Resistenz gegen die Schwarzfäule (Guignardia bidwellii) in der Weinrebe (Vitis spec.) – Etablierung phänotypischer Erfassungsmethoden und genetische Kartierung von Resistenzloci

Institut für Rebenzüchtung Die Rebenkrankheit Schwarzfäule wird durch den Pilz Guignardia bidwellii (Ellis) Viala und Ravaz  hervorgerufen. Die ursprünglich nur in Nordamerika vorkommende Rebenkrankheit, wurde mit Rebmaterial nach Europa eingeschleppt. In den deutschen Weinanbaugebieten war sie bislang weitgehend unbedeutend und trat nur regional begrenzt epidemieartig auf. Seit 2002 wird jedoch ein verstärkter Schwarzfäulebefall vor allem im Anbaugebiet Mosel beobachtet, der teils erhebliche Schäden verursacht (Lipps und Harms 2004). Im Rahmen der vorliegenden Arbeit wurden verschiedene Resistenztests etabliert, um die Resistenzeigenschaften von Kreuzungseltern sowie einer Nachkommenschaft und weiterer Genotypen zu ermitteln. Der Resistenztest an Topfreben im Klimaraum führte zu den verlässlichsten Resultaten. Zur Charakterisierung des Resistenzgrades der Genotypen wurden neun verschiedene Bonitursysteme entwickelt, von denen sich ein 5-Klassensystem als das geeignetste für die nachfolgenden QTL-Analysen erwies. Mikroskopische Untersuchungen hinsichtlich der Sporenkeimrate und Appressorienbildung lieferten zusätzlich eine qualitative Aussage bezüglich der Resistenz. Für die Identifikation und genetische Kartierung von Resistenzloci in der für die Schwarzfäule resistenten Unterlagssorte und Arthybride ‘Börner’ wurde die für dieses Merkmal aufspaltende Kreuzungspopulation V3125 (‘Trollinger’ x ‘Riesling’) x ‘Börner’ (V. riparia Gm183 x V. cinerea Arnold) eingesetzt. Auf Basis der phänotypischen Evaluierung einer 202 Pflanzen umfassenden F1-Population und der vorhandenen genetischen Karte (Zhang et al. 2009) erfolgten QTL-Berechnungen, mit denen Resistenzloci im Genom lokalisiert wurden. Nahezu alle Berechnungen führten zu einem Haupt-QTL auf dem Chromosom 14 (Rgb1), der bis zu 21,8% der Merkmalsausprägung erklärt. Dieser Locus wurde durch die Entwicklung eng gekoppelter Marker von 13,1 cM auf 1,6 cM eingeengt. Der dazu im Referenzgenom PN40024 korrespondierende Genombereich entspricht 287 kb, in dem mehrere Kandidatengene für Resistenz lokalisiert sind. Ein weiterer QTL (Rgb2) wurde reproduzierbar auf Chromosom 16 ermittelt. Dieser erklärt etwa 7-8% der Variabilität der Merkmalsausprägung. Durch zusätzliche Resistenztests an ausgewählten Weinreben wurden die Sorten ‘Felicia‘, ‘Merzling‘ und ‘Villard Blanc‘ sowie der Zuchtstamm Gf.Ga-47-42 als neue wichtige Resistenzträger identifiziert.Institute for Grapevine Breeding Die Rebenkrankheit Schwarzfäule wird durch den Pilz Guignardia bidwellii (Ellis) Viala und Ravaz  hervorgerufen. Die ursprünglich nur in Nordamerika vorkommende Rebenkrankheit, wurde mit Rebmaterial nach Europa eingeschleppt. In den deutschen Weinanbaugebieten war sie bislang weitgehend unbedeutend und trat nur regional begrenzt epidemieartig auf. Seit 2002 wird jedoch ein verstärkter Schwarzfäulebefall vor allem im Anbaugebiet Mosel beobachtet, der teils erhebliche Schäden verursacht (Lipps und Harms 2004). Im Rahmen der vorliegenden Arbeit wurden verschiedene Resistenztests etabliert, um die Resistenzeigenschaften von Kreuzungseltern sowie einer Nachkommenschaft und weiterer Genotypen zu ermitteln. Der Resistenztest an Topfreben im Klimaraum führte zu den verlässlichsten Resultaten. Zur Charakterisierung des Resistenzgrades der Genotypen wurden neun verschiedene Bonitursysteme entwickelt, von denen sich ein 5-Klassensystem als das geeignetste für die nachfolgenden QTL-Analysen erwies. Mikroskopische Untersuchungen hinsichtlich der Sporenkeimrate und Appressorienbildung lieferten zusätzlich eine qualitative Aussage bezüglich der Resistenz. Für die Identifikation und genetische Kartierung von Resistenzloci in der für die Schwarzfäule resistenten Unterlagssorte und Arthybride ‘Börner’ wurde die für dieses Merkmal aufspaltende Kreuzungspopulation V3125 (‘Trollinger’ x ‘Riesling’) x ‘Börner’ (V. riparia Gm183 x V. cinerea Arnold) eingesetzt. Auf Basis der phänotypischen Evaluierung einer 202 Pflanzen umfassenden F1-Population und der vorhandenen genetischen Karte (Zhang et al. 2009) erfolgten QTL-Berechnungen, mit denen Resistenzloci im Genom lokalisiert wurden. Nahezu alle Berechnungen führten zu einem Haupt-QTL auf dem Chromosom 14 (Rgb1), der bis zu 21,8% der Merkmalsausprägung erklärt. Dieser Locus wurde durch die Entwicklung eng gekoppelter Marker von 13,1 cM auf 1,6 cM eingeengt. Der dazu im Referenzgenom PN40024 korrespondierende Genombereich entspricht 287 kb, in dem mehrere Kandidatengene für Resistenz lokalisiert sind. Ein weiterer QTL (Rgb2) wurde reproduzierbar auf Chromosom 16 ermittelt. Dieser erklärt etwa 7-8% der Variabilität der Merkmalsausprägung. Durch zusätzliche Resistenztests an ausgewählten Weinreben wurden die Sorten ‘Felicia‘, ‘Merzling‘ und ‘Villard Blanc‘ sowie der Zuchtstamm Gf.Ga-47-42 als neue wichtige Resistenzträger identifiziert

Evaluation of a oxygenate based plant protection treatment in viticulture against fungal diseases

Over the last decades the use of pesticides in vine protection, e.g. copper is under severe discussion and is becoming a major concern in viticulture. Since the effectiveness of oxygenates against various microorganisms had been proven in the medical field a strategy for oxygenate-based plant protection was developed and evaluated over three vintages. The production of the oxygenate is following the Criegee-mechanism using O3 and unsaturated natural plant derived fatty acids forming so called ozonides. Therefore the effect of the treatment has been evaluated in a holistic approach, covering the efficiency against fungal diseases, protection of desired beneficial insects, the micro flora, various secondary metabolites of the grapevine and the resulting sensory profile of the wines. The biological effectiveness has been measured by using different in-vivo and in-vitro studies. The influence on desired berry compounds, e.g. anthocyanins, have been determined by classical GC-MS and HPLC methods. Positive effects against downy and powdery mildew could be demonstrated. No negative effects against insects, naturally occurring microorganisms, and desired berry compounds were observed. Even spontaneous fermentation was not inhibited. Quantitative descriptive sensory analysis as well as CATA/RATA showed no negative effect of the treatment

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.Peer Reviewe

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Funder: Bundesministerium für Bildung und ForschungFunder: Bundesministerium für Bildung und Forschung (BMBF)We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective

MIBiG 3.0 : a community-driven effort to annotate experimentally validated biosynthetic gene clusters

With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

IntroductionThe COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. MethodsExtensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.ResultsResults revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. DiscussionThe key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies

Development of a method for phenotyping Black Rot (_Guignardia bidwellii_) resistance on grapevine (_Vitis_ spp.)

Black Rot of grapevine is caused by the Ascomycet _Guignardia bidwellii_. The pathogen was introduced from North America to Europe in the 19th century. Since 2002, increased effects of the disease have been noticed, causing significant yield losses in the region of Mosel and infections in all German wine-growing regions. For that reason, it is important to breed Black Rot-resistant grapevine cultivars. A method has been developed to characterize lots of vines in a fast and reliable way concerning their susceptibility. Initial data has been collected and can be used for genetic analysis (here QTL). The aim of the project is to develop a molecular marker correlating with Black Rot resistance which can be used to select juvenile plants and therefore support the breeding of resistant cultivars

Ozonized Oleic Acid as a New Viticultural Treatment? Study of the Effect of LIQUENSO® Oxygenate on the Carpoplane Microbial Community and Wine Microorganisms Combining Metabarcoding and In Vitro Assays

In this study, an amplicon metagenomic approach was used to determine the effect of repeated treatments with ozonized oleic acid on the microbial community of grapevine carpoplane. Differences in community composition of treated vineyards were compared to non-treated and conventionally treated samples regarding the prokaryotic and eukaryotic microbiome at two developmental stages (BBCH 83, BBCH 87). The results showed effects both on occurrence and on abundance of microorganisms and the community assembly. Wine-relevant genera such as Acetobacter and members of the former genus Lactobacillus could be identified as part of the natural microbiota. The impact of the new viticultural treatment on these organisms was assessed in liquid culture-based microtiter assays. Therefore, we investigated an array of two acetic acid bacteria (AAB), four lactic acid bacteria (LAB) and nine saccharomyces and non-saccharomyces yeasts. Brettanomyces bruxellensis, Saccharomyces cerevisiae, Pediococcus sp. and Acetobacter aceti revealed the highest sensitivities against ozonized oleic acid (LIQUENSO® Oxygenat). Culture growth of these organisms was significantly reduced at an ozonide concentration of 0.25% (v/v), which corresponded to a quarter of the concentration used in the vineyard. The metabarcoding approach in combination with complementary in vitro assays allow new insights into treatment effects on the community and species scale

Ozonized Oleic Acid as a New Viticultural Treatment? Study of the Effect of LIQUENSO^® Oxygenate on the Carpoplane Microbial Community and Wine Microorganisms Combining Metabarcoding and In Vitro Assays

In this study, an amplicon metagenomic approach was used to determine the effect of repeated treatments with ozonized oleic acid on the microbial community of grapevine carpoplane. Differences in community composition of treated vineyards were compared to non-treated and conventionally treated samples regarding the prokaryotic and eukaryotic microbiome at two developmental stages (BBCH 83, BBCH 87). The results showed effects both on occurrence and on abundance of microorganisms and the community assembly. Wine-relevant genera such as Acetobacter and members of the former genus Lactobacillus could be identified as part of the natural microbiota. The impact of the new viticultural treatment on these organisms was assessed in liquid culture-based microtiter assays. Therefore, we investigated an array of two acetic acid bacteria (AAB), four lactic acid bacteria (LAB) and nine saccharomyces and non-saccharomyces yeasts. Brettanomyces bruxellensis, Saccharomyces cerevisiae, Pediococcus sp. and Acetobacter aceti revealed the highest sensitivities against ozonized oleic acid (LIQUENSO® Oxygenat). Culture growth of these organisms was significantly reduced at an ozonide concentration of 0.25% (v/v), which corresponded to a quarter of the concentration used in the vineyard. The metabarcoding approach in combination with complementary in vitro assays allow new insights into treatment effects on the community and species scale