Extension of a haplotype-based genomic prediction model to manage multi-environment wheat data using environmental covariates.

KEY MESSAGE: A multi-environment genomic prediction model incorporating environmental covariates increased the prediction accuracy of wheat grain protein content. The advantage of the haplotype-based model was dependent upon the trait of interest. The inclusion of environment covariates (EC) in genomic prediction models has the potential to precisely model environmental effects and genotype-by-environment interactions. Together with EC, a haplotype-based genomic prediction approach, which is capable of accommodating the interaction between local epistasis and environment, may increase the prediction accuracy. The main objectives of our study were to evaluate the potential of EC to portray the relationship between environments and the relevance of local epistasis modelled by haplotype-based approaches in multi-environment prediction. The results showed that among five traits: grain yield (GY), plant height, protein content, screenings percentage (SP) and thousand kernel weight, protein content exhibited a 2.1% increase in prediction accuracy when EC was used to model the environmental relationship compared to treatment of the environment as a regular random effect without a variance-covariance structure. The approach used a Gaussian kernel to characterise the relationship among environments that displayed no advantage in contrast to the use of a genomic relationship matrix. The prediction accuracies of haplotype-based approaches for SP were consistently higher than the genotype-based model when the numbers of single-nucleotide polymorphisms (SNP) in a haplotype were from three to ten. In contrast, for GY, haplotype-based models outperformed genotype-based methods when two to four SNPs were used to construct the haplotype.