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

Adelin Barbacci,Mehdi Khafif,Laurence Godiard,Malick Mbengue,Aline Lacaze,Marielle Barascud,Olivier Navaud,Sylvain Raffaele

doi:10.1111/tpj.14747

Abstract

SUMMARYThe 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 enabling high‐throughput disease lesion measurement with high resolution, low footprint at low cost. We could accurately recover contrasted disease responses in several pathosystems using this system. We used our phenotyping pipeline to assess the kinetics of disease symptoms caused by seven S. sclerotiorum isolates on six A. thaliana natural accessions with unprecedented resolution. Large effect polymorphisms common to the most resistant A. thaliana accessions identified highly divergent alleles of the nucleotide‐binding site leucine‐rich repeat gene LAZ5 in the resistant accessions Rubezhnoe and Lip‐0. We show that impaired LAZ5 expression in laz5.1 mutant lines and in A. thaliana Rub natural accession correlate with enhanced QDR to S. sclerotiorum. 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.

Highlights

The fungal pathogen Sclerotinia sclerotiorum is the causal agent of Sclerotinia stem rot (SSR), designated as white mold disease, on numerous crop and vegetable species, including rapeseed, soybean, sunflower, and tomato
Considering that the ectopic activation of LAZ5 triggers cell death (Palma et al, 2010), our results suggest that the broad host range necrotrophic fungus S. sclerotiorum exploits this R gene induced plant cell death to its benefit
Quantification of disease resistance by automated timeresolved image analysis To generate massive, quantitative, and kinetic measurements of disease caused by S. sclerotiorum, we designed mobile imaging cabinets (Navigable automatized phytotron, Navautron) and the associated automatized image analysis pipeline for detached leaves (Figure 1a)

Summary

Introduction

The fungal pathogen Sclerotinia sclerotiorum is the causal agent of Sclerotinia stem rot (SSR), designated as white mold disease, on numerous crop and vegetable species, including rapeseed, soybean, sunflower, and tomato. S. sclerotiorum can be among the most damaging pathogens of rapeseed and soybean when conditions are favourable (Peltier et al, 2012; Derbyshire and Denton-Giles, 2016). As genetic sources of resistance to SSR are lacking for most crop species, adapted cultural practices, the use of fungicides, and biological control methods are frequently employed to limit damages due to S. sclerotiorum (Derbyshire and Denton-Giles, 2016). Instead of a clear demarcation between resistant and susceptible genotypes, plants challenged with S. sclerotiorum generally show a continuum of resistance levels designated as quantitative disease resistance (QDR) phenotype (Perchepied et al, 2010; Roux et al, 2014).

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