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Second-generation biofuels could provide renewable energy while reducing the globaleconomy dependence on oil and mitigating climate change. However, their greenhouse gasemission balances, as well as their energy and environmental balances, are discussed,especially when they are produced from agricultural feedstock. The use of agriculturalfeedstock for energy purposes also raises the issue of competition with food production. Inthis context, this work contributes to the assessment of the sustainability of Miscanthus xgiganteus, a perennial C4 crop candidate to the production of second-generation ethanol. Theobjectives of this work are (i) to achieve a multicriteria evaluation of cropping systems basedon M. Giganteus using data collected in farmers’ fields and (ii) to compare these croppingsystems with cropping systems including other resources Agricultural candidates for biofuelproduction. The main contributions of this work are (i) the study of the variability of yieldsand winter nitrate losses in a network of commercial fields located in Burgundy (France), (ii)the characterization by modeling of M. giganteus long-term yield evolution and (iii) theintegration of these findings in a process of cropping systems design and assessment aimingat comparing M. giganteus with other feedstock candidate to the production of bioethanol.The study of M. giganteus in farmers’ fields shows that the high variability of yields andnitrate losses is linked to (i) crop age, (ii) soil type and (iii) the type of field (i.e. culturalhistory, size, shape, and environment). Contrasting yield scenarios, built by combining datacollected in commercial fields with a long-term yield evolution model, show that thesensitivity of assessment results regarding yields depends on the assessment field. Theinsertion of M. giganteus in a cropping system can significantly improve the greenhouse gasemission balance as well as the environmental balance, compared with a cropping systembased on a short cropping sequence. Economic results depend strongly on M. giganteus yield.Other agricultural feedstocks are also interesting, especially on soils where the yield potentialof M. giganteus is low: this is particularly the case of alfalfa stems, which can be used forsecond-generation ethanol production. / Second-generation biofuels could provide renewable energy while reducing the globaleconomy dependence on oil and mitigating climate change. However, their greenhouse gasemission balances, as well as their energy and environmental balances, are discussed,especially when they are produced from agricultural feedstock. The use of agriculturalfeedstock for energy purposes also raises the issue of competition with food production. Inthis context, this work contributes to the assessment of the sustainability of Miscanthus xgiganteus, a perennial C4 crop candidate to the production of second-generation ethanol. Theobjectives of this work are (i) to achieve a multicriteria evaluation of cropping systems basedon M. Giganteus using data collected in farmers’ fields and (ii) to compare these croppingsystems with cropping systems including other resources Agricultural candidates for biofuelproduction. The main contributions of this work are (i) the study of the variability of yieldsand winter nitrate losses in a network of commercial fields located in Burgundy (France), (ii)the characterization by modeling of M. giganteus long-term yield evolution and (iii) theintegration of these findings in a process of cropping systems design and assessment aimingat comparing M. giganteus with other feedstock candidate to the production of bioethanol.The study of M. giganteus in farmers’ fields shows that the high variability of yields andnitrate losses is linked to (i) crop age, (ii) soil type and (iii) the type of field (i.e. culturalhistory, size, shape, and environment). Contrasting yield scenarios, built by combining datacollected in commercial fields with a long-term yield evolution model, show that thesensitivity of assessment results regarding yields depends on the assessment field. Theinsertion of M. giganteus in a cropping system can significantly improve the greenhouse gasemission balance as well as the environmental balance, compared with a cropping systembased on a short cropping sequence. Economic results depend strongly on M. giganteus yield.Other agricultural feedstocks are also interesting, especially on soils where the yield potentialof M. giganteus is low: this is particularly the case of alfalfa stems, which can be used forsecond-generation ethanol production.

Lentil (Lens culinaris Med.) is an important component of the human diet in the world, but in the meantime, Europe produces only 26% of the lentils it consumes. This is partly due to strong agronomic weaknesses that reduce yield such as lodging, bruchid beetles and weeds, especially in organic farming. Intercropping, the simultaneous growing of two or more species in the same field is tested here as an option to reduce these drawbacks and develop organic lentil production. The aims of this thesis were to (1) assess the potential of lentil-spring wheat intercrops to produce organic lentil, (2) understand the mechanisms that explain their performances, and (3) evaluate the profitability of such intercrops. A two-year field experiment was carried out in southwestern France in 2015 and 2016 under organic farming rules. Four lentil and two wheat cultivars were grown as sole crops and intercrops in multiple additive and substitutive designs. Our results showed that the total intercrop attainable grain yield was higher than the mean of sole crops. Yet, lentil yield in intercrop was lower than in sole crop as the result of a strong competition for resources from wheat in early lentil growth stages reducing the number of branches per plant of lentil. This led to lower gross margins of intercrops. However, lentil lodging was strongly reduced in intercrops thus its mechanical harvest efficiency increased. This led to similar mechanically harvested yields of lentil in intercrop and sole crop. Consequently, after mechanical harvest and grain cleaning, the marketable gross margin of intercrops was higher than that of sole crops. Our results suggest that (1) intercrop had no effect on bruchids, (2) the most effective intercrop is when lentil is at sole crop density and wheat at 15-20%, (3) intercrop performance is due to complementary use of N pools through legume N2 fixation and (4) the intensity of interspecific interactions depends on year, wheat density and genotypes. Our work indicates that lentil-spring wheat intercrop can develop organic lentil production but a better understanding of Genotype x Environment x Cropping system interactions may be useful to design optimized managements.

La demande mondiale de nourriture et d’energie est en constante augmentation. L’accès à de nouvelles terres arables étant limité, les agriculteurs devront produire environ 70% de plus par hectare d'ici 2050. L'optimisation et la rationalisation des systèmes de production agricole sont essentielles pour assurer la sécurité alimentaire des populations dans des conditions durables. La communauté agricole serait en mesure d'optimiser les performances des cultures en ayant accès à une meilleure compréhension des systèmes de production, notamment concernant leur potentiel et principaux facteurs limitants. Dans ce contexte, la caractérisation des conditions de croissance des cultures prenant en compte leurs impacts sur le potentiel de production et sur les pertes de rendement est importante pour identifier les marges de progrès et proposer des systèmes agricoles améliorés.Dans cette étude une approche est proposée pour caractériser l'environnement de grandes zones géographiques prenant en compte les impacts des ressources clés au développement des plantes (température, rayonnement, eau et azote) sur la performance des cultures. Le niveau de disponibilité de ces ressources a été estimé en utilisant des approches de modélisation de culture, intégrant données météorologiques et caractéristiques de sol. L'efficacité d'utilisation des ressources disponibles a été caractérisée par les pratiques culturales ainsi que la stratégie et l’environnement technique des agriculteurs. Une procédure générique d’intégration de la donnée a été établie et utilisée pour décrire la production de maïs grain en Amérique du Nord de 1991 à 2013. Le jeu de données résultant de cette intégration couvre 84% des superficies plantées en maïs, décrites par 1 558 unités spatiales élémentaires, pour un total de 28 303 scénarios indépendants. Cette méthode combine et harmonise les observations de rendement issues des statistiques agricoles avec un large ensemble de descripteurs pertinents de conditions de croissance.Un sous-ensemble de 21 facteurs limitants a été identifié par une analyse de sélection de variables pour expliquer 66% de la variabilité des pertes de rendement observées. Compte tenu du nombre de dimensions du jeu de donnée, la méthode relaxed lasso a été choisie comme un compromis intéressant entre capacité de prédiction et d’interprétation. Les descripteurs sélectionnés montrent la contribution de la gestion des cultures à la variabilité des pertes de rendement, en particulier les niveaux d'intensification de l’agriculture et l’environnement technique des agriculteurs. Le troisième facteur principal est la disponibilité en eau et la sécheresse qui en résulte. L’utilisation des connaissances en physiologie dans la conception de descripteurs a considérablement amélioré la capacité d’interprétation de la proposition et la confiance des utilisateurs finaux dans l'approche.La structure des facteurs limitant le rendement a été utilisée pour identifier les Environnements Types les plus fréquents. Deux approches ont été proposes : l’une axée uniquement sur les facteurs physiologiques et l’autre intégrant également l’identification de marchés de taille homogène. 11 Environnements Types ont été identifiés en fonction des facteurs physiologiques et 8 en combinant facteurs physiologiques et contraintes de taille de marché. Les Environnements Types basés sur les facteurs physiologiques sont très informatifs sur l'évolution historique des pratiques culturales et les changements de stratégie des agriculteurs au cours du temps. Une telle catégorisation des conditions de croissance a montré des capacités à reproduire l'expertise de terrain et à soutenir l'évaluation de génotypes. Trois cas d'utilisation ont servi à illustrer l'intérêt de l'approche pour (i) décrire l'historique environnemental d'un marché, (ii) définir des populations d’Environnements cibles (TPE) et (iii) évaluer la pertinence de l'échantillonnage environnemental de réseaux multi-lieux (MET). / The global demand for food and energy is constantly increasing. As access to spare arable land is limited, growers will have to produce about 70% more per hectare by 2050. Optimization and rationalization of the agricultural production systems is then critical to ensure food security under sustainable conditions. The agricultural community would be in a position to optimize crop performance by better understanding the cropping systems, especially regarding potential production and limiting factors. In this context, the ability to characterize crop growing conditions in regards to their impacts on potential yield and yield gap is important in order to identify margins of progress and propose improved farming systems.An approach is proposed to characterize the crop environment of large geographical areas taking into consideration the impact on crop performance of the key resources for plant development (temperature, solar radiation, water and nitrogen). The level of availability of each resource was estimated by using crop modeling approaches integrating weather data and soil characteristics as inputs. The efficiency of use of the available resources was characterized by crop practices, grower strategy and grower technical environment. A generic integration procedure was established and used to describe corn production for grain in North America from 1991 to 2013. The resulting dataset covers 84% of the total corn planted area, deciphered in 1,558 elementary spatial units, for a total of 28,303 independent scenarios. Such a method combines and harmonizes, at scale, yield observations from agricultural statistics with a large set of relevant descriptors of growing conditions.A subset of 21 main limiting factors was identified through variable-selection analysis to explain 66% of the observed yield-gap variability. The relaxed lasso method resulted in an interesting compromise between interpretability and prediction ability. The selected descriptors highlighted the contribution of crop management in yield-gap variability, especially regarding levels of crop intensification and the technical environment of growers. The third main factor is water availability and resulting drought. The integration of knowledge in crop physiology into descriptor design significantly improved the interpretability of the proposal and the confidence of end-users in the approach.Yield-gap patterns were used to identify the set of most frequent Environment Types. Two approaches were proposed: one focused on crop physiology drivers and another also considered market-size homogeneity among Environment Types. This resulted in 11 Environment Types based on crop physiology drivers and 8 Environment Types when combining crop physiology drivers and market constraints. Crop-physiology Environment Types are very informative on the historical evolution of cultural practices and the changes in grower strategies over the studied period. Such categorization of growing conditions demonstrated the ability to reproduce field expertise and support genotype evaluation. Three business Use Cases were used to illustrate the interest of the approach in (i) describing the environmental history of a market, (ii) defining relevant Target Population Environments (TPE) and (iii) evaluating the environmental sampling relevance of Multi-Environment Trials (MET).

La lentille (Lens culinaris Med.) est une composante importante des régimes alimentaires de nombreuses populations à travers le monde mais sa consommation en Europe est relativement faible. L’Europe produit seulement 26% de sa consommation de lentille et ce déficit est en partie causé par d’importants verrous agronomiques comme la verse, les bruches et la compétition des adventices qui réduisent ses rendements, notamment en agriculture biologique. Les associations de cultures, définies comme la culture simultanée d’au moins deux espèces différentes sur une même surface pendant une durée significative, sont considérées comme une option pour lever ces verrous agronomiques et ainsi développer la production de lentille en agriculture biologique. Les objectifs de cette thèse étaient de (1) évaluer le potentiel des associations de lentille et de blé de printemps pour produire de la lentille en conditions d’agriculture biologique et (2) comprendre les principaux mécanismes sous-jacents à la performance des associations. Des essais agronomiques ont été mis en place en 2015 et 2016 en conditions d’agriculture biologique. Quatre variétés de lentille et de blé de printemps ont été conduites en culture pures et en plusieurs associations de type substitutif et additif. Nos résultats montrent que le rendement moyen des associations avant récolte mécanique était plus élevé que le rendement moyen des cultures pures. Néanmoins, le rendement de lentille en association était inférieur à celui de la lentille en culture pure en raison d’une compétition forte et précoce du blé pour les ressources qui a causé la diminution nombre de ramifications par plante de la lentille. Le prix de la lentille étant environ quatre fois plus élevé que celui du blé, la marge brute des associations avant récolte était inférieure à celle de la lentille en culture pure. Cependant, la verse de la lentille a été fortement réduite en association, entrainant une augmentation de l’efficacité de sa récolte mécanique. En conséquence les rendements de lentille issus de la récolte mécanique se sont avérés similaires en association et en culture pure. Enfin, après tri et nettoyage des graines, la marge brute des associations sur le rendement commercialisable était supérieure à celle des cultures pures. Nos résultats montrent que (1) les associations n’ont pas eu d’effet sur le taux de bruchage des lentilles, (2) l’association la plus performante est constituée de lentille à densité équivalente à la culture pure dans laquelle on ajoute 15-20% de blé, (3) la performance des associations est due à une utilisation complémentaire de l’azote rendue possible par la fixation symbiotique de l’azote par la lentille et (4) l’intensité des compétitions entre espèces dépendent de l’année, de la densité de blé et des génotypes. En conclusion, nos travaux indiquent que les associations de lentille et de blé de printemps peuvent permettre de développer la production de lentille en agriculture biologique mais qu’une meilleure compréhension des interactions de type génotype x environnement x conduite pourrait permettre de mettre au point des couverts encore plus performants. / Lentil (Lens culinaris Med.) is an important component of the human diet in the world, but in the meantime, Europe produces only 26% of the lentils it consumes. This is partly due to strong agronomic weaknesses that reduce yield such as lodging, bruchid beetles and weeds, especially in organic farming. Intercropping, the simultaneous growing of two or more species in the same field is tested here as an option to reduce these drawbacks and develop organic lentil production. The aims of this thesis were to (1) assess the potential of lentil-spring wheat intercrops to produce organic lentil, (2) understand the mechanisms that explain their performances, and (3) evaluate the profitability of such intercrops. A two-year field experiment was carried out in southwestern France in 2015 and 2016 under organic farming rules. Four lentil and two wheat cultivars were grown as sole crops and intercrops in multiple additive and substitutive designs. Our results showed that the total intercrop attainable grain yield was higher than the mean of sole crops. Yet, lentil yield in intercrop was lower than in sole crop as the result of a strong competition for resources from wheat in early lentil growth stages reducing the number of branches per plant of lentil. This led to lower gross margins of intercrops. However, lentil lodging was strongly reduced in intercrops thus its mechanical harvest efficiency increased. This led to similar mechanically harvested yields of lentil in intercrop and sole crop. Consequently, after mechanical harvest and grain cleaning, the marketable gross margin of intercrops was higher than that of sole crops. Our results suggest that (1) intercrop had no effect on bruchids, (2) the most effective intercrop is when lentil is at sole crop density and wheat at 15-20%, (3) intercrop performance is due to complementary use of N pools through legume N2 fixation and (4) the intensity of interspecific interactions depends on year, wheat density and genotypes. Our work indicates that lentil-spring wheat intercrop can develop organic lentil production but a better understanding of Genotype x Environment x Cropping system interactions may be useful to design optimized managements.