Genetic response from marker assisted selection in an outbred population for differing marker bracket sizes and with two identified quantitative trait loci

Effect of flanking quantitative trait loci (QTL)-marker bracket size on genetic response to marker assisted selection in an outbred population was studied by simulation of a nucleus breeding scheme. In addition, genetic response with marker assisted selection (MAS) from two quantitative trait loci on the same and different chromosome(s) was investigated. QTL that explained either 5% or 10% of phenotypic variance were simulated. A polygenic component was simulated in addition to the quantitative trait loci. In total, 35% of the phenotypic variance was due to genetic factors. The trait was measured on females only. Having smaller marker brackets flanking the QTL increased the genetic response from MAS selection. This was due to the greater ability to trace the QTL transmission from one generation to the next with the smaller flanking QTL-marker bracket, which increased the accuracy of estimation of the QTL allelic effects. Greater negative covariance between effects at both QTL was observed when two QTL were located on the same chromosome compared to different chromosomes. Genetic response with MAS was greater when the QTL were on the same chromosome in the early generations and greater when they were on different chromosomes in the later generations of MAS.