Relative efficiency of marker assisted selection when marker and QTL are incompletely linked

The relative superiority in selection response of two basic marker-assisted selection strategies, marker-assisted BLUP (MBLUP) and two-stage selection, in comparison to standard BLUP was investigated using stochastic simulation of a closed nucleus herd. In marker-assisted BLUP the marker information and the phenotypic information were utilized simultaneously for selecting parental animals, whereas in two-stage selection they were utilized separately in two stages. Different heritabilities and QTL sizes were considered in the simulation. The QTL was assumed to be referred only via flanking markers, which were incompletely linked to the QTL. It was shown that both MBLUP and two-stage selection increased the QTL response but decreased the polygenic response. When the heritability was low or the QTL effect was large MBLUP was superior to standard BLUP by up to 5% with respect to total genetic response. While the two-stage selection did not show any superiority although it gave extremely large increase in QTL response due to a rapid increase in favorable QTL allele frequency. The relative responses of MAS were stark associated with the generations of selection. The superiority or inferiority of MAS was large in the early generations and became small or vanished in the later generations.