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

TL;DR

This paper reviews linear mixed models for predicting genotype-environment interactions in plant breeding, focusing on methods to improve predictions in unseen environments and assessing prediction uncertainty within a unified model framework.

Contribution

It unifies various regression-based methods for genotype-environment modeling under a common prediction framework, including new approaches for uncertainty estimation.

Findings

Methods effectively predict in new environments.

Uncertainty assessment improves prediction reliability.

Models are demonstrated on rice variety trial data.

Abstract

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 modelled 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.