Maximizing quantitative traits in the mating design problem via simulation-based Pareto estimation

Potential pairings are evaluated before the growing season using Monte Carlo simulation, and a mating design is created to allocate a fixed breeding budget across the parent pairs to achieve desired population outcomes. We introduce a novel objective function for this mating design problem that accurately models the goals of a certain class of breeding experiments.

The resulting mating design problem is a computationally burdensome simulation optimization problem on a combinatorially large set of feasible points. We propose a two-step solution to this problem: (i) simulate to estimate the performance of each parent pair and (ii) solve an estimated version of the mating design problem, which is an integer program, using the simulation output. To reduce the computational burden when implementing steps (i) and (ii), we analytically identify a Pareto set of parent pairs that will receive the entire breeding budget at optimality.