Biology subjects

Mestre, P.

Publications and source records attributed to Mestre, P..

5 recordsLinked to original sources

bioRxiv2025

Metabolic biomarker-based phenotyping unveils quantitative effects of plant resistance and pathogen aggressiveness in the grapevine (Vitis spp.) - downy mildew (Plasmopara viticola) pathosystem.

Grapevine resistance to downy mildew has been primarily associated with major "Resistance to Plasmopara viticola" (Rpv) loci, which are extensively used in breeding programs. Resistant varieties represent an effective solution to mitigate the environmental impact of fungicide application in viticulture, but P. viticola strains able to overcome major Rpv have become a main threat to their cultivation. Pyramiding resistance loci in the same variety enhances plant resistance, but interactions involving stacked and defeated Rpv and different P. viticola strains are poorly documented. Investigation of these interactions may uncover new information for the development of efficient breeding strategies, the optimal exploitation of Rpv, and the building of durable resistance. In the present study, a grapevine offspring carrying single and pyramided Rpv1, Rpv3.1 and Rpv10 was phenotyped in laboratory conditions for the resistance to P. viticola using a naive strain and a strain virulent towards Rpv10. By using a high-resolution phenotyping strategy based on P. viticola metabolic biomarkers, we demonstrated that the efficacy of Rpv combinations and aggressiveness of P. viticola strains can be quantified in the early phase of infection and were often related to sporulation outcome. Furthermore, we described how a limited residual effect of a defeated Rpv may become significant in pyramiding. In conclusion, in addition to providing the keys to streamlining resistance utilization in grapevine, our research presents a distinctive case study that provides valuables information for breeding new resistant varieties, thanks to an innovative "omic"-based phenotyping approach, which may be adapted to other plant pathosystems.

plant biology↗

bioRxiv2025

Rpv2 is part of a cluster of NLRs specific to Vitis rotundifolia and confers extreme resistance to grapevine downy mildew.

Downy mildew caused by the oomycete Plasmopara viticola is one of the most important diseases affecting grapevine. Resistant varieties are an environmentally-friendly tool to control grapevine downy mildew. Efficient breeding for durable resistance requires knowledge of the underlying mechanisms. Here we aimed at identifying the molecular basis of Rpv2, a gene for extreme resistance to downy mildew derived from Vitis rotundifolia, and at characterizing its effect on pathogen development. Individuals from two populations segregating for Rpv2 were evaluated for resistance to downy mildew and genotyped. Following genetic mapping, markers flanking Rpv2 were used to screen new populations and identify recombinant individuals. Sequencing of recombinants and in silico chromosome painting was used to reduce the interval containing Rpv2. Comparative genomics inside the Vitaceae, involving de novo assembly of the V. rotundifolia Regale genome, allowed narrowing-down the list of candidate genes. We restrict Rpv2 to a 250 kb genomic region that contains two resistance genes of the NLR type. Comparative genomics analyses could not find orthologs of both NLRs in the other Vitis species studied. We also show that Rpv2-mediated resistance leads to pathogen arrest early in the infection cycle. Our results show that Rpv2 belongs to the NLR family of resistance genes, contributing thus to understand the potential and risks of its use in breeding programs and suggesting that combining NLR-type genes may lead to durable resistance KEY MESSAGEThe Rpv2 locus for extreme resistance to grapevine downy mildew is mapped to a 250 kb genomic region containing two NLR-type genes specific to V. rotundifolia.

plant biology↗

bioRxiv2023

An effector deletion leads to the breakdown of partial grapevine resistance to downy mildew

Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is a globally destructive disease that particularly affect the Eurasian wine grape V. vinifera. While genetically resistant varieties are becoming more accessible, populations of P. viticola are demonstrating rapid adaptability, successfully over-coming these resistances. Here we aimed to identify the avirulence genes involved in the interaction with the Rpv3.1-mediated resistance in grapevine. We sequenced the full genome of 136 P. viticola strains sampled in a natural population of Bordeaux (France) and characterized their development on both resistant and sensitive cultivars. The genome-wide association study allowed the identification of a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid-aware reassembly of the P. viticola INRA-Pv221 genome allowed to detect structural variations in this locus, including a major 30 Kbp deletion. At the avrRpv3.1 locus, virulent P. viticola strains presented deletion on both haplotypes indicating that avirulence is recessive. The deletion involves two closely-related genes that encode proteins containing 800-900 amino acids with a signal peptide. The structure of the predicted proteins contains repeats of the LWY-fold structural modules, typical of oomycete effectors. Moreover, when these proteins were transiently expressed, they induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature. The first description of candidate effectors of P. viticola involved in the interaction with resistance gene provides valuable insights into the genetic mechanisms that enable P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this damaging crop pathogen.

evolutionary biology↗

bioRxiv2020

Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen, Plasmopara viticola

Mating types are self-incompatibility systems that promote outcrossing in plants, fungi and oomycetes. Mating-type genes have been widely studied in plants and fungi, but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570 kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions.

evolutionary biology↗

bioRxiv2018

A high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes

Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high continuity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Pl. viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.\n\nDATA AVAILABILITYRaw reads and genome assemblies have been deposited in GenBank (BioProjects PRJNA329579 for Pl. viticola and PRJNA448661 for Pl. muralis). Genome assemblies, gene annotations and analysis files (e.g. orthology relationships, full tables for GO enrichment analyses, pairwise dN/dS values and branch-site tests) have been deposited in Dataverse (Pl. viticola assembly and annotation: doi.org/10.15454/4NYHD6, Pl. muralis assembly and annotation: doi.org/10.15454/Q1QJYK, analysis files: doi.org/10.15454/8NZ8X9). Links to the data and information about the grapevine downy mildew genome project can be found at http://grapevine-downy-mildew-genome.com/.

genomics↗