marker-assisted selection in wheat - ictsd

Chapter 12 – Marker-assisted selection in dairy cattle 213The disadvantages of this model are thatit assumes that both recombination frequencyand the variance due to the QTL areknown a priori. Studies on simulated datahave demonstrated that although restrictedmaximum likelihood methodology can beused to estimate these parameters, theyare completely confounded for a singlemarker locus (van Arendonk et al., 1994).Methods to estimate the variance contributedby QTL with multiple markers weredeveloped by Grignola, Hoeschele and Tier(1996). Furthermore, as each individualwith unknown parents is assumed to havetwo unique alleles, the prediction errorvariances of the effects for any individualwill be quite large and, therefore, not veryinformative. Finally, the assumption of anormal distribution of possible QTL alleleeffects may not be realistic.Israel and Weller (1998) proposed analternative method that assumes that onlytwo QTL alleles are segregating in thepopulation, and that either a daughter orgranddaughter design has been applied todetermine QTL genotypes of the familyancestors. The QTL effect is then includedin the complete animal model analysis asa fixed effect. For individuals that arenot genotyped, probabilities of receivingeither allele are included as regressionconstants. These probabilities can be readilycomputed for the entire population usingthe segregation analysis method of Kerrand Kinghorn (1996). Israel and Weller(1998) assumed complete linkage betweenthe QTL and a single marker. Israel andWeller (2002) extended the method to QTLanalysis based on flanking marker, usingthe method of Whittaker, Thompsom andVisscher (1996) to estimate QTL effectsand location from the regression estimatesof flanking markers. This method has beentested extensively on simulated populations,and was able to derive unbiased estimatesof QTL effect and location. It has alsobeen applied to actual data from the IsraeliHolstein population for a segregatingQTL on chromosome 14 that affectedmilk production traits (Weller et al., 2003).However, in this case the QTL effectwas underestimated. Further research isrequired to determine the reason for thisdiscrepancy.Methods for QTL detection andMAS in developing countriesAs noted previously, dairy cattle breedingin tropical and subtropical countries is generallybased on crossbreeding between highproduction breeds adapted to temperateclimates, and tropical strains which areadapted to the local environment, includingresistance to local diseases. In other animalspecies, synthetic strains have been producedby selecting those individuals thatretain the positive characteristics fromboth strains. For example, the Assaf sheepbreed was produced from a cross betweenthe Middle East Awassi breed and theEast Friesian breed (www.sheep101.info/breedsA.html). In dairy cattle, the problemof an appropriate strategy for future generationshas not been adequately solved,for reasons considered previously. If theeconomically important genes were identified,then the time and effort required forproduction of the desired synthetic strainscould be reduced.Visscher, Haley and Thompson (1996)considered the situation in which therecipient strain is an outbred populationin an ongoing selection programme, andthe introgressed genes are QTL. Markersflanking the QTL will be required in orderto select backcross progeny that received thedonor QTL allele. As there will be uncertaintywith respect to the QTL location,