Genetic basis ofArabidopsis thalianaresponses to infection by naïve and adapted isolates of turnip mosaic virus

Abstract

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.

Cauliflower mosaic virusdisease spectrum uncovers novel susceptibility factor NCED9 inArabidopsis thaliana

“…The defiance of pathogenload/symptom connections ("tolerance") has been reported in other infection-systems, including bacteria and fungi (Gambetta et al, 2007;Chen et al, 2004), although, examples of clear resistance trajectories also exist, for example for Pseudomonas syringae on Arabidopsis that shows strong positive correlation between symptom severity and bacterial density (Kover & Schaal, 2002). CaMV causes moderate symptoms in most accessions, a trend also seen with TuMV in 1050 Arabidopsis accessions (Butkovic et al, 2022) and in line with the theory that viruses evolve for an intermediate severity to balance replication and host survival (Torres-Barceló et al, 2010).…”

“…Plant viruses are ubiquitous in wild and cultivated habitats with profound impacts on host populations (Prendeville et al ., 2012). As obligate intracellular parasites, they are fully dependent on host-compatibility to complete their replication cycle, and genetic variation within both the plant and viral species can have major effects on the disease outcome (Butkovic et al ., 2022; Cecchini et al ., 1998). Of particular interest is the continuum of two mechanisms, tolerance and resistance, plants employ against invading pathogens.…”

“…Even though, thanks to the extensive 1001 genomes project, Arabidopsis is a superb resource for GWA studies, with over 1000 sequenced naturally inbred accessions collected worldwide (Consortium, 2016). To our knowledge six recent GWA studies have been conducted on RNA virus infections in Arabidopsis (Butkovic et al ., 2022; Liu et al ., 2022; Butković et al ., 2021; Montes et al ., 2021; Rubio et al ., 2019; Pagny et al ., 2012) and successfully identified genetic loci impacting viral infections.…”

Stress & Granules : regulation of Cauliflower mosaic virus disease in Arabidopsis thaliana

“…Arabidopsis has evolved in the presence of viruses and exhibits a broad range of symptoms after infection. Notably, the GWAS studies have all but one focused on either virus accumulation (Liu et al, 2022;Pagny et al, 2012) as the tested trait or plant disease (Butković et al, 2022;Butković et al, 2021;Montes et al, 2021) CaMV infects Arabidopsis in the wild (Pagán et al, 2010), which makes this host-pathogen pair suitable for GWA studies, as CaMV could be a selective pressure on Arabidopsis evolution. The dynamics of CaMV disease in Arabidopsis in response to drought have been studied in a limited number of accessions (Bergès et al, 2021;Bergès et al, 2020;Bergès et al, 2018), but no systemic analyses of CaMV disease in Arabidopsis or an examination of the underlying genetics had been performed before this thesis.…”

Genome-wide association studies of viral infections—A short guide to a successful experimental and statistical analysis

“…While in human studies, many small effect loci explain a trait and require genotyping of thousands of individuals in order to detect them (The Wellcome Trust Case Control Consortium, 2007;Korte and Farlow, 2013;Genissel et al, 2017). So far, in infectious disease GWAS an increase in sample sizes identified more meaningful associations (McLaren et al, 2015;Butković et al, 2021;Butković et al, 2022). Since viral infectious diseases are highly prevalent and are governed by common variants, a moderate increase in sample size should lead to enough statistical power needed to identify meaningful associations.…”