PostGram | Plant

This course introduces you to the basics of R programming applied to biological data analysis. It covers fundamental concepts such as variables, scripts, the working environment, and user interactions (console reading/writing, type conversions). You will learn how to create and manipulate the main data structures: vectors, factors, dataframes, and lists; how to modify, combine, or filter them; and how to extract subsets according to logical criteria. The module also introduces the concepts of environment cleaning, missing data management, and dataset import/export. The final part is devoted to graphical visualization, using bar plots, box plots, histograms, and scatter plots depending on the type of variable (qualitative, quantitative, ordinal, continuous). Datasets such as iris or roseflowers are used for training, through guided exercises aimed at automating the statistical analysis of real datasets.

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OVERVIEW OF THE FOUR LESSONS

1. Fungal diseases as a worldwide threat to crop and ecosystems
   The course “Fungal Diseases as a Worldwide Threat to Crops and Ecosystems” offers an immersion into the diversity of pathogenic and fungiform fungi affecting plants. It explores their infection strategies (biotrophic, necrotrophic, hemibiotrophic), their life cycles, their modes of dispersal, and their effects on crops and natural ecosystems. Historical and contemporary examples illustrate their role in major agricultural crises (coffee rust, Dutch elm disease, late blight, etc.). The course also addresses emerging threats linked to climate change, intensive agriculture, and resistance to treatments, while presenting the main fungal and fungiform pathogens.
   
   2. On plant pathogenic bacteria
   This course offers a comprehensive exploration of phytopathogenic bacteria, from their effects on plants to their identification and management. It begins with an overview of the main symptoms they cause (watery spots, necrosis, wilting, etc.), then addresses their taxonomic diversity, the different levels of classification (species, pathovars, races) and their host specificities. The analysis continues with a study of their parasitic cycles and control strategies (selection of resistant varieties, biological control, epidemiological surveillance). Finally, the course presents methods of identification by molecular phylogeny and typing, in line with international phytosanitary policies.
   
   3. Parasitic plants
   The “Parasitic Plants” course explores the diversity, biology, and agronomic impacts of parasitic plants, true “plant vampires” capable of diverting water and nutrients from their hosts. After an introduction to the different forms of parasitism, the course presents the main families concerned, their strategies (hemiparasites or holoparasites) and the importance of the haustorium, the vascular connection organ. Two major genera are studied: witchweeds (Striga) and broomrapes (Orobanche, Phelipanche), formidable crop parasites. Finally, the course addresses germination signals, spoliation mechanisms, and the challenges posed by current control methods.
   
   4. Study of the rose resistance against black spot disease
   This course explores the rose as a model for studying ornamental plants through resistance to black spot disease (Diplocarpon rosae). It presents the challenges associated with this disease, the limitations of chemical control, and qualitative and quantitative genetic approaches to resistance. The course covers evaluation methods, fungal strain diversity, QTL mapping, and alternative solutions such as bioprotection, illustrated by the ROBIO project.

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OVERVIEW OF THE THREE LESSONS

1. Plant-Microbe Symbioses
The “Plant-Microbe Symbiosis” course invites you to discover the mutualistic interactions between plants and certain microorganisms, particularly mycorrhizal fungi and nitrogen-fixing bacteria. Sequence 1 lays the theoretical foundations of symbiosis and specifies its different forms. The following sequences explore two main types of symbiosis: mycorrhizae, in particular arbuscular mycorrhiza (AM), which plays a key role in nutrient absorption and the evolution of terrestrial plants; and nitrogen-fixing symbiosis between legumes and Rhizobium, which enables the formation of root nodules and the integration of atmospheric nitrogen. These symbioses are discussed in terms of their molecular mechanisms, development, immune regulation, and applications in sustainable agriculture.

2. Chronic loss of apple scab immunity
The course “Chronic Loss of Apple Scab Immunity” addresses the evolution of varietal resistance in apple trees to scab, a fungal disease caused by Venturia inaequalis. Using an evolutionary ecology framework, the course explores how the introduction of the Rvi6 resistance gene from Malus floribunda has changed the structure of pathogen populations.

Through an in-depth case study in Europe, the various sequences analyze the origin of virulence, the identification of the AvrRvi6 gene, and the role of wild reservoirs in the loss of immunity. Genetic tools (GWAS, crossing, heterologous expression) are used to trace the emergence of virulent strains and assess the consequences of their hybridization with local populations. The course concludes with implications for breeding programs, sustainable resistance management, and health policies in arboriculture.

3. Parasitic strategies
The “Parasitic Strategies” course invites you to explore the mechanisms used by phytopathogenic bacteria to invade, colonize, and infect host plants. It draws on a comparative study of two major species, Xylella fastidiosa and Xanthomonas spp., to illustrate the diversity of infectious strategies. The sequences cover their life cycles, transmission routes (vectors, plant material), secretion systems involved in virulence, and molecular interactions with plants. The course also sheds light on the environmental and human factors that promote the emergence of new diseases, as well as epidemiological surveillance tools (typing, modeling, genomics).

Each of these three courses includes a comprehension test to help you assess your knowledge and identify concepts to review before the evaluation.

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OVERVIEW OF THE THREE LESSONS

1. Culture-independent approaches to improve our understanding of microbial communities
This course presents culture-free approaches used to explore the diversity of microbial communities associated with plants. It highlights metabarcoding and metagenomics techniques, which enable the taxonomic and functional composition of microbiotas to be characterized without isolating strains. The course also covers genome reconstruction, diversity indices (alpha, beta), and the ecological roles of microorganisms in plant-environment interactions.

2. Seed microbiome characterization and future applications for plant health
This course explores the seed microbiome, which remains largely unknown despite its key role in plant health and vigor. It presents the diversity, origin, and dynamics of microbial communities associated with seeds, as well as the factors that influence their composition (production site, pollination, microbial interactions). The course also discusses the prospects for bioengineering the seed microbiome as an alternative to pesticides, through the use of beneficial strains or synthetic communities. These approaches aim to improve germination, stress tolerance, and pathogen resistance.

3. Plant microbiota : focus on the mycobiota The incredible power of fungi
This course highlights the central role of fungi in plant-associated microbial communities, from the earliest terrestrial symbioses to current interactions. It explores how mycorrhizae function, their impact on plant nutrition and resilience, and their ability to structure the microbiome of the hyphosphere. The course also addresses more recent cases such as the mucilaginous microhabitat of aerial roots, or the role of the seed mycobiome in the intergenerational transmission of beneficial microorganisms. These examples illustrate the functional and evolutionary power of fungi in plant ecosystems.

4. The French Collection for Plant-associated Bacteria: strategic resources for plant health
A 20-minute video will be available for you to visit the CIRM-CFBP website.

The first three courses include a self-assessment to evaluate your knowledge and guide your revision for the final assessment.

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Le module "Plant Genomics" a pour objectif de vous faire découvrir les mécanismes complexes de l’expression des gènes chez les plantes, en mettant
l’accent sur la régulation à différents niveaux et sur les spécificités végétales. Ce module vous permettra d’acquérir des connaissances approfondies sur les
grandes étapes de la régulation génétique, en lien avec le fonctionnement cellulaire et les réponses environnementales des plantes.
Le cours introductif (séquence 1) vous propose une vue d’ensemble de l’expression génique dans les cellules eucaryotes, depuis l’ADN jusqu’à la synthèse protéique. Vous découvrirez notamment les quatre grands niveaux de régulation : épigénétique, transcriptionnelle, maturation de l’ARNm et post-transcriptionnelle.
Les séquences suivantes (2 à 6) approfondissent ces niveaux :
Séquence 2 : les modifications épigénétiques (méthylation de l’ADN, modifications des histones) et leur rôle dans la mémoire cellulaire des plantes ;
Séquence 3 : la régulation transcriptionnelle, avec l’étude des promoteurs, des facteurs de transcription et des domaines fonctionnels propres aux génomes
végétaux ;
Séquence 4 : la maturation de l’ARN messager, incluant le capping, l’ajout de la queue poly-A et l’épissage, avec un focus sur l’épissage alternatif en tant que modalité de régulation qualitative ;
Séquence 5 : l’édition et la stabilité des ARNm dans le cytoplasme, ainsi que le rôle crucial des petits ARN (miARN et siARN) dans le silençage post-transcriptionnel.

Chaque séquence combine vidéo commentée, support écrit, illustrations, exemples végétaux concrets (Arabidopsis, riz, maïs...), ainsi qu'un test de
compréhension pour valider vos acquis.

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