Biology subjects

Paineau, M.

Publications and source records attributed to Paineau, M..

5 recordsLinked to original sources

bioRxiv2026

TPS Expression, Not Copy Number, Explains Aroma Diversity among Grapevine (Vitis vinifera L.) Cultivars

Terpenoids are major contributors to grapevine berry and wine aroma, with mono- and sesquiterpenoids exhibiting substantial variation among cultivars. However, the genetic basis of cultivar-specific terpenoid profiles remains only partially understood due to gene duplications that expanded the terpenoid synthase (TPS) gene family across different cultivars. Here, we compared haplotype-resolved genome assemblies for seven cultivars to analyze copy number variation and expression profiles of terpenoid biosynthesis genes and terpenoid accumulation throughout flower and berry development. These assemblies resolved duplicated TPS loci at the haplotype level, revealing extensive copy number variation across cultivars and between haplotypes within a cultivar, with up to 44 mono-TPS genes on a single haplotype. We identified eight specific monoterpenoids as key drivers of cultivar-specific profiles in ripe berries. Total TPS transcript abundance correlated strongly with total terpenoid accumulation over time. In contrast, TPS copy number was largely decoupled from both expression and terpenoid accumulation, indicating that expression regulation, rather than gene dosage, underlies aroma differences among cultivars. Transcript-metabolite network analysis revealed both expected correlations between specific TPS genes and putative products as well as novel associations. We functionally validated selected candidate TPS in Nicotiana benthamiana, characterizing -farnesene, {beta}-ocimene, and multi-product -terpineol synthases. The in vivo characterization demonstrated that minor sequence variations can alter catalytic activity and product profile. Together, these findings show that the extensive duplication of TPS genes in grapevine does not itself determine terpenoid output; instead, cultivar-specific aroma arises from how these genes are expressed and from sequence differences that shape enzyme activity.

plant biology↗

bioRxiv2025

Parallel adaptation and admixture drive the evolution of virulence in the grapevine downy mildew pathogen

O_LIPlasmopara viticola is a biotrophic oomycete responsible for grapevine downy mildew, one of the most destructive diseases in viticulture. Breeding for resistant varieties relies on the introgression of partial resistance factors from wild grapes, but virulent strains are rapidly emerging. C_LIO_LITo decipher the genetic bases of the adaptation to plant resistance in P. viticola, we carried out a QTL mapping study using two F1 populations segregating for the ability to overcome Rpv3.1, Rpv10 and Rpv12. Trajectories of virulence emergence were also compared by conducting a population structure analysis on a panel of diversity. C_LIO_LIWe confirmed the position of AvrRpv3.1 and identified the AvrRpv12 locus, in which strains overcoming Rpv12 presented large deletions encompassing several RXLR genes. Distinct virulent alleles were selected independently in different winegrowing regions. Unlike this standard case of recessive virulence, partial breakdown of Rpv10 was determined by a dominant locus, suggesting a suppressor activity. The virulent haplotype exhibits structural rearrangements and an extended effector repertoire. It corresponds to an admixed genomic segment likely originating from a secondary introduction of P. viticola into Europe. C_LIO_LIOn top of the identification of candidate effectors, these results illustrate the range of evolutionary pathways through which plant pathogen populations can adapt to plant resistances. C_LI

plant biology↗

bioRxiv2025

Smoke exposure triggers rapid transcriptional changes and reveals glycosyltransferases linked to smoke taint in ripening grape berries

With the increasing frequency of wildfires, vineyards are more often exposed to smoke, resulting in a higher risk of smoke taint in wine. This taint imparts undesirable "smoky" and "ashy" aromas and causes significant economic losses. Smoke-derived volatile phenols (VPs) in grape berries, metabolized into stable, non-volatile glycoconjugates via glycosyltransferases (GTs), underlie smoke taint formation. Here, we present the dwarf grapevine cultivar Pixie as a model system for smoke taint research. We generated a phased, telomere-to-telomere diploid genome using HiFi long-read sequencing, along with an expression atlas spanning 30 replicated samples across various tissues and developmental stages. We also constructed a second telomere-to-telomere assembly for Pinot Noir to assess GT expression during berry ripening in the field. Controlled smoke-exposure experiments profiled GT expression and enabled transcriptome-wide analyses at multiple time points. We measured VPs in both smoke-exposed and control samples, revealing 12 GT1 genes significantly upregulated by smoke, named Vitis vinifera smoke-inducible UGTs (VviSIUGTs). Their expression peaked one day post-exposure and declined by day three, mirroring glycoside accumulation dynamics. Gene co-expression network analyses highlighted stress-responsive modules enriched in these VviSIUGTs, while transcription factor binding site analyses pinpointed stress-related regulatory elements in their promoters. These findings provide new insights into the molecular basis of smoke taint and identify potential targets for breeding and biotechnological interventions aimed at developing grapevine cultivars with reduced susceptibility to smoke damage.

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↗

bioRxiv2021

The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions

AO_SCPLOWBSTRACTC_SCPLOWUnderstanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no or minor parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.

pathology↗