Sample size determination for training set optimization in genomic prediction

KEY MESSAGE: A practical approach is developed to determine a cost-effective optimal training set for selective phenotyping in a genomic prediction study. An R function is provided to facilitate the application of the approach. ABSTRACT: Genomic prediction (GP) is a statistical method used to select quantitative traits in animal or plant breeding. For this purpose, a statistical prediction model is first built that uses phenotypic and genotypic data in a training set. The trained model is then used to predict genomic estimated breeding values (GEBVs) for individuals within a breeding population. Setting the sample size of the training set usually takes into account time and space constraints that are inevitable in an agricultural experiment. However, the determination of the sample size remains an unresolved issue for a GP study. By applying the logistic growth curve to identify prediction accuracy for the GEBVs and the training set size, a practical approach was developed to determine a cost-effective optimal training set for a given genome dataset with known genotypic data. Three real genome datasets were used to illustrate the proposed approach. An R function is provided to facilitate widespread application of this approach to sample size determination, which can help breeders to identify a set of genotypes with an economical sample size for selective phenotyping. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-023-04254-9.