Data S1. 	List of canola lines utilised in this study
Data S2. 	Overview of experimental design
Data S3. 	Phenotypic data (BLUEs), heritabilities and coefficients of variation
Data S4. 	List of annotated metabolite peaks
Data S5. 	Genotype data set (SNP and CNV markers)
Data S6. 	List of genes in candidate regions
Data S7. 	Pairwise LD matrices for all chromosomes
Data S8. 	List of prediction accuracies for all traits and models
Data S9. 	Pearson correlations between all traits
Data S10. 	Top 100 regulatory links obtained from the network analysis
Data S11. 	List of all associations detected for metabolites, transcripts and phenotypic traits 
Data S12.	Correlation matrix for the correlogram of -omics data
Data S13.	Filtered and outlier-corrected transcriptome (RNA-Seq) data
Data S14.	Input data for the gene ontology (GO) term enrichment analyses
Data S15.	Candidate genes with the GO term ‘intracellular ribonucleoprotein complex’