Improving genomic prediction in wheat with random regression models with genotype-specific phenology-driven...

Wheat (Triticum aestivum L.), a crucial cereal crop for global food security, faces growing challenges from climate change. Future production requires varieties that are resilient to environmental extremes and fluctuations. The goal of this study was to assess strategies to increase selection response through genomic selection in wheat by integrating genotypic-specific phenology-derived environmental covariates (ECs) and random regression models (RRM) in multi-environment trials. We analyzed phenotypic and genomic data from 1683 genotypes from 2010 to 2020 across 71 environments using 45 ECs derived from vegetative, reproductive, and grain-filling phenological phases. Seven key ECs were selected via partial least squares regression to model genotype by environment interaction (GEI) and evaluate their integration in three different genomic prediction scenarios (CV0, CV1, and CV2). Genomic best linear unbiased prediction models (GBLUP), GBLUP models with GEI (GBLUP_{G × E}) modeled as a factor analytic (FA) model, and RRM were compared for their predictive ability performance. RRM with three ECs outperformed GBLUP achieving 50%-100% higher accuracy in CV1 and CV2. The FA exhibited the highest accuracy overall for CV2 but not for CV1. At least one RRM model improved predictions in >89% of environments when predicting new, un-phenotyped environments. Integrating ECs into the RRM enhances genomic prediction by effectively capturing the GEI with a limited number of covariates.