Thèse Ecologie des Virus Causant la Jaunisse Nanisante des Céréales Rôle du Compartiment Sauvage Comme Réservoir pour les Virus et leurs Pucerons Vecteurs. H/F

Doctorat.Gouv.Fr

Établissement : Université de Bordeaux
École doctorale : Sciences de la Vie et de la Santé
Laboratoire de recherche : BFP - Biologie du Fruit et Pathologie
Direction de la thèse : François MACLOT ORCID 0000000331965369
Début de la thèse : 2026-10-01
Date limite de candidature : 2026-05-20T23:59:59

Les virus de la jaunisse nanisante des céréales (YDVs) figurent parmi les maladies les plus dommageables des cultures céréalières (orge, blé, avoine, maïs, riz), avec des épidémies pouvant provoquer jusqu'à 80 % de pertes de rendement. Ils forment un complexe de 12 espèces virales, historiquement classées dans les Luteoviridae puis récemment réassignées aux familles Tombusviridae et Solemoviridae. Ce complexe est transmis de manière persistante par au moins 25 espèces de pucerons, et infecte plus de 150 espèces de poacées sauvages ou cultivées dans divers agro-écosystèmes (cultures, prairies, pelouses, bandes enherbées, lisières). À la fin de l'été, les graminées sauvages peuvent assurer le maintien inter-saisonnier du virus entre la récolte et le semis suivant via un réservoir viral (« green bridge »). Lors des vols de pucerons à l'automne, les vecteurs colonisent ces plantes infectées, acquièrent le virus, puis le retransmettent aux jeunes cultures. Il est donc crucial d'élucider le rôle des graminées estivales dans le maintien et l'émergence des YDVs, en amont des migrations vectorielles. Le développement des technologies de séquençage à haut débit (HTS/NGS) permet aujourd'hui de décrire les communautés virales (viromes) au sein d'échantillons de plantes et d'insectes vecteurs, et d'analyser les dynamiques de circulation virus-hôtes-vecteurs ainsi que la phylodynamique de transmission entre compartiments sauvages et cultivés.
L'objectif général est de caractériser, par métagénomique et écologie virale, la diversité des populations de YDVs chez les céréales et les poacées sauvages, de cartographier la circulation des virus du complexe BYDV/CYDV dans les agro-écosystèmes français, et d'identifier les espèces de poacées jouant un rôle de réservoir viral en fin d'été (green bridge) contribuant à la contamination des céréales à l'automne.
La thèse reposera sur deux axes méthodologiques complémentaires : tout d'abord la réalisation d'un screening viromique des céréales et graminées estivales pour estimer la richesse et la composition en espèces et variants de YDVs par espèce hôte. L'analyse intégrera des poacées annuelles et pérennes, indigènes et exotiques, en tenant compte de leurs traits biologiques et phénologiques.
Plusieurs graminées exotiques C4 présentent une croissance active en juillet-août et constituent des candidats plausibles au rôle de réservoir viral estival, contrairement à certaines poacées indigènes sénescentes en été, peu attractives pour les vecteurs. L'étude comparée de ces styles de vie et origines permettra d'évaluer différentes configurations de réservoirs hôtes, incluant les espèces exotiques en expansion en France sous l'effet du changement climatique, susceptibles de modifier le cycle épidémiologique des YDVs dans les céréales.
Ensuite, l'analyse expérimentale en condition contrôlée de la propagation et de la transmission inter-hôtes des deux espèces virales majoritaires en France : BYDV-PAV et BYDV-PAS, inoculées via le puceron vecteur principal Rhopalosiphum padi. Les virus seront transmis à cinq espèces de poacées sauvages, puis entre les poacées et le blé. Les espèces hôtes seront choisies selon leur sensibilité à l'infection et/ou les résultats du virome. La prévalence de PAV et PAS sera estimée comme proxy du taux d'infection des hôtes. Chez les vecteurs, le taux de survie et la fécondité seront mesurés après la période d'accès à l'inoculation, via le nombre d'insectes vivants et la descendance totale par femelle.
Ce projet présente des implications fondamentales et appliquées : (1) améliorer les connaissances sur l'écologie et l'émergence des YDVs dans les réseaux hôtes-vecteurs, (2) décrypter les voies de transmission virale, et (3) identifier les réservoirs viraux assurant le maintien inter-saisonnier. Les résultats permettront ainsi d'orienter le développement de stratégies culturales et agro-écologiques durables pour la gestion des YDVs dans les systèmes céréaliers français.

Yellow dwarf viruses (YDVs) are extremely damaging diseases for cereal crops (barley, wheat, oat, maize, rice), with the most severe epidemics causing up to 80% yield loss. It is characterized by a reduction in plant size of up to 66% compared to a healthy plant, as well as yellowing of the leaves caused by chlorosis. This disease is caused by a complex of viral species formerly members of the Luteoviridae family and newly assigned to the Tombusviridae and Solemoviridae families. The ICTV (International Committee on Taxonomy of Viruses) currently recognizes 12 viral species associated with the YDV complex, 6 of which are assigned to the genus Luteovirus within the Tombusviridae (BYDV-PAV, BYDV-PAS, BYDV-MAV, BYDV-SGV, BYDV-kerII, and BYDV-kerIII), five are assigned to the genus Polerovirus within the Solemoviridae (CYDV-RPV, CYDV-RPS, MYDV-RMV, MaYMV, and ScYLV), and one is not assigned to any genus (BYDV-GPV). This viral complex is one of the most widespread in the world, due to its wide range of hosts (more than 150 species of wild and cultivated Poaceae) distributed in various agro-ecosystems (cereal crops, pastures, grasslands, meadows, grass strips, etc.) within the same landscape window. The wild compartment can thus serve as virus reservoir at the end of summer, between the cereal harvest and the next crop sowing (so-called green bridge). YDVs also present numerous species of aphid vectors present on different continents (at least 25 species identified, with a certain vector specificity for the YDV species) that transmit the viruses in a persistent manner. However, to identify these potential green bridge grasses is not a trivial task and it requires to consider the biology and ecology of both the wild grasses and the aphid vectors. In addition, climate change and introduction of exotic grasses (e.g. new crops and ornamental grasses) are modifying the interactions between YDVs and their hosts and vectors, which can in turn change the disease ecology in cereals.
Historically, control of the B/CYDV viral species complex has involved several disease management strategies combining cultural, chemical, and biological methods. Much attention has been paid to the development of resistant varieties of cereals to reduce the risk of yellow dwarf virus infection. However the resistance present a limited durability or restricted spectrum of action, targeting only certain species or strains of the complex. This resulted in a few wheat and barley varieties with strong resistance to YDV, most commercial varieties remain susceptible or moderately tolerant. Vector control is another strategy to reduce virus transmission. For decades, insecticides, and in particular neonicotinoids, have been widely used to control aphid vector populations, via seed treatment or vegetation treatment. Nevertheless, numerous studies have warned about the environmental harm caused by neonicotinoids, in particular through their toxicity to non-target insect pollinators. These findings led to a total ban on their use in the European Union. Instead, vector control relied on the use of pyrethrinoids, but with the potential risk of insect resistance.
Integrating cultural and biological control strategies into an integrated pest management (IPM) approach can contribute to manage yellow dwarf viruses in cereals while minimizing reliance on chemical pesticides. These strategies include delayed sowing, optimizing cereal density, crop rotation, crop mixture and introducing natural enemies of aphids such as parasitoid wasps, predatory insects (e.g., ladybugs), and entomopathogenic fungi. These strategies can potentially reduce the aphid number in the field or avoid the peak of aphid activity to limit virus transmission. However, the analysis of the impact of agro-ecological strategies on the viral populations is not a trivial task, in particular for the complex B/CYDV. Its wide host range within Poaceae and the numerous aphid vector species make complex virus-host-vector interactions. It is therefore essential to better understand the structure and functioning of the B/CYDV populations in their host reservoirs and insect vectors in order to better control YDV disease in cereals. For that matter, virus metagenomics can provide new insights on the diversity of the B/CYDV complex in France, the virus circulation in agroecosystems, and the phylodynamic analysis of virus transmission between cultivated and wild compartments by aphid vectors.

The main aim of the PhD thesis is to identify and characterize the circulation in France of the different viruses forming the B/CYDV complex in the cereals, the wild host reservoirs and the aphid vectors.
More specifically, the thesis aims to determine which wild grass species can serve as virus reservoir at the end of summer, between the cereal harvest and the next crop sowing (so-called green bridge). For that matter, the PhD thesis will be divided into two work packages (WPs):
-WP1: In situ virome study on summer grasses (i.e. active growing season in July-August) to identify the richness and composition of YDV species and variants in each grass species. Plant lifestyle and origin will be considered, comparing annual vs. perennial grasses, and exotic vs. indigenous grasses.
-WP2: In controlled conditions, analyze the contribution of the wild grasses to the ecology of the two main YDV species present in France (BYDV PAV and PAS). These two virus species will be inoculated by their aphid vector in ten grass species, and both plant-virus interactions (i.e. infection rate of PAV and PAS) and plant-vector (i.e. survival and fecundity) will be monitored.

Work package 1 of the PhD thesis will be a virome study performed in August on summer grasses (annual, perennial, indigenous and exotic species) and cereal crops to identify the richness and composition of YDV species and variants. The virome study will be replicated in three contrasted pedo-climatic regions in France (North West for oceanic climate, North East for semi-continental climate and South West for climate of the southwestern basin). In each region, five sites will be surveyed for floristic inventories and 50 individual plants will be collected by wild grass species. The ten most abundant grass species within each site will be sampled. In each site, cereal crops will be surveyed in the fall or next spring (10 individual plants per crop, preferentially symptomatic plants). Then, a dual metagenomic approach will be applied to process the samples. For cereals, RNASeq will be performed on individual plants in order to reconstruct the YDV isolate in each sample. For wild grasses, pools of 50 plants will be processed to extract the viral nucleic acids using enrichment protocols developed in the laboratory. In total, 300 viral libraries (i.e. 150 cereals and 150 wild grass librairies) will be sent to high throughput sequencing. Bioinformatics analyses will be performed to reconstruct the YDV genomes, followed by ecological analyses (virus richness and composition, virome network in the different grass species, sites and regions, etc.). Individual plants from each species pool will also be analyzed through targeted RT-PCR, in order to provide other ecological information such as virus prevalence, co-infection and spatial distribution of the virus infection. This first study will enable to determine which grass species can serve as YDV reservoir during the off-season. These species will be used for the second research project.
WP2 will analyze in controlled conditions the contribution of the wild grasses to the propagation and circulation of the two main YDV species present in France (BYDV PAV and PAS) in the wild and cultivated compartments. These two virus species will be inoculated by their aphid vector (Rhopalosiphum padi) in five wild grass species. Viruliferous aphids (2 vectors per plant) will be used to inoculate sets of 20 plantlets/grass species for a three days inoculation access period (IAP). At the end of IAP, alive and dead insects, and total offspring per female will be monitored for each inoculated plant, and plants will be sprayed with insecticides. Then, plants will be transferred in an insect-proof greenhouse for 45 days before being sampled and stored at -20°C until the characterization of their sanitary status. The whole inoculation procedures will be repeated three times. For each species, non-inoculated plants will be used as healthy controls. In a second time, virus-free aphids (2 vectors per plant) will be placed on infected wild grasses for another three days inoculation access period (IAP). Then the supposedly viruliferous aphids they will be used to inoculate healthy wheats using the above methodology. Afterwards, PAV and PAS prevalence in wild grasses and wheat will be calculated as a proxy of the virus infection rate. For the aphid vectors, survival rate and fecundity will be determined based on the number of alive insects and total offspring per female after the IAP, respectively.