Why usefulness is rarely useful.

Abstract

Mate selection plays an important role in breeding programs. The Usefulness Criterion was proposed to improve mate selection, combining information on both the mean and standard deviation of the potential offspring of a cross, particularly in clonally propagated species where large family sizes are possible. Predicting the mean value of a cross is generally easier than predicting the standard deviation, especially in outbred species when the linkage of alleles is unknown and phasing is required. In this study, we developed a method for estimating phasing accuracy from unphased genotype data on possible parental lines and evaluated whether the accuracy was sufficient to predict family standard deviations of possible crosses. We used simulations spanning a wide range of genetic architectures and used genotypes from a real strawberry breeding population to evaluate the conditions when usefulness could be accurately predicted. We found that with highly accurate computational phasing, predicting family standard deviations and usefulness criteria for potential crosses yields benefit over simply selecting crosses based on predicted family means only at high selection intensity and high heritability and with small numbers of QTL. However, even then the gain from using the family usefulness is small.