Biology subjects

Foulongne-Oriol, M.

Publications and source records attributed to Foulongne-Oriol, M..

9 recordsLinked to original sources

bioRxiv2026

Additive and epistatic QTL contribute to the adaptation of the fungus Leptosphaeria maculans to Brassica carinata

Leptosphaeria maculans is a plant-pathogenic fungus that infects Brassica species, including Brassica napus (oilseed rape). Breeding oilseed rape varieties with genetic resistance is an efficient way to control the disease; however, L. maculans can adapt and overcome these resistances. Understanding the mechanisms that enable L. maculans to adapt is crucial for managing the emergence of better-adapted isolates. Brassica carinata, the Ethiopian Mustard, although closely related to B. napus, is considered a nonhost species of L. maculans because this fungus cannot infect it. Despite the extreme resistance of B. carinata, one natural L. maculans isolate has been identified as unable to infect B. napus, causing moderate and atypical symptoms on this species. We performed a cross between this isolate and an isolate adapted to B. napus, followed by a QTL analysis, which identified seven QTL, each encompassing candidate genes involved in L. maculans adaptation to B. carinata or B. napus. Additionally, we observed transgression in the progeny, wherein a few strains caused significantly more or less aggressive symptoms on both species of Brassica. We found that epistasis within the L. maculans genome contributes to the observed transgression. These initial findings provide further opportunities to study the adaptive capacities of L. maculans, as well as data to initiate analysis of the extreme resistance of B. carinata to L. maculans. HighlightsO_LISeven pathogenicity QTL identified, carrying several interesting candidate genes C_LIO_LITransgression of some progeny isolates on B. napus and B. carinata was reported C_LIO_LIEpistasis plays a significant role in the adaptation of L. maculans toward host and nonhost Brassica species C_LI

genetics↗

bioRxiv2026

A Bayesian multidimensional approach to decipher the genetic basis of dynamic phenotypes in multiple species

Deciphering the genetic architecture of complex quantitative phenotypes remains challenging in quantitative genetics. These traits not only depend of multiple genetic factors but are also established over time and environments. Although quantitative genetics has investigated the genetic determinism of phenotypic plasticity in contrasted environmental conditions, the time related phenotypic plasticity has received less attention. Here we proposed a multivariate Bayesian framework, the Bayesian Varying Coefficient Model, designed for analysing the genetic architecture of the time related phenotypic plasticity by a multilocus approach. We applied the BVCM to time series phenotypes measured at various time scales (daily, monthly, yearly) across a diverse set of biological species. We included in this study: yeast (Saccharomyces cerevisiae), fungi (Fusarium graminearum), eucalyptus (Eucalyptus urophylla x E. grandis), and sweet cherry tree (Prunus avium). The BVCM results were compared with those obtained with a known genome-wide association method carried out time by time. For all species and traits, the BVCM was able to detect the major QTL identified by marker-trait association methods and revealed additional genetic regions of weak effect. It also increased the phenotypic variance explained for most of the phenotypes considered. It revealed dynamic QTLs with transitory, increasing or decreasing effects over time. By considering both the temporal and genetic multivariate structures in a single statistical model, we increased our understanding of the genetic architecture of complex traits notably by reducing the issue of missing heritability. More broadly, this work raises the foundation for extended applications in functional genomics, evolutionary ecology, and crop breeding programs, in which time-related phenotypic plasticity remains crucial for predicting and selecting key quantitative complex traits. Key messageBy capturing the genetic factors influencing the time related phenotypic plasticity, our approach contributes to a deeper understanding of the dynamic nature of genotype-phenotype relationships.

genetics↗

bioRxiv2025

A multivirulent Plasmopara viticola strain from Cilaos on Reunion Island breaks down Rpv1, Rpv3.1 and Rpv10 mediated resistance of grapevine

AbstractGrapevine downy mildew, caused by Plasmopara viticola, is one of the most destructive diseases in viticulture. Resistance-based management strategies rely on grapevine varieties carrying major resistance loci (Rpv). Although breakdown of several loci has been reported, Rpv1 had remained effective until now. Here, we provide the first evidence of Rpv1 breakdown by P. viticola in Cilaos on Reunion Island (France) and the first case of a strain simultaneously overcoming three resistances of grapevine. We combined pathogenicity assays with whole-genome sequencing to characterize a P. viticola strain collected in Cilaos in 2023, alongside a panel of eight reference strains of known virulence. Hypersensitive response and sporulation were assessed for each strain on Chardonnay (susceptible variety) and four resistant varieties carrying Rpv1, Rpv3.1, Rpv10, or Rpv12. The strain collected in Cilaos was able to overcome not only Rpv1 but also Rpv3.1 and Rpv10. On Rpv1, we observed a complete loss of host recognition with high sporulation. On Rpv3.1, the phenotype was consistent with previous breakdowns, and the strain carried the vir1 allele previously described in France. By contrast, the breakdown of Rpv10 differed from that reported in European populations: whereas European strains displayed only partial breakdown of resistance, the strain of Cilaos showed complete loss of host recognition with high sporulation. Moreover, genomic analyses revealed a novel mutation, a large homozygous deletion in the corresponding avr locus. Our genomic data analyses further suggests that this P. viticola strain shares a genetic background with populations from mainland France, raising serious concerns about the potential emergence and spread of multivirulent lineages in Europe. These findings highlight the need for large-scale virulence monitoring of P. viticola and improved strategies for the sustainable management of grapevine resistance in Europe.

plant biology↗

bioRxiv2025

Stress-dependent responses of grapevine wood and fungal pathogen activity under esca and drought

O_LIBiotic and abiotic stresses alter the physiology of perennial plants, with consequences for fungal endophytes and disease expression. In grapevine, one of the worlds most valuable crops, drought inhibits esca disease expression, but the underlying molecular interactions between plant and fungi are unknown. C_LIO_LIWe combined wood metatranscriptomics, metabolomics, and metabarcoding to investigate these interactions in 30-year-old grapevines and eight wood-pathogenic fungi under conditions of drought or esca leaf symptom expression. C_LIO_LIBoth esca and drought decreased grapevine transpiration, but with different transcriptomic and metabolic signatures. Similar pathways were also activated, including the phenylpropanoid and stilbenoid synthesis pathways. These stress responses could potentially confer cross-tolerance, and elicit different fungal molecular responses. The levels of putative fungal virulence factors increased significantly under both stresses. Under drought, only the relative abundance of Phaeomoniella chlamydospora and gene expression involved in anti-oxidative mechanisms, growth, and reproduction increased. Under esca expression conditions, only the relative abundance of Fomitiporia mediterranea and gene expression involved in wood degradation, competition, detoxification, and growth increased. C_LIO_LIThe grapevine defense mechanisms induced by drought coupled with a low transpiration rate and a low abundance and virulence of F. mediterranea may account for esca leaf symptom inhibition upon water deficit. C_LI

plant biology↗

bioRxiv2025

A population genetic study of Fusarium graminearum, the causal agent of Fusarium Head Blight, provides insights into patterns of inoculum dispersal in wheat fields at a regional scale

Fusarium graminearum is the primary pathogen responsible for Fusarium Head Blight (FHB) in cereals, causing yield losses and mycotoxin contamination. The present study investigated the genetic diversity and population structure of F. graminearum from wheat grains and maize residues, which were the primary inoculum sources of FHB. A total of 588 isolates from four different fields were genotyped using a sequence-based microsatellite genotyping method of 34 SSR markers (SSRseq) and characterized for chemotype distribution. The results revealed high genetic diversity with 453 distinct multilocus genotypes (MLGs) without significant genetic differentiation by geographic location or substrate, suggesting a single metapopulation at the regional scale. This absence of substrate genetic differentiation strongly supports the fact that residue-borne inoculum contributed to FHB infection, although we failed to demonstrate any field-specific dispersal pattern from residues to grains. The findings underscore the importance of maize residues as a critical inoculum source and highlight the need to consider both local and regional sources in FHB management.

genetics↗

bioRxiv2024

Ecophysiological Behaviour Of Major Fusarium Species In Response To Combinations Of Temperature And Water Activity Constraints

Fusarium Head Blight (FHB) is a devastating fungal disease affecting cereals, caused by Fusarium species that can produce harmful mycotoxins. Fusarium species share the same ecological niche, and their population dynamic and associated mycotoxin patterns are driven by the environment. The aim of the present study was to investigate ecophysiological characteristics of the major Fusarium species causing FHB under abiotic factors. Growth and mycotoxin production of different strains of Fusarium avenaceum, Fusarium graminearum, Fusarium langsethiae, Fusarium poae and Fusarium tricinctum were characterized under a combined effect of temperature ({Theta} = 15, 20, 25 and 30{degrees}C) and water activity (aw = 0.99, 0.98, 0.97, 0.96, 0.95 and 0.94). Using innovative statistical analyses, we demonstrated that those Fusarium species greatly differ in their responses to the studied environmental constraints. Our findings indicated that {Theta}, aw, and their interaction were the major factors with a significant impact on the species behaviour. The intraspecific variation was demonstrated as less pronounced than the interspecific one. Understanding the ecophysiological requirements of Fusarium species is crucial in the context of climate change that is predicted to worsen disease outbreaks. Our data constitute a valuable knowledge base for improving the reliability and robustness of FHB prediction models and anticipating the associated mycotoxin risk. IMPORTANCEFusarium species pose a significant threat to major cereal crops, including wheat. These fungi not only reduce yield but also produce mycotoxins harmful to animals and humans. The prevalence of each Fusarium species is influenced by environmental conditions and shifts in pathogen populations, leading to changes in mycotoxin patterns have already been observed in relation to climate changes. This study revealed distinct ecophysiological behaviours, including mycelium growth and mycotoxin production, among the five major Fusarium species when exposed to varying temperature and water activity conditions. Our findings provide a valuable foundation for a more comprehensive understanding of the challenge of mycotoxin contamination and for the development of more effective mitigation strategies in the near future.

microbiology↗

bioRxiv2024

Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola

Plasmopara viticola, the causal agent of grapevine downy mildew, is a biotrophic oomycete engaged in atight coevolutionary relationship with its host. Rapid adaptation of the pathogen is favored by annual sexual reproduction which generates genotypic diversity. With the aim of studying the recombination landscape across the P. viticola genome, we generated two half-siblings F1 progenies (N=189 and 162). Offspring were genotyped by targeted sequencing of a set of 5,000 informative SNPs. This enabled the construction of unprecedented high-density linkage maps for this species. The reference genome could be assembled into 17 pseudo-chromosomes, anchoring 88% of its physical length. We observed a strong collinearity between parental genomes and extensive synteny with the downy mildew Peronospora effusa. In the consensus map, the median recombination rate was 13.8 cM/Mb. The local recombination rate was highly variable along chromosomes and recombination was suppressed in putative centromeric regions. Recombination rate was found negatively correlated with repeats coverage and positively correlated with gene coverage. However, genes encoding secreted proteins and putative effectors were under-represented in highly recombining regions. In both progenies, about 5% of the individuals presented karyotypic anomalies. Aneuploidies and triploidies almost exclusively originated from the male-transmitted chromosomes. Triploids resulted from fertilization by diploid gametes, but also from dispermy. Obligatory sexual reproduction each year may explain the lower level of karyotypic variation in P. viticola compared to other oomycetes. The linkage maps will be useful to guide future de novo chromosome-scale assemblies of P. viticola genomes and to perform forward genetics. SummarySexual reproduction contributes to the rapid adaptation of plant pathogens thanks to the recombination of genetic variants. By crossing strains of grapevine downy mildew, we built a set of linkage maps and describe the recombination landscape along the 17 chromosomes of the genome. The recombination rate varied greatly and was higher in gene-rich regions, but not in effector-rich regions. We observed an abnormal number of chromosomes in 5% of the offspring, which was mostly due to the male parent.

genetics↗

bioRxiv2024

Generation of diversity in the blue cheese mold Penicillium roqueforti and identification of pleiotropic QTL for key cheese-making phenotypes

Elucidating the genomic architecture of quantitative traits is essential for our understanding of adaptation and for breeding in domesticated organisms. Penicillium roqueforti is the mold used worldwide for the blue cheese maturation, contributing to flavors through proteolytic and lipolytic activities. The two domesticated cheese populations display very little genetic diversity, but are differentiated and carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging to cheese and non-cheese populations. Analyses of high-quality genome assemblies of the parental strains revealed five large translocations, two having occurred via a circular intermediate. Offspring genotyping with genotype-by-sequencing (GBS) revealed several genomic regions with segregation distortion, possibly linked to degeneration in cheese lineages. We found transgressions for several traits relevant for cheese making, with offspring having more extreme trait values than parental strains. We identified quantitative trait loci (QTLs) for colony color, lipolysis, proteolysis, extrolite production, including mycotoxins, but not for growth rates. Some genomic regions appeared rich in QTLs for both lipid and protein metabolism, and other regions for the production of multiple extrolites, indicating that QTLs have pleiotropic impacts. Some QTLs corresponded to known biosynthetic gene clusters, e.g., for the production of melanin or extrolites. F1 hybrids constitute valuable strains for cheese producers, with new traits and genetic diversity, and allowed identifying target genomic regions for traits important in cheese making, paving the way for strain improvement. The findings further contribute to our understanding of the genetic mechanisms underlying rapid adaptation, revealing convergent adaptation targeting major regulators.

evolutionary biology↗

bioRxiv2020

QTL mapping for aggressiveness variation in F. graminearum revealed one causal mutation in FgVe1 velvet protein

Fusarium graminearum is one of the most frequent causal agents of the Fusarium Head Blight in the world, a cereal disease spread throughout the world, reducing grain production and quality. F. graminearum isolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population, for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel of in planta and in vitro proxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a mutation was identified and functionally validated in the gene FgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.

microbiology↗