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International audience; Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.

Les bananiers cultivés sont constitués de deux espèces majeures : Musa acuminata (génome A) et Musa balbisiana (génome B). Le bananier plantain est un hybride triploïde naturel de ces deux espèces, AAB. Le génome B contient naturellement des intégrations du Banana streak virus (BSV), responsable de la mosaïque en tiret du bananier qui affecte habituellement la croissance et la production fruitière. Suite à des stress, ces séquences endogènes appelées " eBSV " peuvent déclencher une infection. Le plant spontanément infecté devient alors un réservoir d'inoculum viral disponible pour les cochenilles, vectrices de la maladie. A ce jour, aucune épidémie n'a été décrite dans les parcelles de plantain où des pieds de bananiers sont pourtant infectés. L'hypothèse testée durant cette thèse propose la mise en place par le bananier plantain d'un contrôle de l'infection virale au cours de la coévolution avec ces séquences virales endogènes, basé sur un mécanisme d'interférence par ARN. Mes travaux de thèse visent à comprendre le fonctionnement du pathosystème en 1) suivant la distribution du virus dans la plante et la dynamique de la charge virale lors d'une infection d'origine endogène grâce à des outils moléculaires (IC-PCR, qPCR), puis en 2) caractérisant les ARN antiviraux impliqués dans la régulation de ces infections (TGS, PTGS) via leur séquençage profond. Par ailleurs, l'intensification des cultures de plantains dans un contexte de changement climatique multipliant les stress abiotiques, pose la question du risque épidémiologique pour les cultures environnantes de bananiers Cavendish, sans génome B et plus sensibles aux infections BSV. Une partie de mes travaux de thèse visent également à 3) définir la localisation histologique des particules virales BSV pour estimer leur accessibilité pour les cochenilles vectrices de l'infection, puis à tester leur transmission à partir de plantains infectés vers des bananiers Cavendish sains, afin d'évaluer le risque que représentent ces infections d'origine endogène chez le plantain pour les cultures environnantes.

Plantain is a natural hybrid coming from interspecific crossing between two major banana species: Musa acuminata (genome A) and Musa balbisiana (genome B). All B genomes contain viral integrations of Banana streak virus (BSV), responsible for the banana streak disease, which affects plant growth and fruit production. The plantain genome (AAB) contains viral integrations of two BSV species (referred as endogenous BSV, or eBSV) and can develop eBSV-derived infections following biotic and abiotic stresses. However, no banana streak disease epidemic has been reported so far on plantain cultures. We suppose that plantain can regulate eBSV-derived infections, probably through RNA silencing acquired through the co-evolution history between B genome and BSV.During my PhD, I followed eBSV-derived infections kinetics in naturals (plantain) and artificial AAB hybrids, on whole mats and for a complete crop cycle. Virus distribution was heterogeneous across the mats, with some suckers showing severe infection while others remained un- or slightly infected. I observed viral titter fluctuations across time, with extreme cases of complete recovery in natural hybrids. Overall, average viral charge was higher in artificial hybrids compared to natural hybrids.Analysis of small virus-derived RNA profiles (from northern blots and deep sequencing) from contrasted samples taken at different stages of the infection, and from both artificial and natural hybrids are in progress. The results aiming to a better understanding of the defence mechanism involved in the infection control will be presented.

Banana streak virus (BSV) is a badnavirus infecting Musa species and inducing Banana streak disease, affecting plant growth and fruit production. BSV exists under two forms: episomal and/or integrated in host genome (referred as “endogenous BSV”, eBSV). Among these viral integrations, four BSV species (BSGFV, BSIMV, BSOLV, and BSMYV) are known to induce eBSV-derived infections under biotic and abiotic stresses.My PhD project aims to follow eBSV-derived infections kinetics in interspecific Musa hybrids (hosting eBSV sequences), over an entire crop cycle. I used qPCR as a quantitative tool to compare BSV infection between different samples, and across time. Because sequence similarity between eBSV and BSV overcomes 99%, I used relative quantification between infected and healthy samples of the same banana genotype hosting eBSV. I refer the healthy, viral particles-free samples as “calibrator”. Viral DNA amplification in the calibrator was supposed to be constant, since eBSV DNA matrix is stable. However, I observed significant variability in eBSV-DNA amplification among a large population of calibrators. This might result from transitory eBSV-DNA expresssion, not encaspidated and therefore escaping serological diagnostics.This result makes this “calibrator” system unreliable for a diagnostic purpose of low infections in banana plants having viral integrations, as standard IC-PCR (immune-capture) and RCA methods have shown better sensibility. Nevertheless, I still use this protocol in my experiments for relative quantification analysis by including a “buffer area” on both sides of the amplification baseline, reflecting viral DNA amplification variations I observed.

Cultivated bananas mainly stem from intra- and interspecific crosses between two species: Musa acuminata (A genome) and Musa balbisiana (B genome). The B genome harbors viral sequences of Banana streak virus (BSV), inducing the banana streak disease and affecting growth and fruits production. The plantain is a natural hybrid (AAB) containing these integrations. BSV integrations can release functional virus following stresses, leading to spontaneous infections. However, no epidemic has been reported so far. We suspect the plantain to control this viral infection using a RNA silencing mechanism, resulting from the co-evolution between viral integrations and B genome. My PhD work aims to investigate BSV infections in plantain, from eBSV activation to complete recovery (qPCR, immunolabelling); as well as the defense mechanism set up by the host (Northern blot, NGS, in situ hybridization). I aim to propose a BSV infection evolution profile in plantain, to further test the virus transmission to a healthy plant. Indeed, other banana trees among which Cavendish cultivar (AAA, producing “dessert bananas”), without B genome, are extremely susceptible to BSV. The plantain culture intensification, associated with global changes, could threat the dessert bananas culture. My project will help answering this arising question of BSV epidemic risk.

The majority of cultivated bananas are intra and interspecific hybrids of the two main species Musa acuminata (denoted genome A) and Musa balbisiana (denoted genome B). The Banana streak virus (BSV) is responsible of the banana streak mosaic disease and causes severe damage on the Musa acuminata hybrids, which are extremely susceptible. The virus is mealybugs- vector transmitted from plant to plant. Curiously, BSV also exists as endogenous sequences named (eBSV) within all B genomes and can give rise active viruses leading to a systemic infection in banana plants. The banana plantain is a natural triploid interspecific hybrid AAB and harbors viral sequences for two BSV species within its B genome. It spontaneously develops BSV infections following abiotic stresses by releasing active viral genome from eBSVs. However, no epidemic has been reported so far, whereas several plantains regularly show infections in the fields. We suspected that the banana plantain regulates such endogenous viral infections by a gene silencing-based plant defense mechanism resulting from a co-evolution process. Our project aims understanding how this pathosystem works by following after an endogenous infection the kinetic of the virus distribution in the plant via molecular (IC-PCR, qPCR) and histologic (serological detection) markers as well as the small viral RNA profiles involved in gene silencing (TGS, PTGS) via Northern blots, NGS and LNA probes.

To face global warming and fossil fuel depletion crisis, plant biomass will provide a renewable source of energy, materials and chemicals. Accordingly, agriculture will have to adapt not only to avoid competition between food-feed and non-food non-feed uses but also to ensure the economical and environmental sustainability of these productions. In this context, we are developing an integrative strategy merging genetics, breeding, material sciences, energy production, animal nutrition and socio economic analyses to accelerate the development of multipurpose sorghum value chains for both Mediterranean and tropical semi-arid conditions (West Africa). As a first step, new products (biocomposites) and uses (biomethane production) are being developed. Then the plant traits impacting the production and quality of the different end-products and uses are being identified taking advantage of the genetic diversity of sorghum. As a third step, the set-up of these key traits in the plant is being analyzed in order to describe their patterns of development / accumulation, their susceptibility to environmental constraints and provide some insights regarding their molecular determinism. Taking advantage of these functional information, the genomic regions impacting the key traits are being deciphered and used to develop new breeding tools and breeding strategies. In parallel, to maximize the probability to convert scientific results in local impacts, the different stakeholders of the value chains are being mobilized and territorial analyses aiming to assess the relevance of the different value chains are performed.