Accounting for Correlation Between Traits in Genomic Prediction

Abstract

Genomic enabled prediction is playing a key role for the success of genomic selection (GS). However, according to the No Free Lunch Theorem, there is not a universal model that performs well for all data sets. Due to this, many statistical and machine learning models are available for genomic prediction. When multitrait data is available, models that are able to account for correlations between phenotypic traits are preferred, since these models help increase the prediction accuracy when the degree of correlation is moderate to large. For this reason, in this chapter we review multitrait models for genome-enabled prediction and we illustrate the power of this model with real examples. In addition, we provide details of the software (R code) available for its application to help users implement these models with its own data. The multitrait models were implemented under conventional Bayesian Ridge regression and best linear unbiased predictor, but also under a deep learning framework. The multitrait deep learning framework helps implement prediction models with mixed outcomes (continuous, binary, ordinal, and count, measured on different scales), which is not easy in conventional statistical models. The illustrative examples are very detailed in order to make the implementation of multitrait models in plant and animal breeding friendlier for breeders and scientists.

Keywords: Bayesian methods; Deep learning methods; Genomic selection; Multitrait; Plant breeding.