ENVIROME-WIDE ASSOCIATIONS ENHANCE MULTI-YEAR GENOME-BASED PREDICTION OF HISTORICAL WHEAT BREEDING DATA

Abstract

Linking high-throughput environmental data (enviromics) into genomic prediction (GP) is a cost-effective strategy for increasing selection intensity under genotype-by-environment interactions (GxE). This study developed a data-driven approach based on Environment-Phenotype Associations (EPA) aimed at recycling important GxE information from historical breeding data. EPA was developed in two applications: (1) scanning a secondary source of genetic variation, weighted from the shared reaction-norms of past-evaluated genotypes; (2) pinpointing weights of the similarity among trial-sites (locations), given the historical impact of each envirotyping data variable for a given site. Then, the EPA outcomes were integrated into multi-environment GP models through a new single-step GBLUP. The wheat trial data used included 36 locations, 8 years and 3 target populations of environments (TPE) in India. Four prediction scenarios and 6 kernel-models within/across TPEs were tested. Our results suggest that the conventional GBLUP, without enviromic data or when omitting EPA, is inefficient in predicting the performance of wheat lines in future years. However, when EPA was introduced as an intermediary learning step to reduce the dimensionality of the GxE kernels while connecting phenotypic and environmental-wide variation, a significant enhancement of GxE prediction accuracy was evident. EPA revealed that the effect of seasonality makes strategies such as "covariable selection" unfeasible because GxE is year-germplasm specific. We propose that the EPA effectively serves as a "reinforcement learner" algorithm capable of uncovering the effect of seasonality over the reaction-norms, with the benefits of better forecasting the similarities between past and future trialing sites. EPA combines the benefits of dimensionality reduction while reducing the uncertainty of genotype-by-year predictions and increasing the resolution of GP for the genotype-specific level.