Biology subjects

Vailleau, F.

Publications and source records attributed to Vailleau, F..

5 recordsLinked to original sources

bioRxiv2026

Natural habitats are reservoirs of Fusarium lineages highly pathogenic on Triticum aestivum

Fungal plant diseases are a major cause of crop loss worldwide. Understanding the processes driving these diseases is therefore crucial to anticipate and control epidemics while improving crop yield production. Moreover, the new European Green Deal aims to reduce the use of pesticides, while, few alternatives are currently available on the market. There is therefore an urgent need to better track and anticipate fungal crop epidemics in the current context of fungicide reduction. In light of this, our study aims to understand Fusarium spill overs from non-agricultural habitats in order to better characterise potential non-host Fusarium reservoirs that may be implicated in the emergence of Fusarium diseases. To address this question, we isolated Fusarium lineages from natural populations of Brassica rapa. We characterised their phylogenomic affiliation and found that they display high diversity, with a population structure related to the locality of isolation. By inoculation assays, we identified Fusarium strains from non-agricultural habitats that were highly aggressive on wheat. In addition, we observed a strong effect of wheat variety on disease development. We monitored the Fusarium colonisation through a microscopy approach in both wheat and Brassica plants. We observed that while the fungus is mostly on root surface in Brassica plants, it spreads inter-cellularly in wheat roots with vascular colonisation in the wheat shoots. Finally, we showed that most aggressive Fusarium strains were isolated from Brittany, a French region where wheat is vastly cultivated.

ecology↗

bioRxiv2026

Natural selection acting on the genetics of host response to commensal bacteria

BackgroundMicrobiota members collectively contribute to individual performance in humans, animals, and plants. This led to the quest for probiotics to improve host health and reproductive performance. Although the efficacy of probiotics is known to be strongly affected by environmental factors, microbe-microbe interactions, and microbial strain identity, the effects of host genotype and the underlying genetic architecture have been overlooked. In addition, the evolutionary causes of such genetic variation are typically not addressed. In this study, we aimed to describe the genetic architecture of the adaptation of the host plant Arabidopsis thaliana to commensal bacterial members of its native microbiota by identifying candidate genes associated with fitness proxies and presenting signatures of natural selection. ResultsA Genome-Wide Association study conducted under field conditions revealed extensive variation within a new mapping population of 162 genotypes of A. thaliana scored for total seed production and its two underlying components, namely fruit number and mean seed number per fruit, in response to 13 commensal strains. In agreement with the strong host genotype x commensal strain identity interactions observed for each reproductive trait, the polygenic genetic architecture was highly flexible among the 13 commensal strains. Candidate genes exhibited a significant enrichment in signatures of both local adaptation and balancing selection. In line with the phenotyped reproductive traits, we identified seven candidate genes with functions specifically and strongly linked to seed germination and fertility. ConclusionsOur findings reveal the importance of genotype-by-genotype interactions when measuring fitness proxies on a wild plant species inoculated with key members of its native microbiota. In addition, this study improves our understanding of the genetic signatures of natural selection acting on native host-microbiota adaptive interactions.

evolutionary biology↗

bioRxiv2025

New resistance to bacterial wilt in heat-stressed tomato is revealed by two-reference Genome Wide Association

Bacterial wilt, caused by bacterial strains of the Ralstonia solanacearum species complex, is one of the most harmful diseases striking many crops including tomato. Its spread is dependent upon temperature and humidity, which are expected to fluctuate strongly due to climate change. Previous results have highlighted that temperature elevation led to an increase in disease severity in commercial cultivars, whose resistance is quantitative and mostly relies on the Quantitative Trait Loci (QTL) bwr-6 and bwr-12. In this study, we focused on temperature-dependent quantitative disease resistance (QDR) to bacterial wilt with the aim to unravel new resistance mechanisms that remain efficient at higher temperatures. For this purpose, a new panel of 189 accessions composed of tomato wild relatives, was assembled and sequenced thus creating a unique genomic resource. Its response to the Ralstonia pseudosolanacearum strain GMI1000 from three- to ten-days post-inoculation at 28{degrees}C and 32{degrees}C was explored. To discover the genetic basis underlying the responses of the panel, Genome-Wide Association (GWA) studies were conducted using the disease symptom scores recorded daily and monitored throughout the kinetics of the infection. To improve QTL detection, we have proposed a new approach using two reference genomes from within the panel. By correcting part of a single reference genome, especially when the only reference genome is a cultivar, this approach may be considered an alternative to pangenomic studies. As panel sequencing was highly resolutive, QTL positions allowed the identification of 44 candidate genes, which seemed to follow a temporal dynamic of activation after pathogen inoculation. Interestingly, no candidate genes were found to be common between the two phenotyping temperatures, highlighting the importance of the experimental design in addressing this type of question. Most of our quantitative disease resistance candidate genes belong to gene families described as being involved in immunity. Moreover, a significant proportion appears to be expressed in roots where bacterial infection occurs. Among them, two candidates are closely linked to the genomic positions of the bwr-6 and bwr-12 QTLs, the main QTLs of bacterial wilt Quantitative Disease Resistance (QDR) studied whose mechanisms of action are still unknown. Author summaryBacterial wilt is a plant disease that affects more than 200 crop species (including tomato, potato and banana) leading to high yield losses. The most efficient way to deal with this disease is still the use of genetic resistance. However, previous studies have shown that numerous sources of resistance are negatively affected when plants face heat stress, which is alarming in a context of global warming. In this study, we have developed a new approach for discovering candidate genes in tomato capable of conferring thermostable resistance to bacterial wilt. Forty-four genes were sequentially detected over time, reflecting different temporal dynamics of induction after inoculation. Even if none were found to be common between the two temperatures, available information on their transcriptional regulation in roots and their involvement in immune processes confirms their relevance. Finally, we provide a short list of the candidate genes identified, some of which are currently undergoing functional validation and will be used in breeding programs to help overcome epidemics in future years.

genetics↗

bioRxiv2022

The genetic architecture of Arabidopsis thaliana in response to native non-pathogenic leaf bacterial species revealed by GWA mapping in field conditions

Non-pathogenic bacteria can largely contribute to plant health by mobilizing and supplying nutrients and by providing protection against pathogens and resistance to abiotic stresses. Yet, the number of GWAS reporting the genetic architecture of the response to individual members of the beneficial microbiota remains limited. In this study, we established a GWAS under field conditions to estimate the level of genetic variation and the underlying genetic architecture, among 162 accessions of Arabidopsis thaliana originating from 54 natural populations located south-west of France, in response to 13 strains of seven of the most abundant and prevalent non-pathogenic bacterial species isolated from the leaf compartment of A. thaliana in the same geographical region. Using a high-throughput phenotyping methodology to score vegetative growth-related traits, extensive genetic variation was detected within our local set of A. thaliana accessions in response to these leaf bacteria, both at the species and strain levels. The presence of crossing reaction norms among strains indicates that declaring a strain as a plant-growth promoting bacterium is highly dependent on the host genotype tested. In line with the strong genotype-by-genotype interactions, we detected a complex and highly flexible genetic architecture between the 13 strains. Finally, the candidate genes underlying the QTLs revealed a significant enrichment in several biological pathways, including cell, secondary metabolism, signalling and transport. Altogether, plant innate immunity appears as a significant source of natural genetic variation in plant-microbiota interactions and opens new avenues for better understanding the ecologically relevant molecular dialog during plant-microbiota interactions.

genetics↗

bioRxiv2022

Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats

Plants interact simultaneously with highly diversified microbes defined as the plant microbiota. Microbiota modulates plant health and appears as a promising lever to develop innovative, sustainable and eco-friendly agro-ecosystems. Key patterns of microbiota assemblages in plants have been revealed by an extensive number of studies based on taxonomic profiling by metabarcoding. However, understanding the functionality of microbiota and identifying the genetic and molecular mechanisms underlying the interplay between plants and their microbiota are still in its infancy and relies on reductionist approaches primarily based on the establishment of representative microbial collections. In Arabidopsis thaliana, most of these microbial collections include one strain per OTU isolated from a limited number of habitats, thereby neglecting the ecological potential of genetic diversity within microbial species to affect the plant-microbiota molecular dialog. With this study, we aimed at estimating the extent of genetic variation between strains within the most abundant and prevalent leaf-associated non-pathogenic bacterial species in 163 natural populations of A. thaliana located south-west of France. By combining a culture-based collection approach consisting of the isolation of more than 7,000 bacterial colonies with an informative-driven approach, we isolated 35 pure strains from eight non-pathogenic bacterial species. We detected significant intra-specific genetic variation at the genomic level and for growth rate in synthetic media. In addition, significant host genetic variation was detected in response to most bacterial strains in in vitro conditions, with the presence of both negative and positive responses on plant growth. Our study provides new genetic and genomic resources for a better understanding of the plant-microbe ecological interactions at the microbiota level. We also highlight the need of considering genetic variation in both non-pathogenic bacterial species and A. thaliana to decipher the genetic and molecular mechanisms involved in the ecologically relevant dialog between hosts and leaf microbiota.

microbiology↗