ASHS 2024 Conference

Multi-location genomic prediction models have been proposed as a strategy for aggregating disconnected phenotypic datasets to enable performance prediction of individuals into new environments. This approach also offers improved prediction accuracy and understanding of environmental stability. Multi-location GBLUP prediction models have been developed and used to study patterns in genotype-by-environment interaction for: flowering date in cherry across four locations in USA, France, and Italy; for sweetness in peach across four locations in USA; in strawberry across eight locations in USA, Australia, and Europe; and for fruit firmness in apple across five locations in USA and Europe. Here we present an online bioinformatics platform for the deployment of these models via the Breeding Information Management System (BIMS) in the Genome Database for Rosaceae (GDR). This platform enables performance of new material that has not been physically tested to be predicted for the traits across the environmental space included in the multi-environment GBLUP models. The predicted genetic value of each individual included in the GBLUP models for each trait in each environment was used with the GBLUP individual-by-marker allele frequency matrix to predict the genetic effect of each marker allele for each trait in each environment. A portal was then developed on BIMS to host this vector of marker effects and enable new users to upload tables of new individual-by-SNP marker data for the loci used in the original GBLUP model. Predictions for the new individuals are produced by multiplying the new sample-by-marker frequency matrix by the vector of predicted allelic effects. Predictions of the new material for each trait across environments are delivered alongside predicted performance of publicly available genetic material to enable comparison and evaluation of reliability of predictions. The use of this portal is demonstrated with genome-wide SNP genotypic data collected on new apple selections evaluated for an Australian genetic improvement program.