PT - JOURNAL ARTICLE AU - Anamarija Butković AU - Thomas James Ellis AU - Rubén González AU - Benjamin Jaegle AU - Magnus Nordborg AU - Santiago F. Elena TI - A globally distributed major virus-resistance association in <em>Arabidopsis thaliana</em> AID - 10.1101/2022.08.02.502433 DP - 2022 Jan 01 TA - bioRxiv PG - 2022.08.02.502433 4099 - http://biorxiv.org/content/early/2022/08/03/2022.08.02.502433.short 4100 - http://biorxiv.org/content/early/2022/08/03/2022.08.02.502433.full AB - Plant viruses account for enormous agricultural losses worldwide, and the most effective way to combat them is to identify genetic material conferring plant resistance to these pathogens. Here, we screen a large panel of Arabidopsis thaliana natural inbred lines for four disease-related traits in response to infection by A. thaliana-naïve and -adapted isolates of the natural pathogen turnip mosaic virus (TuMV). We detected a strong, replicable association in a 1.5 Mb region on chromosome 2 with a 10-fold increase in relative risk of necrosis in response to infection. The region contains several plausible causal genes as well as abundant structural variation, including an insertion of a Copia transposon into an NBS-LRR coding gene, that could be either a driver or a consequence of the disease-resistance locus. Susceptible alleles are found worldwide, and their distribution is consistent with a trade-off between resistance during viral outbreaks and a cost of resistance otherwise, leading to negative frequency-dependent selection.Author summary Plant viruses are an enormous burden to agriculture worldwide. The best way to combat these losses is to use plants that are naturally resistant, so identifying and characterizing genes associated with viral resistance is a priority. Because it is closely related to many crop species and excellent genetic resources, Arabidopsis thaliana is a useful model to investigate the genetic basis of virus resistance. We inoculated a large sample of natural lines of A. thaliana with two isolates of its natural pathogen turnip mosaic potyvirus, and looked for genes associated with variation in resistance. We found a cluster of several genes that showed a strong association with whether the infection was fatal or not. We also compared the fine-scale structure of a subset of the available genomes assembled using long-read DNA sequencing technology, and found enormous variation in the local structure of the genome between individuals. How this variation interacts with disease resistance is unclear, though a transposon insertion in a resistance-related gene, might be relevant. Finally, alleles associated with increased susceptibility to the virus are found at low frequency all over the world. Since potyvirus outbreaks are common in nature, but short-lived, this is consistent with virus resistance being beneficial during outbreaks, but costly when the virus is absent.Competing Interest StatementThe authors have declared no competing interest.