Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity

Abstract

Quantitative genetics states that phenotypic variation is a consequence of genetic and environmental factors and their subsequent interaction. Here, we present an enviromic assembly approach, which includes the use of ecophysiology knowledge in shaping environmental relatedness into whole-genome predictions (GP) for plant breeding (referred to as E-GP). We propose that the quality of an environment is defined by the core of environmental typologies (envirotype) and their frequencies, which describe different zones of plant adaptation. From that, we derive markers of environmental similarity cost-effectively. Combined with the traditional genomic sources (e.g., additive and dominance effects), this approach may better represent the putative phenotypic variation across diverse growing conditions (i.e., phenotypic plasticity). Additionally, we couple a genetic algorithm scheme to design optimized multi-environment field trials (MET), combining enviromic assembly and genomic kinships to provide in-silico realizations of the future genotype-environment combinations that must be phenotyped in the field. As a proof-of-concept, we highlight E-GP applications: (1) managing the lack of phenotypic information in training accurate GP models across diverse environments and (2) guiding an early screening for yield plasticity using optimized phenotyping efforts. Our approach was tested using two non-conventional cross-validation schemes to better visualize the benefits of enviromic assembly in sparse experimental networks. Results on tropical maize show that E-GP outperforms benchmark GP in all scenarios and cases tested. We show that for training accurate GP models, the genotype-environment combinations representativeness is more critical than the MET size. Furthermore, we discuss theoretical backgrounds underlying how the intrinsic envirotype-phenotype covariances within the phenotypic records of (MET) can impact the accuracy of GP and limits the potentialities of predictive breeding approaches. The E-GP is an efficient approach to better use environmental databases to deliver climate-smart solutions, reduce field costs, and anticipate future scenarios.