more than 50 loci,these being either QTL identified in theexperimental population where MARS wasbeing initiated, QTL identified in otherpopulations, or genes. Marker genotypesare generated for all markers flanking QTLincluded in the selection indices (Ragotet al., 2000). Plants are genotyped at eachcycle and specific combinations of plantsare selected for crossing, as proposed byvan Berloo and Stam (1998). Several, probablythree to four, cycles or MARS areconducted per year using continuous nurseries.In maize, early versions of suchschemes have been tested and implemented(Johnson, 2004; Crosbie et al., 2006).Results reported in these recent communicationsabout private MARS experiments(Ragot et al., 2000; Eathington, 2005) are insharp contrast to those in earlier publications(Openshaw and Frascaroli, 1997; Moreau,Charcosset and Gallais, 2004). Several factorscan explain these discrepancies:• Size of the populations submitted to selectionat each cycle. Given reports thatincreasing population size should resultin higher genetic gain through MARS(van Berloo and Stam, 2001,) it is likelythat populations submitted to selectionin private programmes are rather large,larger than the 160 and 300 individualsreported respectively by Openshaw andFrascaroli (1997) and Moreau, Charcossetand Gallais (2004).• Use of flanking versus single markers.The use of flanking markers for QTLunder selection allows better predictionof the genotype at the QTL than whenusing single markers. When single markersare used, recombination events thatoccur between the marker and the QTLlead to loss of linkage between the markerand the QTL much faster than whenflanking markers are used, thereby rapidlyreducing the predictive power of thesingle marker.• Early selection, pre-flowering. The abilityto select plants before flowering ensuresoptimal mating schemes as the genotypesof plants being selfed or intercrossed arefully known. However, this is not thecase when selection cannot take placebefore flowering and involves intercrossingselfed progenies of selected plants, thegenotypes of which might have driftedsignificantly from those of their genotypedparents.• Number of generations per year. To theauthors’ knowledge, none of the simulationor experimental studies of MARS hasassessed the effects of cycle length on itsefficiency despite its direct relationshipto the rate of genetic gain. In maize,cycle length can be reduced three- to sixfoldwhen using marker-only recurrentselection compared with phenotypicrecurrent selection. Consequently, markeronlyrecurrent selection will be superiorto phenotypic selection as soon as thegenetic gain achieved through one cycleof MARS is, respectively, more than athird or a sixth of that achieved throughone cycle of phenotypic selection. Privatemaize breeding programmes have accessto off-season nurseries. Furthermore,they have often established efficientcontinuous nurseries where three to fourgenerations of maize can be grown peryear. The use of such nurseries allowsthem to carry MARS continuously, i.e.