Fig. 2

Graphical abstract illustrating the main steps of our analysis workflow. (1) First step of GWAS: detection of the associations among LC-MS features (orange boxes) and reference SNPs (red vertical bars); (2) Second step of GWAS: reference SNPs are linked to co-inherited SNPs sets (blue vertical bars); (3) Co-localization among co-inherited SNPs and SNPs belonging to abiotic stress-related QTLs (green vertical bar). Co-inherited SNPs falling in a 50 kb interval downstream or upstream of an SNP belonging to a QTL are considered co-localizing with the same QTL. All the SNPs in complete linkage disequilibrium (LD) with co-localizing SNPs and mapping to exons (yellow transparent boxes) are then used to identify putative candidate genes; (4) LC-MS features associated to reference SNPs in complete LD with co-localizing SNPs are selected and tentatively annotated