Plant secondary metabolism is an active research area because of the unique and important roles the specialized metabolites have in the interaction of plants with their biotic and abiotic environment, the diversity and complexity of the compounds and their importance to human medicine. Thousands of natural accessions of Arabidopsis thaliana characterized with increasing genomic precision are available, providing new opportunities to explore the biochemical and genetic mechanisms affecting variation in secondary metabolism within this model species. In this study, we focused on four aromatic metabolites that were differentially accumulated among 96 Arabidopsis natural accessions as revealed by leaf metabolic profiling. Using UV, mass spectrometry, and NMR data, we identified these four compounds as different dihydroxybenzoic acid (DHBA) glycosides, namely 2,5-dihydroxybenzoic acid (gentisic acid) 5-O-b-D-glucoside, 2,3-dihydroxybenzoic acid 3-O-b-D-glucoside, 2,5-dihydroxybenzoic acid 5-O-b-D-xyloside, and 2,3-dihydroxybenzoic acid 3-O-b-D-xyloside. Quantitative trait locus (QTL) mapping using recombinant inbred lines generated from C24 and Col-0 revealed a major-effect QTL controlling the relative proportion of xylosides vs. glucosides. Association mapping identified markers linked to a gene encoding a UDP glycosyltransferase gene. Analysis of Transfer DNA (T-DNA) knockout lines verified that this gene is required for DHBA xylosylation in planta and recombinant protein was able to xylosylate DHBA in vitro. This study demonstrates that exploiting natural variation of secondary metabolism is a powerful approach for gene function discovery. P LANTS produce .200,000 diverse low-molecular weight compounds, known as secondary or specialized metabolites (Dixon and Strack 2003; Yonekura-Sakakibara and Saito 2009). These metabolites are not essential to shortterm survival but play important roles in many aspects of plant life, including growth regulation, defense against herbivores, UV protection, and other adaptations to the environment (Hartmann 2007). Apart from their roles in plant adaptation, plant specialized metabolites are rich sources for industrial and medicinal materials such as dyes, flavors, and pharmaceuticals (Balandrin et al. 1985).Studies of Arabidopsis thaliana have greatly advanced our understanding of the biochemical pathways and gene networks involved in a variety of specialized metabolism. For example, genetic analysis of artificially induced Arabidopsis mutants has led to the discovery of genes responsible for the biosynthesis of flavonoids, sinapate esters, and lignin (Shirley et al. 1995;Ruegger and Chapple 2001). Exploiting natural variation between different accessions in the accumulation of glucosinolates and terpenoids has led to the identification of genes involved in their biosynthesis and alleles regulating their variation that are under strong selection (Kliebenstein et al. 2001a,b;Kroymann et al. 2001;Chen et al. 2003;Tholl et al. 2005). Despite this progress, there are many mo...