Biology subjects

Saintenac, C.

Publications and source records attributed to Saintenac, C..

6 recordsLinked to original sources

bioRxiv2026

Interaction-specific early wheat responses to Zymoseptoria tritici share enhanced defense-related transcription during incompatibility

Despite the recent cloning of RLK-encoding resistance genes and the identification of a common point of hyphal arrest at the stomatal level in incompatible interactions, the molecular mechanisms leading to the establishment of wheat resistance against Septoria tritici blotch (STB) remain poorly characterized. Here, we use long-read RNA-sequencing data to compare the early transcriptomic responses of two wheat cultivars carrying major, isolate-specific resistances to Zymoseptoria tritici via differential expression, differential transcript usage (DTU), functional- and pathway enrichment analyses. We show that both magnitude and composition of the responses depend strongly on the combination of host cultivar and pathogen isolate and that DTU appears to be uncommon at this infection stage. We do not detect a set of genes exclusively differentially expressed across incompatible interactions, but genes coding for proteins involved in several defense-related processes consistently show higher expression levels in incompatible than compatible interactions, including receptors and ROS homeostatic, antifungal hydrolytic, phenylpropanoid and diterpenoid biosynthetic enzymes. Our results suggest that whilst interaction-specific differences in magnitude and composition may also shape resistance, different major STB resistances may quantitatively enhance overlapping defense machinery, providing a basis for its functional investigation.

plant biology↗

bioRxiv2025

From Canopy Images to Organ-Level Disease Assessments: A Scalable Approach to Measure Quantitative Resistance in the Field

Breeding for quantitative, polygenic resistance is widely considered the most durable, cost-effective, and environmentally safe approach to crop disease control. However, progress in resistance breeding is hindered by the limited capability of current approaches to measure highly quantitative disease phenotypes under field conditions with high precision and sufficient throughput. Here, we present an imaging protocol and a modular image processing pipeline that enables wheat disease detection and severity estimation directly from very-high-resolution canopy imagery, eliminating the need for physical interaction with the monitored plants as required in previously proposed sensor-based methods capable of symptom-level diagnosis. The pipeline combines deep-learning-based semantic segmentation, keypoint detection, and depth estimation to diagnose and quantify disease symptoms and extract the analyzable reference plant surfaces for severity estimation. By leveraging estimated relative depth and analyzing image texture, well-focused areas with sufficient quality were accurately segmented. Despite the challenging nature of canopy images and frequent symptom ambiguity, symptom detection and segmentation models trained on a new dataset reached a similar performance as already described in more simplified scenarios where detached, flattened leaves were analyzed. Plot-level severity estimates of Septoria Tritici Blotch, a major wheat disease, obtained using the new method and a precise but more laborious reference method were highly correlated (Pearson R = 0.83) across a range of morphologically contrasting cultivars. Validation of the new method on data collected by different operators at different sites demonstrated the robustness of the approach. The ability of the method to process imagery acquired in a contact-free manner can enable deployment on autonomous ground vehicles, paving the way for automated, scalable phenotype acquisition.

biochemistry↗

bioRxiv2024

Diversification, loss, and virulence gains of the major effector AvrStb6 during continental spread of the wheat pathogen Zymoseptoria tritici

Interactions between plant pathogens and their hosts are highly dynamic and mainly driven by pathogen effectors and plant receptors. Host-pathogen co-evolution can cause rapid diversification or loss of pathogen genes encoding host-exposed proteins. The molecular mechanisms that underpin such sequence dynamics remains poorly investigated at the scale of entire pathogen species. Here, we focus on AvrStb6, a major effector of the global wheat pathogen Zymoseptoria tritici, evolving in response to the cognate receptor Stb6, a resistance widely deployed in wheat. We comprehensively captured effector gene evolution by analyzing a global thousand-genome panel using reference-free sequence analyses. We found that AvrStb6 has diversified into 59 protein isoforms with a strong association to the pathogen spreading to new continents. Across Europe, we found the strongest differentiation of the effector consistent with high rates of Stb6 deployment. The AvrStb6 locus showed also a remarkable diversification in transposable element content with specific expansion patterns across the globe. We detected the AvrStb6 gene losses and evidence for transposable element-mediated disruptions. We used genome-wide association mapping data to predict virulence emergence and found marked increases in Europe, followed by spread to subsequently colonized continents. Finally, we genotyped French bread wheat cultivars for Stb6 and monitored resistant cultivar deployment concomitant with AvrStb6 evolution. Taken together, our data provides a comprehensive view of how a rapidly diversifying effector locus can undergo large-scale sequence changes concomitant with gains in virulence on resistant cultivars. The analyses highlight also the need for large-scale pathogen sequencing panels to assess the durability of resistance genes and improve the sustainability of deployment strategies. Author summaryInteractions between plants and their specialized pathogens are often mediated by a sophisticated molecular dialogue. Effectors produced by pathogens serve to manipulate the host but may also be used by the host to trigger defence mechanisms upon recognition. Deploying plants carrying a resistance gene against a specific effector could lead to rapid adaptation in the pathogen. Here, we unraveled such dynamics at the scale of the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. The effector is encoded by the gene AvrStb6 located in a polymorphic region of a chromosome near the telomere. We find selfish elements (i.e. transposable elements) repeatedly inserted nearby the gene, which has likely facilitated the rapid sequence evolution. The effector diversified among continents, and we could predict that the sequence changes likely helped escape recognition by the host receptor. Our study provides one of the most comprehensive views how a crop pathogen diversified a major effector in response to host resistance factors. Such studies facilitate devising more durable deployment strategies of host resistance in order to maintain crop yield.

genomics↗

bioRxiv2023

Estimating the frequency of virulence against an Stb gene in Zymoseptoria tritici populations by bulk phenotyping on checkerboard microcanopies of wheat NILs

Monitoring virulent strains within fungal pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in genomes based on high-throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms and in planta phenotyping remains necessary. We developed a method for bulk phenotyping on checkerboard microcanopies of wheat near-isogenic lines (BPC) for estimating the frequency of virulence against an Stb gene in populations of Zymoseptoria tritici, the causal agent of Septoria tritici blotch in wheat, without the need for strain-by-strain phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines - one with the resistance gene and the other without it - with a multi-strain cocktail representative of the population to be characterized, followed by the differential quantification of infection points (lesions). Using Stb16q, a resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, and synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with recently developed molecular methods.

microbiology↗

bioRxiv2023

Septoria tritici blotch resistance gene Stb15 encodes a lectin receptor-like kinase

Septoria tritici blotch (STB), caused by the Dothideomycete fungus Zymoseptoria tritici, is of one of the most damaging diseases of bread wheat (Triticum aestivum)1 and the target of costly fungicide applications2. In line with the fungus apoplastic lifestyle, STB resistance genes isolated to date encode receptor-like kinases (RLKs) including a wall-associated kinase (Stb6) and a cysteine-rich kinase (Stb16q)3,4. Here, we used genome-wide association studies (GWAS) on a panel of 300 whole-genome shotgun-sequenced diverse wheat landraces (WatSeq consortium) to identify a 99 kb region containing six candidates for the Stb15 resistance gene. Mutagenesis and transgenesis confirmed a gene encoding an intronless G-type lectin RLK (LecRK) as Stb15. The characterisation of Stb15 exemplifies the unexpected diversity of RLKs conferring Z. tritici resistance in wheat.

genetics↗

bioRxiv2020

Remarkable recent changes in genetic diversity of the avirulence gene AvrStb6 in global populations of the wheat pathogen Zymoseptoria tritici

Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is one of the most economically important diseases of wheat. Recently, both factors of a gene-for-gene interaction between Z. tritici and wheat, the wheat receptor-like kinase Stb6 and the Z. tritici secreted effector protein AvrStb6, have been identified. Previous analyses revealed a high diversity of AvrStb6 alleles present in historic Z. tritici isolate collections, with up to ~ 18% of analysed isolates possessing the avirulence isoform of AvrStb6 identical to that originally identified in the reference isolate IPO323. With Stb6 present in many commercial wheat cultivars globally, we aimed to assess potential changes in AvrStb6 genetic diversity and the incidence of alleles allowing evasion of Stb6-mediated resistance in more recent Z. tritici populations. Here we show, using targeted re-sequencing of AvrStb6, that this gene is universally present in field isolates sampled from major wheat-growing regions of the world between 2013-2017. However, in contrast to the data from studies of historic isolates, our study revealed a complete absence of the originally described avirulence isoform of AvrStb6 amongst modern Z. tritici isolates. Moreover, a remarkably small number of alleles, each encoding AvrStb6 protein isoforms conditioning virulence on Stb6-containing wheat, were found to predominate among modern Z. tritici isolates. A single virulence isoform of AvrStb6 was found to be particularly abundant throughout the global population. These findings indicate that, despite the ability of Z. tritici to sexually reproduce on resistant hosts, AvrStb6 avirulence alleles tend to be eliminated in subsequent populations.

microbiology↗