A Bayesian optimization R package for multitrait parental selection

Abstract

Selecting and mating parents in conventional phenotypic and genomic selection are crucial. Plant breeding programs aim to improve the economic value of crops, considering multiple traits simultaneously. When traits are negatively correlated and/or when there are missing records in some traits, selection becomes more complex. To address this problem, we propose a multitrait selection approach using the Multitrait Parental Selection (MPS) R package—an efficient tool for genetic improvement, precision breeding, and conservation genetics. The package employs Bayesian optimization algorithms and three loss functions (Kullback–Leibler, Energy Score, and Multivariate Asymmetric Loss) to identify parental candidates with desirable traits. The software's functionality includes three main functions—EvalMPS, FastMPS, and ApproxMPS—catering to different data availability scenarios. Through the presented application examples, the MPS R package proves effective in multitrait genomic selection, enabling breeders to make informed decisions and achieve strong performance across multiple traits.