Association mapping analysis of Cd, Cu and H (2)O (2) tolerance, judged by relative root length (RRL: % of root length in stress condition relative to that in control condition), and Cd and Cu translocation ratios (amount of metal in the shoot to the total) were performed using 90 accessions of Arabidopsis thaliana. Using 140 SNPs that were distributed across the genome, association mapping analysis was performed with a haploid setting by the Q + K method, which minimizes detection of false associations by combining the Q-matrix of the structured association (Q) with kinship (K) to control for the population structure. Six, five and five significant (-log (10)P-value is 1.3 > or =) linkages were detected between the SNPs and Cd, Cu and H(2)O(2) resistant RRLs, respectively. In addition, six significant linkages were identified with translocation capacities of Cd and Cu. Among those detected loci, two each of Cu and Cd tolerance RRLs were collocated with those of H(2)O(2) tolerance RRL, while one locus each was detected by Cu and Cd tolerance RRLs that collocated with their translocation ratios. These results suggested that these factors might partly explain the phenotypic variation of tolerance RRLs to Cd and Cu of Arabidopsis thaliana. Finally, using a different approach to analyze interactions between individual phenotypes, namely clustering analysis, we found an expected segregation of resistant SNPs (single-nucleotide polymorphisms) of the multiple RRLs in the typical accession groups carrying multiple traits. Almost none of the loci detected by association mapping analysis were linked to the loci of previously identified critical genes regulating the traits, suggesting that this could be useful to identify complex architecture of genetic factors determining variation among multiple accessions.