Marker assisted selection for genetic improvement of animal populations when a single QTL is marked

A Monte Carlo simulation study to evaluate the benefits of marker assisted selection (MAS) in small populations with one marked bi-allelic quantitative trait locus (QTL) is described. In the base generation, linkage phase equilibrium between the markers, QTL and polygenes was assumed and frequencies of 0.5 for the two QTL alleles were used. Six discrete generations of selection for a single character measured on both sexes followed. An additive genetic model was used with the QTL positioned midway between two highly polymorphic markers. Schemes were simulated with a distance of 10 cM between the QTL and either of the two markers and with the QTL explaining 1/8 of the total genetic variance in the base generation. Values of 0.5, 0.25 or 0.1 were assumed for the heritability. Eight males and 16, 32 or 64 females were selected each generation with each dam producing four sons and four daughters as candidates for the next generation. Animals were evaluated with a conventional BLUP animal model or with a model using marker information. MAS resulted in substantially higher QTL responses (4-54%), especially with low heritabilities, than conventional BLUP but lower polygenic responses (up to 4%) so that the overall effect on the total genetic response, although in the majority of cases favourable, was relatively small. With QTLs of larger size (explaining 25% of the genetic variance) comparable results were found. When the distance between the QTL and the markers was reduced to 2 cM, genetic responses were increased very slightly with a heritability of 0.5 whereas with a heritability of 0.1 responses were increased by up to 10%, compared with conventional BLUP. Results emphasize that MAS should be most useful for lowly heritable traits and that once QTLs for such traits have been identified the search for closely linked polymorphic markers should be intensified.