marker-assisted selection in wheat

Chapter 12 – Marker-assisted selection in dairy cattle 219the sire is heterozygous will be denotedthe “type I” error. Deciding that the QTLis heterozygous in a specific sire, whilethe sire is in reality homozygous will bedenoted the “type II” error. In the firstcase, segregating QTL will be missed while,in the second case, selection for the positiveQTL allele will be applied to no advantage.All three studies found that geneticgains will be maximized with a relativelylarge proportion of type I errors, between5 and 20 percent. This is due to the factthat as type I error increases, type II errordecreases, and more real effects will bedetected and applied in selection. A thirdtype of error is theoretically possible, i.e.determining correctly that the ancestor isheterozygous for the QTL, but incorrectdetermination of QTL phase relative tothe genetic markers. However, Israel andWeller (2004) showed by simulation thatthis error never occurred even when thetype I error rate was set at 20 percent.Spelman, Garrick and van Arendonk(1999) considered three different breedingschemes by deterministic simulation:• a standard PT with the inclusion of QTLdata;• the same scheme except that young bullswithout PT could also be used as bullsires based on QTL information;• a scheme in which young sires could beused as both bull sires and cow sires inthe general population, based on QTLinformation.It was assumed that only bulls weregenotyped but that, once genotyped, theinformation on QTL genotype and effectwas known without error. It was then possibleto conduct a completely deterministicanalysis. They varied the fraction of thegenetic variance controlled by known QTLfrom zero to 100 percent. Even withoutMAS, a slight gain was obtained by allowingyoung sires to be used as bull sires, and agenetic gain of 9 percent was obtained ifyoung sires with superior evaluations werealso used directly as both sires of sires andin general service. As noted previously, thegenetic gain was limited where MAS wasused only to increase the accuracy of youngbull evaluations for a standard PT schemebecause the accuracy of the bull evaluationswas already high. Thus, even if all thegenetic variance was accounted for by QTL,the genetic gain was less than 25 percent.However, if young sires are selected forgeneral service based on known QTL, therate of genetic progress can be doubled. Themaximum rate of genetic gain that can beobtained in the third scheme, the “all bulls”scheme, was 2.2 times the rate of geneticgain in a standard PT. Theoretically, withhalf of the genetic variance due to knownQTL, the rate of genetic gain obtainedwas greater than that possible with nucleusbreeding schemes.The final scheme, with use of geneticmarkers to reduce parentage errors, is themost certain to produce gains, as it doesnot rely on QTL genotype determination,which may be erroneous. Weller et al.(2004) genotyped 6 040 Israeli Holsteincows from 181 Kibbutz herds for 104microsatellites. The frequency of rejectedpaternity was 11.7 percent, and most errorswere due to inseminator mistakes. Mostadvanced breeding schemes already usegenetic markers to confirm parentage ofyoung sires. Israel and Weller (2002) foundby simulations that if the parentage of bulldams and the test daughters of young siresare also verified, genetic gain increasedby 4.3 percent compared with a breedingprogramme with 10 percent incorrectpaternity. This scheme is economicallyjustified if genotyping costs per individualare no more than US$15.