biostudies-literatureUnknown127(3)Sasaki EGenome-wide association studies (GWAS) have become a standard approach for exploring the genetic basis of phenotypic variation. However, correlation is not causation, and only a tiny fraction of all associations have been experimentally confirmed. One practical problem is that a peak of association does not always pinpoint a causal gene, but may instead be tagging multiple causal variants. In this study, we reanalyze a previously reported peak associated with flowering time traits in Swedish Arabidopsis thaliana population. The peak appeared to pinpoint the AOP2/AOP3 cluster of glucosinolate biosynthesis genes, which is known to be responsible for natural variation in herbivore resistance. Here we propose an alternative hypothesis, by demonstrating that the AOP2/AOP3 flowering association Heredity245-252https://www.ebi.ac.uk/biostudies/studies/S-EPMC8405673biostudies-literatureRevisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity.PMC8405673Filiault DLSasaki ENordborg MKocher TfalseRevisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity.Genome-wide association studies (GWAS) have become a standard approach for exploring the genetic basis of phenotypic variation. However, correlation is not causation, and only a tiny fraction of all associations have been experimentally confirmed. One practical problem is that a peak of association does not always pinpoint a causal gene, but may instead be tagging multiple causal variants. In this study, we reanalyze a previously reported peak associated with flowering time traits in Swedish Arabidopsis thaliana population. The peak appeared to pinpoint the AOP2/AOP3 cluster of glucosinolate biosynthesis genes, which is known to be responsible for natural variation in herbivore resistance. Here we propose an alternative hypothesis, by demonstrating that the AOP2/AOP3 flowering association 2021-01-01T00:00:00Z2021 Sep2025-04-04T09:37:48.523Z2025-04-04T09:37:48.523ZS-EPMC84056733422667210.1038/s41437-021-00456-3