Simulation of marker assisted breeding in an applied tree improvement project: A case study based on the Western Gulf Forest Tree Improvement Program

Marker assisted selection (MAS) was evaluated by Monte Carlo simulation in the context of an applied tree improvement program. Selection was modeled for a quantitative trait where 1, 3, or 5 quantitative trait loci (QTL) explained 60% of the additive genetic variation in a single family used for QTL detection. The remainder of the additive variation was explained by 20 minor genes. The QTL were initially at a frequency of 5% in the breeding population which reduced their contribution to 36% and 22% of the additive genetic variation for QTL originally detected in the backcross (Aa:aa) or intercross (AA:Aa:aa) configuration, respectively. The trait in breeding population was moderately heritable (h 2 = 0.2) and expressed an inbreeding depression as a 5% reduction in phenotype for each 0.1 increase in F. The breeding population consisted of 360 individuals subdivided into 20 sublines.; Breeding using a complementary mating system was simulated for 10 generations with and without MAS using both dominant and codominant marker systems with a modification of Breeding System Model (Bridgwater et al. 1993). Markers and traits were assumed to be in linkage equilibrium, therefore MAS was appropriate for within-family selection only. Under these conditions, MAS was not effective for population level improvement. Simulation of MAS in a smaller, highly selected elite-breeding population demonstrated that MAS became more effective as markers became more reliable, within-family selection increased in importance, and the penalty for inbreeding depression increased.; Economic analysis of MAS to improve a single quantitative trait indicated the presence of considerable risk with an average negative net present value (NPV) for a large mainline breeding program at a discount factor of 7%. However, the analysis indicated that the uncertainty surrounding this prediction was large and that significantly better returns were achieved in iterations where MAS was effective. NPV was positive for the elite-breeding population although a large amount of uncertainty was present. Shortening the breeding cycle resulted in large positive values for NPV. The most appropriate program for the successful implementation of MAS was likely to be a small elite-breeding population where inbreeding depression prevented efficient individual selection. The correct choice of populations and traits were critical for MAS to be successful.