Accession-associated metabolomic variation in wild type Arabidopsis thaliana under control and heat shock conditions

Abstract Arabidopsis thaliana exhibits extensive natural variation, raising questions about the generalization of stress-response studies performed in single accessions. This issue is particularly relevant for metabolomic analyses, where accession-specific baselines may influence interpretation. Here, we compared two widely used Columbia accessions, Col-0 and Col-4, under control conditions and an acute heat-stress regime using untargeted metabolomics. We observed broadly shared heat-associated metabolic-feature patterns in both accessions, together with a limited number of features that met the within-accession significance criteria in only one accession. Although Col-0 and Col-4 displayed high metabolic similarity under control conditions, descriptive analyses indicated subtle accession-associated patterns in specific metabolic features during heat stress; however, no genotype × treatment interaction remained significant after FDR correction. These data provide a concise comparative reference describing shared and accession-associated metabolic patterns and underscore the importance of considering genetic background when interpreting metabolomic studies of stress responses in Arabidopsis.