Quantitative disease resistance (QDR) is an immune response limiting pathogen damage in plants. It involves transcriptomic reprogramming of numerous genes, each having a small contribution to plant immunity. Despite the broad-spectrum nature of QDR, the evolution of its underlying transcriptome reprogramming remains largely uncharacterized. Here, we analyzed global gene expression in response to the necrotrophic fungus Sclerotinia sclerotiorum in 23 Arabidopsis (Arabidopsis thaliana) accessions of diverse origin and contrasting QDR phenotypes. Over half of the species pan-transcriptome displayed local responses to S. sclerotiorum, with global reprogramming patterns incongruent with accession phylogeny. Due to frequent small-amplitude variations, only ∼11% of responsive genes were common across all accessions, defining a core transcriptome enriched in highly-responsive genes. Co-expression and correlation analyses showed that QDR phenotypes result from the integration of the expression of numerous genes. Promoter sequence comparisons revealed that variation in DNA-binding sites within cis-regulatory regions contributes to gene expression rewiring. Finally, transcriptome–phenotype maps revealed abundant neutral networks connecting diverse QDR transcriptomes with no loss of resistance, hallmarks of robust and evolvable traits. This navigability associated with regulatory variation in core genes highlights their role in QDR evolvability. This work provides insights into the evolution of complex immune responses, informing models for plant disease dynamics.

Acclimation enables plants to adjust to immediate environmental fluctuations and is therefore key to the resilience of plant disease resistance in a time of climate change. Here, we report on the acclimation of Arabidopsis thaliana quantitative immune responses against the fungal pathogen Sclerotinia sclerotiorum to daily environmental fluctuations. We analyzed disease resistance phenotypes and global gene expression in plants grown in three acclimation regimes, revealing the rewiring of regulatory networks during this process. We identified pathogen-induced genes weakly sensitive to acclimation as promising bases for acclimation-proof immunity. Fluctuations in Mediterranean-like acclimation resulted in an increased disease susceptibility and the misregulation of many pathogen-responsive genes. We identified A. thaliana mutants in novel immune components contributing positively to quantitative disease resistance following temperate but not Mediterranean acclimation. Quantitative disease resistance was maintained under Mediterranean acclimation in NAC42-like mutants and associated with a switch in the repertoire of pathogen-responsive targets of this transcription factor. Our work reveals the role of immune gene networks' plasticity in acclimation and suggests new strategies to maintain plant immune function in a warming climate.

Efficient plant immune response requires concerted reprogramming of cellular transcriptomes both globally and locally at the site of infection. Upon inoculation by the fungal pathogen Sclerotinia sclerotiorum, plants show quantitative disease resistance characterized by transcriptional reprogramming of numerous genes with small phenotypic effect. To study transcriptional heterogeneity across cells during quantitative disease resistance, we combine end-point single-nucleus RNA-sequencing and time-course RNA-seq of mock-treated and S. sclerotiorum-inoculated Arabidopsis thaliana leaves. We observe heterogeneity of plant immune responses across cell types and in sub-populations of mesophyll cells, and reconstruct the sequence of immune responses activation over time. The quantification of gene expression heterogeneity reveals a transient increase in intrinsic transcriptional noise followed by the activation of key defense genes and the rise of extrinsic transcriptional noise in infected cells. Using the R-GECO1 cytoplasmic calcium reporter, we find that the intensity of calcium variations upon S. sclerotiorum inoculation coincides with variations to transcriptional noise in space and time. These results provide evidence that stochastic cell–cell variability plays a key role in commitment to plant immunity and in the coordination of plant defense at the organ scale. Our study offers new insights into the mechanisms underlying plasticity and robustness of plant immune responses that can inform the design of strategies to reduce pathogen damage to crops in unstable environments.

Self-organized Turing patterns, arising from the dynamic interplay of reaction and diffusion processes, are instrumental in modeling natural morphogenesis and deciphering the biological functions of diverse structures. These patterns exhibit complex spatial arrangements that can be analyzed through the lens of statistical mechanics, particularly in relation to hyperuniformity-a state characterized by suppressed long-range density fluctuations. Despite this, the connection between Turing patterns and hyperuniformity remains relatively unexplored. In this study, we examine the spatial distribution of generic Gray-Scott patterns and Arabidopsis thaliana trichome patterns, linking their morphogenesis to disordered hyperuniform patterns. Our findings demonstrate that hyperuniformity emerges in Turing patterns as a solution to a reaction-diffusion equation system, reaching its apex in a specific region of the Gray-Scott phase space marked by dotlike spatial patterns. Mapping the hyperuniformity classes in this region reveals patterns with class III hyperuniformity surrounding special class I solutions. By extending this framework to biological systems currently under investigation for mechanosignalling triggrered immunity, we show that A. thaliana trichomes form class III disordered hyperuniform systems. Such exotic organization, as described by Turing patterning, has a strong potential to influence mechanically triggered immune response, offering novel insights into plant mechanoperception.

Facilitating plant defense through priming holds significant promise for advancing sustainable crop health practices. The primed state of plants is correlated with a more rapid and efficient response, achievable by subjecting plants to recurrent stressors. Consequently, priming constitutes a dynamic transitional process between two distinct biological states, necessitating the establishment and maintenance of transcriptional memory mechanisms. Research on transcriptional memory has revealed molecular mechanisms including protein and transcription factor accumulation, as well as epigenetic modulations. Nonetheless, there remains a dearth of understanding regarding the interplay among the dynamics of transcriptional stress memory, its preservation, and the resultant emergent properties conferred upon the organism once primed. Here, we found that the robustness of transcriptional memory associated with repeated mechanical stimuli played an antagonistic role in the priming of plant defense. Incorporating experiments and computational modeling, we have analyzed the transcriptional stress memory of Arabidopsis thaliana subjected to daily acoustic stimulations. The observed enhanced resistance to the pathogen Sclerotinia sclerotiorum following three rounds of repeated acoustic stimulations is attributed to three primary mechanisms: the activation of a first line of defense in non-inoculated plants, an increase defense-associated gene diversification, and gene priming. These mechanisms are sustained by a transcriptional stress memory involving thousands of genes, likely regulated mostly by transcription factor cascades. Upon comparing the predictions of the transcriptional stress memory model with experimental outcomes, we propose that priming does not arise from the sequential activation of different pathways but rather from the simultaneous modulation of a broad spectrum of pathways. Pathway redundancy in the transcriptional memory topology imparts robustness to plant defense priming. Consequently, primed plants exhibit independence from limited genetic variations, preventing critical loss of resistance observed in naive plants. Pathway redundancies also imply strong limitations in increasing plant defense. Thus, plants remain unaffected by an increase in the daily rate of RAS and exhibited a stress memorization time limited to 1.5 days.### Competing Interest StatementThe authors have declared no competing interest.

Acclimation enables plants to adapt to immediate environmental fluctuations, supporting biodiversity and ecosystem services. However, global changes are altering conditions for plant disease outbreaks, increasing the risk of infections by pathogenic fungi and oomycetes, and often undermining plant immune responses. Understanding the molecular basis of plant acclimation is crucial for predicting climate change impacts on ecosystems and improving crop resilience. Here, we investigated how Arabidopsis thaliana quantitative immune responses acclimates to daily temperature fluctuations. We analyzed responses to the fungal pathogen Sclerotinia sclerotiorum following three acclimation regimes that reflect the distribution areas of both species. Mediterranean acclimation, characterized by broad diurnal temperature amplitudes, resulted in a loss of disease resistance in three natural A. thaliana accessions. Global gene expression analyses revealed that acclimation altered nearly half of the pathogen-responsive genes, many of which were down-regulated by inoculation and associated with disease susceptibility. Phenotypic analysis of A. thaliana mutants identified novel components of quantitative disease resistance following temperate acclimation. Several of these mutants were however more resistant than wild type following Mediterranean acclimation. Notably, mutant lines in the NAC42-like transcription factor did not show a loss of resistance under Mediterranean acclimation. This resistance was linked to an acclimation-mediated switch in the repertoire of NAC42-like targets differentially regulated by inoculation. These findings reveal the rewiring of immune gene regulatory networks by acclimation and suggest new strategies to maintain plant immune function in a warming climate. ### Competing Interest Statement The authors have declared no competing interest.

Besides the well-understood qualitative disease resistance, plants possess a more complex quantitative form of resistance: quantitative disease resistance (QDR). QDR is commonly defined as a partial but more durable form of resistance and, therefore, might display a valuable target for resistance breeding. The characterization of QDR phenotypes, especially of wild crop relatives, displays a bottleneck in deciphering QDR’s genomic and regulatory background. Moreover, the relationship between QDR parameters, such as infection frequency, lag-phase duration, and lesion growth rate, remains elusive. High hurdles for applying modern phenotyping technology, such as the low availability of phenotyping facilities or complex data analysis, further dampen progress in understanding QDR. Here, we applied a low-cost (<1.000 €) phenotyping system to measure lesion growth dynamics of wild tomato species (e.g., Solanum pennellii or Solanum pimpinellifolium). We provide insight into QDR diversity of wild populations and derive specific QDR mechanisms and their cross-talk. We show how temporally continuous observations are required to dissect end-point severity into functional resistance mechanisms. The results of our study show how QDR can be maintained by facilitating different defense mechanisms during host–parasite interaction and that the capacity of the QDR toolbox highly depends on the host’s genetic context. We anticipate that the present findings display a valuable resource for more targeted functional characterization of the processes involved in QDR. Moreover, we show how modest phenotyping technology can be leveraged to help answer highly relevant biological questions.

Additional file 5: Table S1. Parameters values used to model the effect of fungal-derived hydrolysis heterogeneities on the principal strain patterning and the dependency of the overstretched length on the lesion radius.

Additional file 14: File S5. Pictures used in this work (raw and analyzed).

BACKGROUND:The ongoing adaptation of plants to their environment is the basis for their survival. In this adaptation, mechanoperception of gravity and local curvature plays a role of prime importance in finely regulating growth and ensuring a dynamic balance preventing buckling. However, the abiotic environment is not the exclusive cause of mechanical stimuli. Biotic interactions between plants and microorganisms also involve physical forces and potentially mechanoperception. Whether pathogens trigger mechanoperception in plants and the impact of mechanotransduction on the regulation of plant defense remains however elusive.RESULTS:Here, we found that the perception of pathogen-derived mechanical cues by microtubules potentiates the spatio-temporal implementation of plant immunity to fungus. By combining biomechanics modeling and image analysis of the post-invasion stage, we reveal that fungal colonization releases plant cell wall-born tension locally, causing fluctuations of tensile stress in walls of healthy cells distant from the infection site. In healthy cells, the pathogen-derived mechanical cues guide the reorganization of mechanosensing cortical microtubules (CMT). The anisotropic patterning of CMTs is required for the regulation of immunity-related genes in distal cells. The CMT-mediated mechanotransduction of pathogen-derived cues increases Arabidopsis disease resistance by 40% when challenged with the fungus Sclerotinia sclerotiorum.CONCLUSIONS:CMT anisotropic patterning triggered by pathogen-derived mechanical cues activates the implementation of early plant defense in cells distant from the infection site. We propose that the mechano-signaling triggered immunity (MTI) complements the molecular signals involved in pattern and effector-triggered immunity.

Plants memorize events associated with environmental fluctuations. The integration of environmental signals into molecular memory allows plants to cope with future stressors more efficiently—a phenomenon that is known as ‘priming’. Primed plants are more resilient to environmental stresses than non-primed plants, as they are capable of triggering more robust and faster defence responses. Interestingly, exposure to various forms of mechanical stimuli (e.g. touch, wind, or sound vibration) enhances plants’ basal defence responses and stress tolerance. Thus, mechanostimulation appears to be a potential priming method and a promising alternative to chemical-based priming for sustainable agriculture. According to the currently available method, mechanical treatment needs to be repeated over a month to alter plant growth and defence responses. Such a long treatment protocol restricts its applicability to fast-growing crops. To optimize the protocol for a broad range of crops, we need to understand the molecular mechanisms behind plant mechanoresponses, which are complex and depend on the frequency, intervals, and duration of the mechanical treatment. In this review, we synthesize the molecular underpinnings of plant mechanoperception and signal transduction to gain a mechanistic understanding of the process of mechanostimulated priming.

Comparative transcriptome analyses reveal a major contribution of regulatory divergence in conserved genes during the response of Pentapetalae plants to the fungal pathogen Sclerotinia sclerotiorum. Quantitative disease resistance (QDR) is a conserved form of plant immunity that limits infections caused by a broad range of pathogens. QDR has a complex genetic determinism. The extent to which molecular components of the QDR response vary across plant species remains elusive. The fungal pathogen Sclerotinia sclerotiorum, causal agent of white mold diseases on hundreds of plant species, triggers QDR in host populations. To document the diversity of local responses to S. sclerotiorum at the molecular level, we analyzed the complete transcriptomes of six species spanning the Pentapetalae (Phaseolus vulgaris, Ricinus communis, Arabidopsis [Arabidopsis thaliana], Helianthus annuus, Solanum lycopersicum, and Beta vulgaris) inoculated with the same strain of S. sclerotiorum. About one-third of plant transcriptomes responded locally to S. sclerotiorum, including a high proportion of broadly conserved genes showing frequent regulatory divergence at the interspecific level. Evolutionary inferences suggested a trend toward the acquisition of gene induction relatively recently in several lineages. Focusing on a group of ABCG transporters, we propose that exaptation by regulatory divergence contributed to the evolution of QDR. This evolutionary scenario has implications for understanding the QDR spectrum and durability. Our work provides resources for functional studies of gene regulation and QDR molecular mechanisms across the Pentapetalae.

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.

Pathogen infection triggers extensive reprogramming of the plant transcriptome, including numerous genes the function of which is unknown. Due to their wide taxonomic distribution, genes encoding proteins with Domains of Unknown Function (DUFs) activated upon pathogen challenge likely play important roles in disease. In Arabidopsis thaliana, we identified thirteen genes harboring a DUF4228 domain in the top 10% most induced genes after infection by the fungal pathogen Sclerotinia sclerotiorum. Based on functional information collected through homology and contextual searches, we propose to refer to this domain as the pathogen and abiotic stress response, cadmium tolerance, disordered region-containing (PADRE) domain. Genome-wide and phylogenetic analyses indicated that PADRE is specific to plants and diversified into 10 subfamilies early in the evolution of Angiosperms. PADRE typically occurs in small single-domain proteins with a bipartite architecture. PADRE N-terminus harbors conserved sequence motifs, while its C-terminus includes an intrinsically disordered region with multiple phosphorylation sites. A pangenomic survey of PADRE genes expression upon S. sclerotiorum inoculation in Arabidopsis, castor bean, and tomato indicated consistent expression across species within phylogenetic groups. Multi-stress expression profiling and co-expression network analyses associated AtPADRE genes with the induction of anthocyanin biosynthesis and responses to chitin and to hypoxia. Our analyses reveal patterns of sequence and expression diversification consistent with the evolution of a role in disease resistance for an uncharacterized family of plant genes. These findings highlight PADRE genes as prime candidates for the functional dissection of mechanisms underlying plant disease resistance to fungi.

Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta. Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.

Relations between the apple cortex viscoelastic properties, water dynamics, histological, and chemical characteristics were investigated. Water mobility in four apple genotypes was studied by low-field NMR relaxometry prior and after plasmolysis of the cortex tissue. A discrete and a continuous method for decomposing the multi-exponential T2 curves were implemented and compared. The results show that both methods of relaxation curve decomposition had close ability to discriminate genotypes before and after plasmolysis. Although the sensitivity of T2 relaxometry allowed distinguishing microstructures among genotypes even after cellular fluids were mixed and diffused in plasmolyzed tissues, no relaxation component correlated with apple viscoelasticiy. Galactose and arabinose cell wall content were correlated with the storage modulus (E') prior and after plasmolysis though the correlation signs were opposite and pointed to a potential key role of pectin RGI side chains in regulating apple texture in turgid tissue.

The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Consistent with previous reports on oomycete parasites, our findings suggest that host jump and radiation, possibly combined with low speciation rates, could associate with the emergence of generalist pathogens. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.

The viscoelastic mechanical properties of water-rich plant tissues are fundamental for many aspects of organ physiology and plant functioning. These properties are determined partly by the water in cellular vacuole and partly by the mechanical properties of the cell wall, the latter varying according to the composition and organization of its polysaccharides. In this study, relationships between the viscoelastic properties of apple cortex parenchyma tissue and cell wall pectin, hemicelluloses, and cellulose structures were studied by infusing the tissue with selected sets of purified enzymes in a controlled osmoticum. The results showed that tissue elasticity and viscosity were related, and controlled to variable extents by all the targeted polysaccharides. Among them, pectic homogalacturonan domains, crystalline cellulose, and fucosylated xyloglucan were revealed as being of prime importance in determining the viscoelastic mechanical properties of apple cortex tissue.