The data published here is the raw multi-omics data used for the paper titled "Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations" (bioRxiv 2021.05.03.442386). In this paper, we integrated genomic DNA markers, transcripts and metabolites to predict agronomic and seed nutritional traits across environments and in distantly related populations in addition to the single-environment prediction. The GBS data used in this study was downloaded from T3/Oat (https://oat.triticeaetoolbox.org/), so here we publish the phenotypic, RNAseq and metabolomics data.