Rapid identification of an Arabidopsis NLR gene conferring susceptibility to Sclerotinia sclerotiorum using time-resolved automated phenotyping

Abstract

The broad host range necrotrophic fungus Sclerotinia sclerotiorum is a devastating pathogen of many oil and vegetable crops. Plant genes conferring complete resistance against S. sclerotiorum have not been reported. Instead, plant populations challenged by S. sclerotiorum exhibit a continuum of partial resistance designated as quantitative disease resistance (QDR). Because of their complex interplay and their small phenotypic effect, the functional characterization of QDR genes remains limited. How broad host range necrotrophic fungi manipulate plant programmed cell death is for instance largely unknown. Here, we designed a time-resolved automated disease phenotyping pipeline and assessed the kinetics of disease symptoms caused by seven S. sclerotiorum isolates on six A. thaliana natural accessions with unprecedented resolution. We hypothesized that large effect polymorphisms common to the most resistant A. thaliana accessions, but absent from the most susceptible ones, would point towards disease susceptibility genes. This identified highly divergent alleles of the nucleotide-binding site leucine-rich repeat gene LAZ5 in the resistant accessions Rubenzhnoe and Lip-0. Two LAZ5-deficient mutant lines in the Col-0 genetic background showed enhanced QDR to S. sclerotiorum, whereas plants mutated in the closely related CSA1 gene responded like the wild type. These findings illustrate the value of time-resolved image-based phenotyping for unravelling the genetic bases of complex traits such as QDR. Our results suggest that S. sclerotiorum manipulates plant sphingolipid pathways guarded by LAZ5 to trigger programmed cell death and cause disease.