marker-assisted selection in wheat - ictsd

Chapter 10 – Strategies, limitations and opportunities for marker-assisted selection in livestock 181Meuwissen and Goddard (1996) publisheda simulation study that looked at themain characteristics determining efficiencyof MAS using LE markers. They foundthat MAS could improve the rate of geneticimprovement up to 64 percent by selectingon the sum of QTL and polygenic EBV.Their work also demonstrated that MAS ismainly useful for traits where phenotypicmeasurement is less valuable because of:(i) low heritability; (ii) sex-limited expression;(iii) availability only after sexualmaturity; and (iv) necessity to sacrifice theanimal (e.g. slaughter traits). Selection ofanimals based on (most probable) QTLgenotype will allow earlier and more accurateselection, increasing the short- andmedium-term selection response.Most simulation studies have assumedcomplete marker genotype information butin practice only a limited number of individualswill be genotyped. However, inan advanced breeding programme withcomplete information on phenotype andpedigree information, marker and QTLgenotype probabilities could be derivedfor un-genotyped animals and genotypingstrategies could be optimized to achievea high value for the investments made.Marshall, Henshall and van der Werf (2002)looked at strategies to minimize genotypingcost in a sheep breeding programme. Closeto maximal gain could be achieved whengenotyping was undertaken only for highranking males and animals whose markergenotype probability could not be derivedwith enough certainty based on informationon relatives. Marshall, van der Werfand Henshall (2004) also looked at progenytesting of sires to determine family-specificmarker-QTL phase within a breedingnucleus. Again, testing of a limited numberof males provided a lot of information aboutphase for several generations of breedinganimals, as progeny tested sires have relationshipswith descendants. However, inbreeding programmes for more extensiveproduction systems (beef, sheep), pedigreerecording is often incomplete and only asmall proportion of animals are genotyped.Moreover, these genotyped animals are notnecessarily the key breeding animals. Theutility of linked markers will be even morelimited if pedigree relationships cannotbe used to resolve genotype probabilitiesand marker-QTL phase of un-genotypedindividuals.A second point of caution is that manystudies on MAS have taken a single-traitapproach and shown that genetic markerscould have a large impact on responses fortraits that are difficult to improve by phenotypicselection. However, within thecontext of a multitrait breeding objective,the overall impact of such markers on thebreeding goal may be less because a greaterresponse for one trait often appears at theexpense of another. For example, geneticmarkers for carcass traits improve the abilityto select (i.e. earlier, with higher accuracy)for such traits, but selection emphasisfor other traits is reduced. Therefore, theoverall effect of MAS on the breeding programmewill generally be much smallerthan predicted for single trait MAS-favourablecases. The main effects of MAS wouldbe to shift the selection response in favourof the marked traits, rather than achievingmuch additional overall response. Hence,while it will be easier to select for carcassand disease resistance, further improvementfor these traits will be at the expenseof genetic change for production traits(growth, milk).The impact of MAS on the rate ofgenetic gain may be limited in conventionalbreeding programmes (ranging upto perhaps 10 percent extra gain) unless