Genomic prediction for complex traits across multiples harvests in alfalfa (Medicago sativa L.) is enhanced by enviromics

Abstract

Breeding for dry matter yield and persistence in alfalfa (Medicago sativa L.) can take several years as these traits must be evaluated under multiple harvests. Therefore, genotype-by-harvest interaction should be incorporated into genomic prediction models to explore genotypes’ adaptability and stability. In this study, we investigated how enviromics could help to predict the genotypic performance under multiharvest alfalfa breeding trials by evaluating 177 families across 11 harvests under four cross-validation scenarios. All scenarios were analyzed using six models in a Bayesian mixed model framework. Our results demonstrate that models accounting to the enviromics information led to an increase of genetic variance and a decrease in the error variance, indicating better biological explanation when the enviromic information was incorporated. Furthermore, models that accounted for enviromic data led to higher predictive ability (PA) in a reduced number of harvests used in the training data set. The best enviromic models (M2 and M3) outperformed the base model (GBLUP model—M0) for predicting adaptability and persistence across all cross-validation scenarios. Incorporating environmental covariates also provided higher PA for persistence compared with the base model, as predictions increased from 0 to 0.16, 0.20, 0.56, and 0.46 for CV00, CV1, CV0, and CV2. The results also demonstrate that GBLUP without enviromics term has low power to predict persistence, thus the adoption of enviromics is a cheap and efficient alternative to increase accuracy and biological meaning.