# Regression approaches for modeling genotype-environment interaction and making predictions into unseen environments

## TL;DR

This paper reviews and connects various regression methods used in plant breeding to improve predictions in new environments by incorporating environmental data.

## Contribution

The paper introduces a new approach for estimating prediction uncertainty and unifies diverse regression methods under a common framework.

## Key findings

- Environmental covariates improve prediction accuracy in plant breeding.
- A new method enhances estimation of prediction variance for genotype-environment interactions.
- Various regression approaches are shown to be closely related within a unified model-based framework.

## Abstract

Several seemingly distinct regression methods are closely related. Environmental covariates delivered improved prediction, and a new approach improves estimation of prediction variance.

In plant breeding and variety testing, there is an increasing interest in making use of environmental information to enhance predictions for new environments. Here, we will review linear mixed models that have been proposed for this purpose. The emphasis will be on predictions and on methods to assess the uncertainty of predictions for new environments. Our point of departure is straight-line regression, which may be extended to multiple environmental covariates and genotype-specific responses. When observable environmental covariates are used, this is also known as factorial regression. Early work along these lines can be traced back to Stringfield & Salter (1934) and Yates & Cochran (1938), who proposed a method nowadays best known as Finlay-Wilkinson regression. This method, in turn, has close ties with regression on latent environmental covariates and factor-analytic variance-covariance structures for genotype-environment interaction. Extensions of these approaches – reduced rank regression, kernel- or kinship-based approaches, random coefficient regression, and extended Finlay-Wilkinson regression – will be the focus of this paper. Our objective is to demonstrate how seemingly disparate methods are very closely linked and fall within a common model-based prediction framework. The framework considers environments as random throughout, with genotypes also modeled as random in most cases. We will discuss options for assessing uncertainty of predictions, including cross validation and model-based estimates of uncertainty, the latter one being estimated using our new suggested approach. The methods are illustrated using a long-term rice variety trial dataset from Bangladesh.

The online version contains supplementary material available at 10.1007/s00122-025-05103-7.