Legumes fix atmospheric nitrogen (N) via symbiotic biological N fixation where part of the N fixed by legumes can be transferred to non-legumes. Identification of genotypic variability for N transfer among different legume cultivars enables improving N transfer to non-legumes under mixed stands. Six diverse red clover (RC) cultivars which include three diploid (AC Christie, Tapani and CRS15) and three tetraploid (Tempus, CRS18, CRS39) were selected to evaluate genotypic variability for N transfer. The above RC cultivars were characterized for root hair deformation, nodulation, growth, and N uptake under different levels of N supply during the growing period and for starter N supply under in vitro conditions. Significant genotypic differences among the RC cultivars were found for the above attributes where the cultivars responded differently to N applications during early growth. The above RC cultivars were also evaluated for root exudate N content in the form of NO3--N, NH4+-N and dissolved organic N (DON) during early growth under in vitro conditions. Significant genotypic differences were found for root exudate inorganic and organic N content. In general, root exudate DON content was greater than the inorganic N content and positively correlated with average nodule dry weight and shoot N concentration. The NH4+-N and NO3--N content in root exudates were positively correlated with active nodule number and root growth parameters respectively. Nitrogen fixation, N transfer ability and soil N profiles of the above six RC cultivars were evaluated with bluegrass under field conditions for two post establishment years. Significant genotypic differences were found for N fixation and transfer but, these attributes were not associated with the ploidy nature of the selected RC cultivars. Generally, N transfer increased as the season and production year advanced. Soil mineral N and potential N leaching were affected differently by the RC cultivars included in this study under mixed stands, thus showing genotypic differences for soil N cycling. The results of investigations in this thesis highlight the dynamics of N flow between legumes and companion grasses and may assist in developing management protocols and plant breeding strategies to identify genotypes with efficient N cycling profiles.

Au vu de l’impact croissant du changement climatique global et en particulier de la sécheresse sur les forêts, il est nécessaire de comprendre les mécanismes de réponse des arbres face à des variations de disponibilité en eau. Ces dernières années, des études ont montré un contrôle épigénétique et notamment par la méthylation de l’ADN de la plasticité phénotypique des plantes en réponse aux variations environnementales. Dans ce contexte, cette thèse visait à évaluer le rôle de la méthylation de l’ADN des cellules du méristème apical caulinaire dans la plasticité développementale de la tige feuillée en réponse à des variations de disponibilité en eau chez le peuplier, un arbre modèle. A cette fin, le méthylome de la chromatine non condensée dans le méristème apical caulinaire de Populus trichocarpa a été caractérisé. Ensuite, l’impact de variations de disponibilité en eau sur la méthylation de l’ADN a été étudié dans l’apex caulinaire de différents hybrides (P. × euramericana). Les loci et les réseaux de gènes affectés pour leur expression et leur méthylation ont ainsi été identifiés. Ces travaux ont montré que dans le méristème apical caulinaire, la majorité des gènes étaient dans un état non condensé de la chromatine et méthylés dans leur corps. Ils ont également mis en évidence une forte variation de la méthylation globale de l’ADN selon les génotypes et en réponse à des variations de disponibilité en eau. De plus, des corrélations ont été établies entre les niveaux de croissance des arbres et de méthylation globale de l’ADN dans l’apex caulinaire. Enfin, les variations de la méthylation de l’ADN en réponse aux variations de la disponibilité en eau s’accompagnent de variations d’expression et ont ciblé particulièrement des gènes impliqués dans la signalisation par les phytohormones ou la morphogenèse. Ainsi, les travaux effectués lors de cette thèse suggèrent un rôle de la méthylation de l’ADN dans la plasticité phénotypique en réponse à des variations de disponibilité en eau chez le peuplier via le contrôle de l’expression de réseaux de gènes dans le méristème apical caulinaire. / Predicted climate changes and particularly drought represent a major threat to forest health. Therefore, understanding mechanisms that control trees response to variations in water availability is of great interest. These last years, epigenetic marks such as DNA methylation have been involved in plant phenotypic plasticity in response to environmental stresses. In this context, this work aimed at assessing the role of shoot apical meristem cells DNA methylation in the shoot developmental plasticity towards variations in water availability in poplar, a model tree. For this purpose, the methylome of non condensed chromatin in Populus trichocarpa shoot apical meristem was characterized. Then, the impact of variations in water availability on shoot apex DNA methylation in different hybrids (P. × euramericana) was studied. Loci and gene networks affected by DNA methylation and expression changes were thus identified. This work showed that in shoot apical meristem, most of the genes was in non condensed chromatin state with DNA methylation in their body. A strong variation in DNA methylation depending on genotypes and water availability was highlighted. Moreover, correlations between trees growth and shoot apex DNA methylation levels were established. Lastly, DNA methylation changes in response to variations in water availability correlated to expression variations were identified for genomic loci and gene networks. Thus, the work performed during this thesis suggests a role for DNA methylation in poplar phenotypic plasticity in response to variations in water availability through the control of gene networks transcription in the shoot apical meristem.