The cistrome comprises genomic loci that regulate gene expression, playing a crucial role in defining cellular identity and function. Analyzing cistrome data reveals key molecular mechanisms underlying grapevine growth, development, and environmental responses. Identifying transcription factors that bind specific DNA sequences allows researchers to dissect the complex regulatory networks controlling gene expression. Moreover, this analysis can help pinpoint targets for crop improvement, as traits like fruit quality, disease resistance, and abiotic stress tolerance are often regulated by transcription factors. DNA affinity purification sequencing (DAP-seq) is a high-throughput, cost-effective method for mapping the cistrome, providing valuable insights into transcriptional regulation. This technique relies on the in vitro affinity purification of genomic DNA-protein complexes, followed by high-throughput sequencing of eluted DNA fragments. Unlike other in vitro DNA-binding assays, such as protein-binding microarrays (PBM) and systematic evolution of ligands by exponential enrichment (SELEX), DAP-seq allows transcription factors to interact directly with plant-derived genomic DNA, capturing all potential binding sites. The resulting data closely resemble those from chromatin immunoprecipitation sequencing (ChIP-seq) but are obtained much faster. Initially developed in Arabidopsis, DAP-seq has since been applied to several crops, including maize, tomato, and grapevine, generating extensive cistrome datasets and deepening our understanding of gene regulatory regions. However, despite its power in elucidating crop biology, DAP-seq faces certain limitations, particularly concerning the size and complexity of plant genomes. This chapter presents detailed protocols for DAP-seq studies aimed at the unbiased identification of transcription factor binding sites in crops. Additionally, we outline a standardized pipeline for DAP-seq data analysis, encompassing raw sequencing data processing (i.e., trimming, filtering, and read alignment), as well as peak calling and motif discovery analysis. This approach enables the efficient and scalable identification of transcription factor binding profiles in diverse crop species.

Molecular genotyping is a key factor for plant breeding programming and plant variety protection (PVP). However, its potential still remains to be elucidated when considering ornamental plants like Petunia × hybrida. In this study, a petunia breeding clone collection, including sister line groups, was genotyped through double digest Restriction-site Associated DNA sequencing (ddRADseq), and its genetic diversity and structure were studied. In addition to estimating the high genetic similarity observed among sister lines, this approach allowed the unique discrimination of each clone too. Molecular results agreed with genealogy data, supporting the assessment of genotyping effectiveness. In addition, the minimal number of variants able to uniquely discriminate and/or correctly cluster the experimental lines was investigated. The loci number could be reduced to eight to achieve line discrimination, and a method to identify the specific variant sets is presented. Conversely, to preserve the original clustering with minor adjustments, one hundred loci were required and were obtained through minor allele frequency (MAF) filtering. Moreover, analysis of the chromosomal distribution of variants revealed a predominant accumulation in distal regions. Genetic analyses were repeated considering only variants located in coding sequences and results were in agreement with what previously observed, disclosing the potential of the expressed regions for genotyping purposes. Eventually, the applied approach enabled the investigation of SNPs within genes putatively involved in traits of interest. Our findings encourage the adoption of high-throughput and cost-effective sequencing techniques for petunia genotyping aimed at achieving PVP, supporting new variety registration, and developing marker-assisted breeding (MAB) and marker-assisted selection (MAS) strategies.

ABSTRACT Chromatin organization regulates genome stability and gene expression by controlling DNA accessibility to transcription factors and regulatory complexes. DNA-protein interactions are commonly investigated using chromatin immunoprecipitation (ChIP), which relies on specific antibodies often involving technically demanding protocols. CRISPR-Cas technologies have enabled sequence-specific targeting of genomic loci using catalytically inactive Cas9 (dCas9), but most CRISPR-based chromatin capture approaches in plants require transient or stable transformation to express the CRISPR machinery, limiting their applicability across species, tissues and physiological contexts. Here, we present GRASP (Genomic Region Affinity Sequestration by CRISPR-Purification), a transformation-independent strategy for sequence-specific chromatin isolation operating directly on purified plant nuclei. In GRASP, dCas9-gRNA ribonucleoprotein complexes are used to capture predefined genomic regions from chromatin under native conditions, bypassing the need for transgene expression. Using grapevine and tomato as model systems, we demonstrate efficient and highly specific enrichment of target loci, including telomeric repeats as well as low-copy and single-copy genomic regions, with qPCR and NGS validation. These results establish GRASP as a robust and broadly applicable platform for locus-specific chromatin isolation in plants. Beyond sequence-specific DNA isolation, GRASP establishes a versatile platform for potential downstream analyses of locus-associated chromatin components, including protein complexes, distal DNA-DNA interactions and chromatin-associated RNAs, providing new opportunities to investigate regulatory architecture in plant genomes. GRAPHICAL ABSTRACT

Professor Philippe Jeandet was one of the world’s leading biologists and plant biochemists, best known for his research on the chemical structure of natural products and their bioactivity, particularly that of stilbenoids. His scientific interests primarily focused on resveratrol (trans-3,5,4'-trihydroxystilbene), a stilbene with a wide range of biological activities. Additionally, his work highlighted the potential of combining pharmacological treatments with the use of natural products of plant origin, which have made significant contributions to the treatment of various diseases. He leaves behind a legacy of groundbreaking research and a lasting influence in the field. He was also involved in research on sugar signaling during plant responses to abiotic and biotic stress factors, as well as the role of signaling molecules in fruit development. His scientific achievements demonstrate that he was, first and foremost, a dedicated scientist – but also a honourable colleague who understood and respected the work of others.

Cytological and molecular investigations in chicory revealed crucial aspects related to female gametophyte development, pollen‒stigma interactions, and self-incompatibility responses. The Asteraceae family, one of the largest of angiosperms, comprises approximately 24,000 species and exhibits considerable variation in reproductive biology. Cichorium intybus (commonly known as chicory) is among the most well-known and widespread species of the family. In addition to its economic and commercial value, chicory is considered one of the most interesting species in its family for the study of sporophytic self-incompatibility (SSI). Information regarding megasporogenesis, megagametogenesis, pollen tube development, and embryogenesis in this species is almost entirely absent in the scientific literature. Using confocal laser scanning microscopy (CLSM), we conducted a detailed investigation of female gametophyte development, providing a comprehensive characterization of the cytological stages involved in megasporogenesis and megagametogenesis. To investigate the dynamics and timing of pollen tube development and pollen rejection, we microscopically examined the interactions between pollen and stigmas in both cross- and self-pollinated plants. The response was similar to those documented in other Asteraceae species with a 'semidry' type of stigma. Integrated RNA-seq analyses further highlighted transcriptional changes during self- and non-self-pollen recognition and led to the identification of potential candidate genes involved in pollen tube development and callose deposition (in the case of self-incompatibility reactions). In parallel, for the first time, we characterized both the embryogenesis process and embryo sac degeneration in a compatible and incompatible crosses, respectively.

Lantana camara L. is sold worldwide for ornamental purposes, although it is also characterized by high invasiveness potential. Genetic and molecular data available for L. camara are still poor, and breeding is performed through conventional methods. This study focused on a molecular genotyping analysis through the ddRADseq method on an experimental collection of lantana clonal lines to evaluate the potential of molecular techniques in performing marker-assisted breeding, in favour of variety registration and in guaranteeing plant variety protection for the species. Although high genetic uniformity was observed in the population, a unique molecular profile was assigned to every line, indicating the effectiveness of the approach used. Interestingly, low degrees of heterozygosity were observed. In addition, the possibility of inferring ploidy levels through SNP profiles was assessed since it would avoid the necessity of previous biological knowledge and the use of fresh materials. Ploidy analysis is of high interest for lantana breeding to obtain less invasive triploids. Flow cytometry and chromosome counting were used for inference assessment. An nQuack framework provided correct results for the majority of the clonal lines, confirming its effectiveness. These findings encourage the adoption of molecular systems to help breed minor species such as L. camara.

Plant male sterility (MS) refers to the failure of the production of functional anthers, viable pollen grains and/or fertile sperm cells. This feature has great potential in horticultural crops for the exploitation of heterosis through the development of F1 hybrid varieties. MS in plants can occur spontaneously or can be induced artificially by exploiting biotechnological tools, such as the editing of genes involved in spore formation or pollen development. The success of such an approach strongly depends both on preliminary knowledge of the involved genes and on effective procedures for in vitro transfection/regeneration of whole plants. Furthermore, according to previous studies based on CRISPR/Cas9 technology, the efficacy of targeting and the resulting mutation profile are critically influenced by intrinsic factors, such as the CRISPR target primary sequence sites and chromatin signatures, which are often associated with varying levels of chromatin accessibility across different genomic regions. This relationship underscores the complexity of CRISPR-based genome editing and highlights the need to identify a precise suitable target. Our paper reports the results obtained for site-specific in vivo mutagenesis via a CRISPR/Cas9-mediated strategy applied to the MYB80 gene, which is a promising target for implementing male sterility in horticultural crops. We highlight the main steps that play a key role in the whole experimental pipeline, which aims at the generation of CRISPR/Cas-edited DNA-free tomato plants. This goal was achieved via protoplast-based technology and by directly delivering a ribonucleoprotein complex consisting of the Cas9 protein and in vitro synthesized single guide RNAs that can target different positions of the gene under investigation. Overall findings and insights are presented and critically discussed.

The genus Cichorium, which comprises economically important crops such as chicory and endive, exhibits significant genetic and phenotypic diversity. This study used genome-scale sequencing based on ddRAD technology to explore the genetic diversity and relationships, and to identify multiple discriminant loci within this genus. Moreover, microscopy analysis was conducted to identify morphological traits, such as pappus structure, to aid species-level identifications. Despite this, the genetic complexity within Cichorium remains challenging to resolve based solely on phenotypic characteristics. Our study confirms the efficacy of ddRADseq in generating high-quality genotyping-by-sequencing data, identifying 1,350 multi-allelic polymorphic loci across 368 genotypes and revealing significant genetic differentiation among species, varieties, and biotypes. Lower observed heterozygosity (Ho) compared to expected heterozygosity (Hs) suggests the presence of fixed genotypes within biotype groups, likely due to selection for specific morphological traits. Genetic distance and clustering analyses proved the distinctiveness of self-incompatible species (C. intybus and C. spinosum) from self-compatible species (C. endivia and C. pumilum). Notably, a strong genetic relationship was observed between C. intybus var. foliosum (Witloof) and var. sativum (Root chicory), supporting the hypothesis of a common ancestry. These findings may help refine the taxonomic classification of Cichorium, offering valuable insights for the conservation of genetic resources and their classification, the precise adoption in breeding decisions and genomic selection of suitable genotypes, as well as the genotypic identity determination of registered cultivars with the protection of breeder's rights.

Genome editing technologies, especially those based on the CRISPR/Cas9 system, have revolutionized crop breeding by enabling precise genetic modifications. Specifically, delivering preassembled ribonucleoprotein (RNP) complexes-consisting of the Cas9 endonuclease coupled to specific single guide RNAs (sgRNAs)-into protoplasts offers an effective DNA-free method that prevents the integration of foreign genetic material. Despite the availability of detailed protocols, establishing a standardized and efficient in vitro regeneration procedure-from protoplast isolation to whole plant regeneration-remains challenging due to significant variability in regeneration efficiency across different varieties and biotypes. Therefore, optimizing each step is essential to maximize the recovery of successful edited plants. In this study, we developed an efficient protocol for regenerating whole plants from protoplasts isolated from 12 representative Italian varieties of chicory and endive. We focused on leaf chicory and endive biotypes with high horticultural value, including Radicchio types, which are important targets for quality improvement. Our optimized platform supports protoplast isolation, PEG-mediated transfection, and plant regeneration, demonstrating promising potential for future genome editing applications. Notably, the high responsiveness of protoplasts to PEG-mediated transfection suggests that coupling this method with our regeneration procedure could facilitate the use of advanced biotechnological strategies. The combination of high transient transformation efficiency, versatile encapsulation techniques, and successful plant regeneration establishes chicory and endive as promising candidates for DNA-free genome editing via protoplasts, providing a technically precise approach with reduced environmental and economic impacts compared to conventional breeding methods.

In the frame of the EU Next Generation Europe program, the Italian Minister of University and Research has approved the IRIS project (Innovative Research Infrastructure for applied Superconductivity). IRIS will be active in six poles. The six poles are spread all over Italy: Milano, hub of the infrastructure; Genova, Frascati, Napoli, Salerno, and Lecce. The scope of IRIS is to provide an infrastructure to accompany the development of applied superconductivity for basic research like accelerators. It also aims at developing societal applications of superconductivity, especially in the fields of sustainability and medicine. The new facility will support basic research on magnetism and superconducting materials, wires, tapes and large current cable tests; superconducting magnet construction with advanced instrumentation, superconducting magnet, and power transmission line tests. The program, which represents an investment of about €60 million, has passed halfway of its three-year life; once finished will be followed by at least 10 years of infrastructure exploitation. The IRIS construction program also includes two demonstrators: a 10 T dipole HTS magnet to be operated at 10-20K and an electric superconducting transmission line capable of 1 GW (40kA-25 kV) of about 130 m long.

Botrytis cinerea (Bc) is a major pathogen of cultivated grapevine (Vitis vinifera L.), with cell wall (CW) remodelling playing a critical role in fungal colonisation. CW-modifying enzymes, particularly pectin methylesterases (PMEs), produced by both host and pathogen, influence CW integrity and the outcome of infection. To explore the role of CW composition and remodelling in grapevine's response to Bc, we inoculated three genotypes with varying susceptibility at full flowering. Biochemical analysis of flowers and ripe berry skins revealed that the tolerant genotype exhibited significantly higher PME activity postinfection compared with the susceptible ones. Unbiased transcriptome analysis of infected flower tissues showed a more intense transcriptional response in the susceptible genotype, suggesting an ultimately ineffective attempt to restrict fungus spread. Expression profiling of 62 PME genes in this data set and public Bc-infected berry transcriptomes identified PME10 as the most strongly induced gene upon infection. PME10 knockout mutants displayed reduced PME activity and heightened susceptibility, while overexpression lines showed enhanced PME activity and reduced disease symptoms. Gene co-expression network analysis highlighted WRKY03, a defence-related transcription factor, as a putative regulator of PME10. DAP-seq, DAP-qPCR and dual luciferase assays confirmed direct binding and activation of the PME10 promoter by WRKY03. Altogether, this study demonstrates that PME10 is a functional PME contributing to grapevine immunity against B. cinerea, establishing it as a key component of the grapevine defence machinery against fungal pathogens.

Genome editing (GE) technologies have the potential to completely transform breeding and biotechnology applied to crop species, contributing to the advancement of modern agriculture and influencing the market structure. To date, the GE-toolboxes include several distinct platforms able to induce site-specific and predetermined genomic modifications, introducing changes within the existing genetic blueprint of an organism. For these reasons, the GE-derived approaches are considered like new plant breeding methods, known also as New Breeding Techniques (NBTs). Particularly, the GE-based on CRISPR/Cas technology represents a considerable improvement forward biotech-related techniques, being highly sensitive, precise/accurate, and straightforward for targeted gene editing in a reliable and reproducible way, with numerous applications in food-related plants. Furthermore, numerous examples of CRISPR/Cas system exploitation for non-editing purposes, ranging from cell imaging to gene expression regulation and DNA assembly, are also increasing, together with recent engagements in target and multiple chemical detection. This manuscript aims, after providing a general overview, to focus attention on the main advances of CRISPR/Cas-based systems into new frontiers of non-editing, presenting and discussing the associated implications and their relative impacts on molecular traceability, an aspect closely related to food safety, which increasingly arouses general interest within public opinion and the scientific community.

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

DNA-binding proteins play a pivotal role in critical cellular processes such as DNA replication, transcription, recombination, repair, and other essential activities. Consequently, investigating the interactions between DNA and proteins is of paramount importance to gain insights into these fundamental cellular mechanisms. Several methodologies have been devised to uncover DNA-protein interactions, which can be broadly categorized into two approaches. The "protein-centered" approach focuses on identifying the DNA sequences bound by a specific transcription factor or a set of TFs. Techniques falling within this category include chromatin immunoprecipitation, and protein-binding microarrays. The "gene-centered" approach entails using one or more DNA sequences as bait to explore the TFs that bind to these specific DNA elements. Methods belonging to this approach encompass yeast one-hybrid (Y1H), PICh, and Reverse ChIP. Both methodologies offer distinct advantages and face limitations, largely stemming from challenges related to complexity, efficiency, and specificity. With the emergence of next-generation sequencing (NGS) protocols and the CRISPR/Cas system, new avenues for investigating trans-cis interactions in organisms have opened. In our research focusing on grapevines, we discuss advancements in both protein- and gene-centered approaches. Firstly, we present the implementation of a DNA Affinity Purification (DAP-seq) protocol in grapevines to explore the cistrome associated with various TFs from the WRKY and MYB families. Secondly, we address the challenge of developing an innovative gene-centered approach utilizing a CRISPR/Cas system for in-situ purification of regulatory elements. This approach aims not only to identify proteins associated with specific genomic regions but also to elucidate long-range DNA interactions.

The advent of CRISPR/Cas9 technology has revolutionized genome editing, enabling the attainment of once-unimaginable goals. CRISPR/Cas's groundbreaking attributes lie in its simplicity, versatility, universality, and independence from customized DNA-protein systems, erasing the need for specialized expertise and broadening its scope of applications. It is therefore more and more used for genome modification including the generation of mutants. Beyond such editing scopes, the recent development of novel or modified Cas-based systems has spawned an array of additional biotechnological tools, empowering both fundamental and applied research. Precisely targeting DNA or RNA sequences, the CRISPR/Cas system has been harnessed in fields as diverse as gene regulation, deepening insights into gene expression, epigenetic changes, genome spatial organization, and chromatin dynamics. Furthermore, it aids in genome imaging and sequencing, as well as effective identification and countering of viral pathogens in plants and animals. All in all, the non-editing aspect of CRISPR/Cas exhibits tremendous potential across diverse domains, including diagnostics, biotechnology, and fundamental research. This article reviews and critically evaluates the primary CRISPR/Cas-based tools developed for plants and animals, underlining their transformative impact.

BACKGROUND:In alfalfa (Medicago sativa), the coexistence of interfertile subspecies (i.e. sativa, falcata and coerulea) characterized by different ploidy levels (diploidy and tetraploidy) and the occurrence of meiotic mutants capable of producing unreduced (2n) gametes, have been efficiently combined for the establishment of new polyploids. The wealth of agronomic data concerning forage quality and yield provides a thorough insight into the practical benefits of polyploidization. However, many of the underlying molecular mechanisms regarding gene expression and regulation remained completely unexplored. In this study, we aimed to address this gap by examining the transcriptome profiles of leaves and reproductive tissues, corresponding to anthers and pistils, sampled at different time points from diploid and tetraploid Medicago sativa individuals belonging to progenies produced by bilateral sexual polyploidization (dBSP and tBSP, respectively) and tetraploid individuals stemmed from unilateral sexual polyploidization (tUSP). RESULTS:Considering the crucial role played by anthers and pistils in the reduced and unreduced gametes formation, we firstly analyzed the transcriptional profiles of the reproductive tissues at different stages, regardless of the ploidy level and the origin of the samples. By using and combining three different analytical methodologies, namely weighted-gene co-expression network analysis (WGCNA), tau (τ) analysis, and differentially expressed genes (DEGs) analysis, we identified a robust set of genes and transcription factors potentially involved in both male sporogenesis and gametogenesis processes, particularly in crossing-over, callose synthesis, and exine formation. Subsequently, we assessed at the same floral stage, the differences attributable to the ploidy level (tBSP vs. dBSP) or the origin (tBSP vs. tUSP) of the samples, leading to the identification of ploidy and parent-specific genes. In this way, we identified, for example, genes that are specifically upregulated and downregulated in flower buds in the comparison between tBSP and dBSP, which could explain the reduced fertility of the former compared to the latter materials. CONCLUSIONS:While this study primarily functions as an extensive investigation at the transcriptomic level, the data provided could represent not only a valuable original asset for the scientific community but also a fully exploitable genomic resource for functional analyses in alfalfa.

The recent development of regulatory genomics has raised increasing interest in plant research since transcriptional regulation of genes plays a pivotal role in many biological processes. By shedding light on the target genes of the various transcription factors (TFs), it is therefore possible to infer the influence they exert on the different molecular mechanisms. In this regard, the attention was focused on WRKYs, a family of TFs almost exclusively found in plant species. In grapevine, WRKYs are involved in several biological processes, playing a key role in berry development, hormonal balance and signalling, biotic and abiotic stresses responses, and secondary metabolites biosynthesis. In this study, DAP-Seq was used to investigate the regulatory activity of the whole WRKY family in gDNA from young leaves of Cabernet Franc. This approach allowed the definition of the WRKYs cistrome (i.e., the set of bound genes). 46 out of 59 WRKYs gave results, outlining a total number of 674,407 binding events along whole grapevine genome, of which 459,791 (68%) are localized in the perigenic region, according to its intense regulatory activity. Cistrome maps were integrated with gene centred co-expression networks based on a large transcriptomics dataset, and with the results of an ATAC-Seq. This allowed to isolate some High Confidence Targets, characterized by high degree of co-expression with the related TF and laying down in genomic regions of open chromatin. The networks generated can be used to provide a complete regulatory map of WRKY family, shedding light on its biological role in grapevine.

Cis-acting regulatory elements are DNA sequences that can be bound by transcription factors to regulate the expression of genes in a condition-dependent and tissue-specific way. It is nowadays possible to search for DNA motives and sequences that a given transcription factor is binding or at least can, but it is still hard to have a glance at all the transcription factors that are contemporaneously located at the same locus. Inspired by an existing technique that uses the CRISPR-Cas system in mammal cells, we are trying to develop a protocol to study such regulation in Vitis vinifera. Using the highly sequence-specific binding capacity of a catalytically inactive Cas9 protein (dCas9), our idea is to set up a system to target a desired sequence and precipitate all the crosslinked proteins and distantly interacting chromatin at this locus and analyze them. After conducting preliminary assays on protoplast system, we got introduced to the CRISPR-FISH technique, that uses dCas9 and a fluorescent guide to label telomeres on nuclei directly isolated from a small quantity of fixed leaves with a very simple procedure. We used part of such technique to easily obtain the chromatin that was needed for our trials and eventually performed the pull-down of the targeted DNA sequences directly on these nuclei after transforming them with the dCas9 complex. Sequencing the obtained fragments allows to verify the specificity of the tool. Far from having eliminated the idea of using protoplasts as model system, we proceed developing both approaches in parallel.

PIWI, from the German word Pilzwiderstandsfähig, meaning “fungus-resistant”, refers to grapevine cultivars bred for resistance to fungal pathogens such as Erysiphe necator (the causal agent of powdery mildew) and Plasmopara viticola (the causal agent of downy mildew), two major diseases in viticulture. These varieties are typically developed through traditional breeding, often crossbreeding European Vitis vinifera with American or Asian species that carry natural disease resistance. This study investigates the transcriptional profiles of exocarp tissues in mature berries from four PIWI grapevine varieties compared to their elite parental counterparts using RNA-seq analysis. We performed RNA-seq on four PIWI varieties (two red and two white) and their noble parents to identify differential gene expression patterns. Comprehensive analyses, including Differential Gene Expression (DEGs), Gene Set Enrichment Analysis (GSEA), Weighted Gene Co-expression Network Analysis (WGCNA), and tau analysis, revealed distinct gene clusters and individual genes characterizing the transcriptional landscape of PIWI varieties. Differentially expressed genes indicated significant changes in pathways related to organic acid metabolism and membrane transport, potentially contributing to enhanced resilience. WGCNA and k-means clustering highlighted co-expression modules linked to PIWI genotypes and their unique tolerance profiles. Tau analysis identified genes uniquely expressed in specific genotypes, with several already known for their defense roles. These findings offer insights into the molecular mechanisms underlying grapevine resistance and suggest promising avenues for breeding strategies to enhance disease resistance and overall grape quality in viticulture.

Botrytis cinerea (Bc) is one of the main pathogens affecting the cultivated grapevine. A key role in grapevine tissue colonization is played by cell wall (CW) remodeling driven by CW Modifying Enzymes (CWMEs), expressed both by the host and the pathogen. Their action can impact CW integrity and trigger specific immune signaling, thus influencing Bc infection outcome. To further characterize the role of the CW in the grapevine response to Bc, two contrasting genotypes in their resistance to the fungus were artificially inoculated at full bloom. RNA-seq analysis and biochemical characterization of the CW and its modification in samples collected at 24 hours post-inoculation highlighted significant differences between genotypes. A gene set enrichment analysis indicated several over-represented categories upon infection, with a general down-regulation of those genes related to CW organization and pectin modification, mostly in the resistant genotype. Within the down-regulated CWMEs, Pectin Methyl-Esterase (PME) genes were found highly represented. Unlike, VviPME10 was significantly induced upon infection and was further characterized since its putative ortholog in Arabidopsis was associated with resistance to Bc. VviPME10promoter hosts several predicted binding sites for VviWRKY3, a defense-associated transcription factor, as highlighted by DAP-seq analysis. This evidence is under confirmation by luciferase assays. In addition, the artificial inoculation with Bc of leaves from six VviPME10 knock-out (KO) edited lines showed significantly larger lesion areas when compared to control plants at 5 dpi. Together, these results suggest that pectin modification, mediated by VviPME10, plays an important role in the grapevine response to Bc.