marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 349to acceptable levels when the number offamilies is relatively low.To date, little has been publishedregarding the economic profits arising fromthe extra genetic gain obtained by MASor GAS schemes in aquaculture or terrestrialspecies. Information of this natureis essential because the additional gainsare dependent on the magnitude of theallelic effects and thus the marginal increaseshould offset the costs of applying thetechnology. This trade-off may be moreimportant when a single marked QTL,rather than multiple marked QTL (andmultiple traits), is targeted by selection.Pleiotropic effects can be important ifthe polymorphisms under MAS or GASalso have negative effects on fitness orother traits of economic importance. Forexample, negative genetic correlations havebeen found for resistance to viral and bacterialdiseases (Gjøen et al., 1997; Henryonet al., 2002, 2005), which may be a problemin practical breeding when the goal is toselect fish resistant to a range of pathogens.For example, in natural and selectedpopulations, MHC polymorphism is likelyto be maintained by frequency-dependentselection (Langefors, Lohm and Grahn,2001; Lohm et al., 2002; Bernatchez andLandry, 2003), suggesting that selectionfavours rare alleles, but works against thesame alleles at high frequency. Therefore,it seems likely that a MAS scheme usingMHC information or QTL in LD with diseaseresistance should focus on maintainingpolymorphism rather than on selecting fora particular combination of alleles.MAS in populations in linkageequilibriumWhen populations are in LE betweenmarkers and QTL, the information usedfor selection purposes is given by theMendelian co-segregation of markers andQTL within each of the full-sib familiesin the population under selection. Inpractical terms, this means that co-ancestryconditional on marker information needsto be computed within a family for agiven segment in the genome. In effect,the segregation of regions that individualsshare as identical-by-descent (“more” or“less” than average) is being traced and,under such circumstances, the accuracy ofpredicting breeding values using markerinformation is mainly dependent on theproportion of the within-family variancedue to the QTL (Ollivier, 1998).The effect of family size on the relativeaccuracy of predicting breeding values(comparing MAS and BLUP) using markerinformation was studied in detail using simulations(Table 2; V. Martinez, unpublisheddata). Compared with the GAS schemespresented below, for LE-MAS to be efficient,large full-sib families are requiredfor predicting breeding values for the QTLaccurately. This is because breeding valueprediction is carried out on a within-familybasis; thus, large families are required toobtain breeding values for predicting QTLeffects with reasonable accuracy. Whenindividuals do not have records for thequantitative trait, the extra accuracy ofMAS was highest for the largest family sizesimulated (50 individuals, 25 with recordsand 25 without records; the difference isequal to 7 percent). The accuracy of predictingbreeding values was very similar inBLUP or MAS for individuals that haverecords for the trait in most of the scenariossimulated, suggesting that MAS is expectedto be of little use under these circumstances(Villanueva, Pong-Wong and Woolliams,2002).The advantage of MAS will comeboth from increased accuracy and from