En Amazonie orientale, l’agriculture familiale contribue significativement à la transformation des écosystèmes forestiers en pâturages. La mise en valeur pastorale se fait généralement de manière monospécifique avec une Poacée pérenne d’origine africaine (Brachiaria brizantha cv. Marandu) qui constitue la principale offre fourragère. Mais les pratiques pastorales mises en oeuvre sur une exploitation conduisent souvent à une dégradation des pâturages, qui se manifeste par une prolifération des plantes adventices. Le pâturage a été modifié par l’introduction de deux Fabacées pérennes fourragères originaires d’Amérique Latine, l’une herbacée (Arachis pintoï cv. Amarelo) et l’autre ligneuse (Leucaena leucocephala). Pendant la saison sèche, nous avons étudié les interactions entre B. brizantha et des Fabacées fourragères implantées. Cette étude est la première approche intégrée (écophysiologie) qui étudie les caractéristiques adaptatives et les effets des Fabacées sur la capacité de résistance à la contrainte hydrique des pâturages à partir des évolutions des échanges gazeux foliaires, du potentiel hydrique et de l’état hydrique du sol. Le dispositif expérimental était composé de cinq parcelles de 100 m2 isolées du bétail correspondant à cinq traitements différents. Les trois espèces étudiées ont été cultivées seules et en association. Trois répétitions ont été réalisées pour chaque traitement afin de valider statistiquement les résultats et prendre en compte la variabilité spatiale du sol. En monoculture, les valeurs de conductances stomatiques de B. brizantha sont relativement élevées au regard des conditions climatiques par rapport à des valeurs habituelles de plantes C4 au champ alors que les valeurs d’assimilations nettes sont celles mesurées couramment. A. pintoï et L. leucocephala possèdent des valeurs de conductances stomatiques et d’assimilations mesurées habituellement sur les plantes C3 au champ. En situation de sécheresse, les trois espèces étudiées en monoculture adoptent un mouvement de fermeture stomatique 30 jours après l’arrêt des pluies et ajustent ainsi leur conductance sur l’épuisement de la réserve utile du sol. Cette stratégie permet le maintien de l’activité photosynthétique indispensable à la survie cellulaire et de maintenir une transpiration suffisante pour réguler leur température. Les trois espèces survivent par évitement de la sécheresse, en réduisant leur surface foliaire active et en fermant leurs stomates dès l’abaissement du potentiel hydrique. B. brizantha a le même comportement lorsqu’il est cultivé seul ou associé à A. pintoï que ce soit au niveau de la conductance stomatique, de l’assimilation de CO2 ou de l’efficience instantanée de l’eau. Cependant, son potentiel hydrique est affecté plus précocement au cours d’un stress hydrique lorsqu’il est en concurrence avec A. pintoï. Dans le cas de cette association, notre étude montre que la présence de B. brizantha a un effet négatif sur les activités photosynthétiques et donc sur la production de biomasse d’A. pintoï, espèce considérée pourtant comme sciaphile. Enfin, les fonctions métaboliques de B. brizantha sont réduites lorsqu’il est associé à L. leucocephala du fait de l’ombrage. L. leucocephala évite la sécheresse en réduisant sa surface foliaire. L’augmentation d’insolation en fin de saison sèche affaiblit cependant les plantes associées aux strates inférieures et réduit la quantité de fourrage disponible sur pied. Nous proposons aux agriculteurs de mettre en place une gestion durable de leurs pâturages par la création d’associations végétales fourragères adaptées aux contraintes biotiques et abiotiques. / In the Eastern Amazon region (Pará, Brazil), smallholder farming significantly contributes to the transformation of the Amazonian rain forest ecosystem into pasture land that typically includes a single species, generally a perennial fodder grass (Poaceae) originating from Africa (Brachiaria brizantha cv. Marandu). Such pastures rapidly lose their sustainability and get invaded by weeds. To prevent these effects, two imported perennial fodder species of the Fabaceae family (Arachis pintoï cv. Amarelo and Leucaena leucocephala Lam.) have been mixed with the African grass Brachiaria and the interrelations between B. brizantha and the Fabaceae species have been studied. In this unique ecophysiological study, plant parameters, such as gas exchange and plant water potential have been correlated with soil parameters, such as soil water content. The final goal was to assess the impact of the Fabaceae plants on pasture tolerance to water deficit. The experimental setting included five treatments applied to 100 m2 fenced plots to keep cattle away. Treatments corresponded to various combinations between the grass and the two Fabaceae species. Three biological repeats were set up for each treatment for statistical significance and in order to account for soil structure variability. In monospecific plots, B. brizantha exhibited stomatal conductance values higher than those expected from typical C4 species whereas net CO2 assimilation rates were normal. A. pintoï and L. leucocephala had usual stomatal conductance values for field-cultivated C3 plants. In response to drought, a general adjustment in stomatal conductance was observed 30 days into the dry season (i.e. without rain), suggesting that the plants limited transpiration rates according to the progressive decrease in soil water content. This strategy allowed them to maintain photosynthetic activities and to supply photosynthates to their tissues while limiting rises in temperatures. Upon exhaustion of soil water cotent, decreases in leaf water potentials were observed and plants escaped drought by reducing their leaf area and by abruptly closing their stomata. Brachiaria’s responses to drought were similar in mixed and monospecific plots regarding stomatal conductance, net CO2 assimilation rate or real-time water efficiency. However, when grown in mixed plots with A. pintoï, Brachiaria’s leaf water potential decreased rapidly after the onset of drought, due to the competition for water. In a A. pintoï ! Brachiaria plot, Brachiaria had a negative impact on A. pintoï photosynthetic activities and biomass production, even though the latter was considered as a shade plant species. On the other hand, Brachiaria metabolic activities were reduced in L. leucocephala ! Brachiaria combinations, due to the interception of light supply by L. leucocephala. L. leucocephala avoided water deficit by reducing leaf area. The resulting increase in light intensity reaching the lower strata, toward the end of the dry season weakened the shortest plants and limited fodder production. In conclusion, we propose that farmers implement pasture sustainability by developing crop mixing, using fodder species adapted to abiotic stresses. Furthermore, our results show that several crop combinations represent viable solutions to the perpetuation of new pastures. Each fodder species presents specific drought adaptation features. Combining them could be beneficial if pastoral pressure was allowed to develop according to the plants tolerance level. Improvements in fodder production and diversity could extend the life-span of smallholder settlements and as a result slow down deforestation

Symbiosis between bacteria and single celled eukaryotes, such as ciliates and amoebae, is a widespread phenomenon. In the past years, the number of species characterizations of symbiotic bacteria, has constantly grown. Especially members of the order Rickettsiales (Alphaproteobacteria), which comprises obligate intracellular human and animal pathogens as well as other non-pathogenic intracellular species, got into the focus. However, biodiversity of both, protists and associated bacterial symbionts, is still largely underestimated. Thus, I hypothesised that different kind of bacteria occur naturally in the ciliate Paramecium, that paramecia can serve as potential reservoir for human and animal pathogens, and that the species distribution of Paramecium and its endosymbionts shows geographical patterns. In the present thesis, I provide data on the distribution and diversity of Paramecium species and their endosymbionts isolated from freshwater and brackish habitats from North and South America. The most frequent species were Paramecium biaurelia, Paramecium caudatum and Paramecium multimicronucleatum for the North American samples as well as P. multimicronucleatum and Paramecium calkinsi for the South American samples indicating geographical differences in the species distribution of Paramecium between the two continents. Monoclonal cultures were screened for the presence of endosymbionts by fluorescence in situ hybridization (FISH) using universal and specific probes. I detected bacterial endosymbionts belonging to different taxa of Rickettsiales sensu lato in Paramecium-cultures isolated from eight different habitats. Moreover, I characterized the four novel endosymbiont species “Candidatus Fokinia solitaria”, “Candidatus Fokinia cryptica”, “Candidatus Bealeia paramacronuclearis” and “Candidatus Jurandia parameciophila”, respectively, presenting detailed descriptions. Thus, I did not only detect various bacterial symbionts in different host species from two continents, but I also identified bacteria related to human and animal pathogens. Moreover, phylogenetic information provided by the four novel bacterial species helped me to revise the taxonomic organisation of the order Rickettsiales, which I split into the two orders Rickettsiales sensu stricto and Holosporales ord. nov. The importance and severity of a symbiosis for its host can be estimated, among others, by studying the symbionts transmission modes. Most host-symbiont systems in nature show a mixed mode of transmission, even if one transmission type occurs only rarely. Moreover, evolution of exclusively vertically or horizontally transmitted symbionts is scarce. However, circumstances for horizontal transmission of many symbiont species so far described as vertically transmitted, are completely unknown and still need to be revealed. Therefore, I assumed that both, vector organisms and environmental stress, can trigger horizontal transmission. I performed different sets of infection experiments using vector organisms and environmental stress factors as driving forces to trigger horizontal transmission. In experiments focused on vector-induced transmission, I was not able to confirm vector properties of Holospora towards Caedibacter, as described towards food bacteria. However, I rarely observed vector-independent horizontal transmission of Caedibacter taeniospiralis towards symbiont-free Paramecium species. The here tested genotypes of C. taeniospiralis might still take advantage of additional horizontal transmission, even if it occurs rarely. In addition, I tested the effect of salinity and temperature stress on the transmission of the recently described bacterial symbionts “Candidatus Megaira polyxenophila” and “Ca. Bealeia paramacronuclearis” as potentially interesting representatives. The involved symbiont and host genotypes differed in their response to the induced environmental stress. Results of horizontal transmission turned out to be ambiguous. While temperature stress did not show any effect on transmission, salinity stress could possibly induce horizontal transmission of “Ca. Megaira polyxenophila” at slightly increased salinity concentrations in regard to normal conditions indicating the significance of environmental stress for the selection of the preferred transmission mode. / Symbiosen zwischen Bakterien und einzelligen Eukaryoten wie Ciliaten und Amöben sind weitverbreit. In den vergangenen Jahren stieg die Anzahl der Artbeschreibungen symbiotisch lebender Bakterien stetig an. Besonders Vertreter der Ordnung Rickettsiales (Alphaproteobacteria), welche obligat intrazelluläre Menschen- und Tierpathogene sowie andere nicht-pathogene, intrazelluläre Arten beinhaltet, rückten in den Fokus. Die Biodiversität von Protisten und mit ihnen assoziierte, bakterielle Symbionten wird jedoch weitestgehend unterschätzt. Daher untersuchte ich, welche verschiedenen Bakterienarten im Ciliaten Paramecium vorkommen, ob Paramecien als potentielles Reservoir für menschen- und tierpathogene Bakterien dienen können und ob die Artverbreitung von Paramecium und seiner Symbionten geographische Muster aufweist. In der vorliegenden Arbeit, präsentiere ich Verbreitungs- und Diversitätsdaten von Paramecium-Arten sowie deren Endosymbionten, welche aus nord- und südamerikanischen Süß- und Brackwasserproben isoliert wurden. Die am häufigsten erfassten Arten in nordamerikanischen Proben waren Paramecium biaurelia, Paramecium caudatum und Paramecium multimicronucleatum, sowie P. multimicronucleatum und Paramecium calkinsi in südamerikanischen Proben. Die identifizierten Arten weisen auf geographische Unterschiede in der Artverteilung der beiden Kontinente hin. Monoklonale Massenkulturen wurden unter Verwendung universeller und spezifischer Sonden mittels Fluoreszenz in situ Hybridisierung auf das Vorhandensein von Endosymbionten überprüft. Dabei entdeckte ich bakterielle Endosymbionten verschiedener Rickettsiales sensu lato-Vertreter in Paramecienkulturen aus acht verschiedenen Habitaten. Darüber hinaus charakterisierte ich die vier neuen Endosymbiontenarten “Candidatus Fokinia solitaria”, “Candidatus Fokinia cryptica”, “Candidatus Bealeia paramacronuclearis” und “Candidatus Jurandia parameciophila” und lieferte detaillierte Artbeschreibungen. Somit erfasste ich nicht nur verschiedene Symbionten in unterschiedlichen Paramecium-Arten der beiden Kontinente, sondern identifizierte auch Bakterien, welche nahe mit relevanten Pathogenen verwandt sind. Die phylogenetischen Informationen, die mir diese vier neuen Bakterienarten lieferten, halfen mir die taxonomische Organisation der Ordnung Rickettsiales zu revidieren, welche ich in die zwei Ordnungen Rickettsiales sensu stricto und Holosporales ord. nov. aufspaltete. Die Bedeutung einer Symbiose für seinen Wirt kann unter anderem durch die Erforschung der Übertragungswege abgeschätzt werden. Die meisten natürlichen Wirt-Symbionten-Systeme zeigen gemischte Übertragungswege, auch wenn eine der Übertragungsarten nur wenig genutzt wird. Ferner tritt eine Evolution hin zu sich ausschließlich vertikal oder horizontal übertragenden Symbionten selten auf. Die Bedingungen, unter denen eine horizontale Übertragung der meisten sich als vertikal übertragend beschriebenen Symbionten stattfindet, sind unbekannt und müssen nach wie vor untersucht werden. Deshalb legte ich meiner Arbeit die Annahme zugrunde, dass sowohl Vektororganisen als auch Umweltstress eine horizontale Übertragung begünstigen können. Ich führte verschiedene Infektionsexperimente durch, in denen ich die Effekte von Vektororganismen und verschiedener abiotischer Stressfaktoren als potenzielle Auslöser für eine horizontale Übertragung untersuchte. In den Experimenten, die sich mit einer Vektor-induzierten Übertragung beschäftigten, konnte ich keine möglichen Vektoreigenschaften von Holospora gegenüber Caedibacter nachweisen, wie sie gegenüber Futterbakterien bekannt sind. In seltenen Fällen beobachtete ich jedoch eine Vektor-unabhängige, horizontale Übertragung von Caedibacter taeniospiralis auf Symbionten-freie Paramecium-Arten. Die hier getesteten C. taeniospiralis-Genotypen sind möglicherweise immer noch dazu in der Lage, die Vorteile einer zusätzlichen horizontalen Übertragung zu nutzen. Zusätzlich testete ich die Effekte von Salz- und Temperaturstress auf die Übertragung der kürzlich beschriebenen, bakteriellen Symbionten “Candidatus Megaira polyxenophila” und “Ca. Bealeia paramacronuclearis” als potentiell interessante Vertreter. Die getesteten Symbionten- und Wirtsgenotypen unterschieden sich hinsichtlich ihrer Reaktion auf den ausgelösten abiotischen Stress. Die erzielten Ergebnisse zur horizontalen Übertragung erscheinen jedoch nicht eindeutig. Während Temperaturstress keine Effekte auf die Übertragung hatte, führte leichter Salzstress zu einer möglichen horizontalen Übertragung von “Ca. Megaira polyxenophila”, was auf die Bedeutung abiotischer Stressfaktoren bei der Wahl des bevorzugten Übertragungsweges hinweist. / Le simbiosi fra batteri ed eucarioti unicellulari, come i ciliati e le amebe, è un fenomeno molto diffuso. Negli anni passati, il numero di descrizioni di specie di batteri simbionti è cresciuto costantemente. In particolare, sono venuti alla ribalta i membri dell’ordine Rickettsiales (Alphaproteobacteria), che comprende patogeni intracellulari obbligati umani e di animali, oltre ad altre specie di batteri intracellulari non patogeni. Comunque, la biodiversità dei protisti e dei batteri simbionti a loro associati è ancora largamente sottostimata. Perciò, è stato ipotizzato che ci siano diversi tipi di batteri che vivono in associatione con il ciliato Paramecium in natura, che I parameci possano fungere da possibili serbatoi naturali per patogeni umani e animali, e che la distribuzione delle specie di Paramecium e dei suoi simbionti presenti dei pattern geografici. Nel presente lavoro di tesi, sono presentati dati sulla distribuzione e diversità di specie del genere Paramecium e dei loro batteri endosimbionti, isolate da ambienti dulciacquicoli e salmastri dal nordamerica e sudamerica. Le specie più frequenti sono state Paramecium biaurelia, Paramecium caudatum e Paramecium multimicronucleatum per i campioni nordamericani, e P. multimicronucleatum e Paramecium calkinsi per i campioni sudamericani, il che indica differenze geografiche nella distribuzione della specie di Paramecium fra I gue continenti. Colture monoclonali sono state saminate per la presenza di endosimbionti tramite ibridazione in situ a fluorescenza (FISH), impiegando sonde universali e specifiche. Sono stati rilevati batteri endosimbionti appartenenti a diversi taxa di Rickettsiales sensu lato in colture di paramecio isolate da otto diversi habitat. Inoltre, sono state caratterizzate quattro nuove specie di endosimbionti, rispettivamente, “Candidatus Fokinia solitaria”, “Candidatus Fokinia cryptica”, “Candidatus Bealeia paramacronuclearis” e “Candidatus Jurandia parameciophila”), fornendo descrizioni dettagliate. Perciò non solo sono stati caratterizzati diversi batteri simbionti in differenti specie di ospiti da due continenti, ma sono anche stati identificati batteri affini a patogeni umani e animali. I dati filogenetici forniti dalle quattro nuove specie mi hanno permesso di revisionare l’organizzazione tassonomica dell’ordine Rickettsiales, che è stato diviso nei due ordini Rickettsiales sensu stricto e Holosporales ord. nov. L’importanza e la severità di una simbiosi per l’ospite può essere stimata studiando le modalità di trasmissione del simbionte. La maggior parte dei sistemi ospite-simbionte in natura presentano una modalità mista di trasmissione, anche se una tipo di trasmissione avviene solo occasionalmente. Inoltre, l’evoluzione di simbionti trasmessi eclusivamente per via verticale o orizzontale è scarsa. Comunque, le circostanze per la trasmissione orizzontale di molti simbionti finora descritti come trasmessi orizzontalmente sono completamente sconosciute, e necessitano di essere rivelate. Perciò, è stato ipotizzato che sia organismi vettori che stress ambientali possano indurre la trasmissione orizzontali. Sono stati eseguiti diversi set di esperimenti di infezione, impiegando organismi vettori e fattori di stress ambientali come agenti che potessero indurre tramissione orizzontale. In esperimenti incentrati sulla trasmissione indotta da vettori, non è stato possibile confermare capacità di vettore da parte di Holospora nei confronti di Caedibacter, come invece descritto nei confronti di batteri a vita libera. Comunque, in rari casi è stata osservata trasmissione orizzontale di Caedibacter taeniospiralis verso specie di Paramecium indipendente dal vettore. I genotipi testati di C. taeniospiralis potrebbero comunque trarre un vantaggio dalla possibilità alternativa di trasmissione orizzontale, anche se questa avviene solo di rado. Inoltre, è stato testato l’effetto dello stress da salinità e temperatura sulla trasmissione dei batteri simbionti recentemente descritti “Candidatus Megaira polyxenophila” e “Ca. Bealeia paramacronuclearis” come rappresentanti potenzialmente interessanti. I genotipi coinvolti di ospiti e simbionti hanno risposto diversamente a fattori indotti di stress ambientale. I risultati sono stati ambigui in termini di trasmissione orizzontale. Mentre lo stress da temperatura non ha mostrato un effetto sulla trasmissione, è stata rilevata una possibile induzione della trasmissione di “Ca. Megaira polyxenophila” in presenza di basso stress salino rispetto alle condizioni normali, indicando l’importanza degli stress ambientali per la selezione della modalità di trasmissione.

While animal steroid hormones are very well known and have been studied for a long time, in plants no steroid substances were known until relatively recently. Only in the second half of the past century brassinosteroids were discovered; later on, their hormonal function in plants was confirmed. Still a lot of unknown remains as regards their function in plant cells. This paper presents in its first part the evidence that brassinosteroids control in maize (Zea mays L.) grown under field conditions not only its morphology and yield but also some developmental/reproduction characteristics like e.g. number of female inflorescences or speed of the development of male inflorescences. Particular response of a plant depends, however, on the type of applied brassinosteroid, its concentration, and last but not least also on a particular maize genotype and developmental stage of the plant during applicatin. Impact of brassinosteroids on primary photosynthetic processes in plants has not been proven under these conditions, neither on the activity of photosystem (PS) I nor on the Hill reaction. No statistically significant differences in the content of photosynthetic pigments have been found either. Another topic dealt with in this thesis is the possible protective influence of brassinosteroids on plants...

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).

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Tesis por compendio / [ES] Durante siglos de cultivo en la Península Ibérica después de su introducción en el siglo XVI, las judías se adaptaron a nuevos entornos, evolucionando numerosas variedades locales. Se evaluaron cultivares españoles locales de Phaseolus lunatus (frijol lima) y su resistencia a la salinidad, en dónde se expusieron las plantas a varios tratamientos de sal, con el fin de evaluar el efecto de la salinidad en el crecimiento y el rendimiento del cultivo. Se observó que el estrés salino redujo el peso fresco de los órganos aéreos, lo que permitió clasificar los cuatro genotipos según su tolerancia a la salinidad. la prolina aumentó en todos los cultivares, más notablemente en el cv. VPH-79, con las concentraciones absolutas más altas registradas en los cultivares más tolerantes a la sal. Estos hallazgos indican que P. lunatus es moderadamente tolerante a la sal y que sus principales mecanismos para adaptarse al estrés salino son el mantenimiento de altas concentraciones de K+ y la acumulación de prolina en las hojas. Por otra parte, se analizaron en invernadero 24 genotipos locales de P. vulgaris de España durante dos temporadas consecutivas. De cada genotipo, se cultivaron cinco plantas y se caracterizaron (17 rasgos cuantitativos y 15 cualitativos) utilizando los descriptores del IBPGR. Los resultados obtenidos indican una alta variabilidad para la mayoría de los rasgos, especialmente los relacionados con el rendimiento y sus componentes. Además, se analizaron las respuestas a los tratamientos por déficit hídrico y estrés salino, en cuanto a inhibición del crecimiento y contenido de prolina foliar (Pro), en 47 genotipos de Phaseolus vulgaris de diferentes orígenes. Para la mayoría de las variables de crecimiento analizadas y Pro, los efectos del cultivo, el tratamiento y sus interacciones fueron altamente significativos (p<0.001); los rasgos morfológicos de las raíces, el diámetro del tallo y el número de hojas se debieron principalmente a una variación incontrolada, mientras que la variación del peso fresco y el contenido de agua de los tallos y las hojas fue inducida claramente por el estrés. Bajo las condiciones experimentales, los efectos promedio del estrés salino sobre el crecimiento de las plantas fueron relativamente más débiles que los del déficit hídrico. . Pro, por su parte, fue la única variable que mostró una correlación negativa con todos los parámetros de crecimiento, pero particularmente con los de tallos y hojas mencionados anteriormente, como lo indican los coeficientes de correlación de Pearson y los PCA. Se propone el uso de Pro como un marcador bioquímico adecuado para exámenes simples, rápidos y a gran escala de genotipos de judía, para excluir los más sensibles, aquellos que acumulan concentraciones más altas de Pro en respuesta a tratamientos de estrés hídrico o salino. Asimismo, se han analizado las respuestas a la salinidad en seis cultivares de judía común: cuatro variedades locales de España y dos líneas experimentales de Cuba. La prolina fue usada para clasificar la tolerancia de los cultivares, Las concentraciones de azúcares solubles totales variaron con los tratamientos y entre los genotipos, pero fue difícil evaluar su papel en la tolerancia al estrés de las plantas analizadas. Los cambios en el contenido de malondialdehído (MDA) no indicaron peroxidación de la membrana inducida por sal como resultado del estrés oxidativo secundario; en consecuencia, no se detectó acumulación de compuestos fenólicos totales y flavonoides, como mecanismo de defensa antioxidante. Estos resultados destacan la confiabilidad del uso de prolina como marcador bioquímico del estrés salino en judía y la importancia del mecanismo relacionado con el transporte de potasio a las hojas para conferir tolerancia al estrés a algunos cultivares de judía. / [CA] Durant segles de cultiu a la Península Ibèrica després de la seva introducció en el segle XVI, les mongetes es van adaptar a nous entorns, evolucionant nombroses varietats locals. Es van avaluar conreessis espanyols locals de garrofó (fesol llima) i la seva resistència a la salinitat, a on es van exposar les plantes a diversos tractaments de sal, per tal d'avaluar l'efecte de la salinitat en el creixement i el rendiment de l'cultiu. Es va observar que l'estrès salí va reduir el pes fresc dels òrgans aeris, el que va permetre classificar els quatre genotips segons la seva tolerància a la salinitat. la prolina augmentar en tots els conreessis, més notablement en el cv. VPH-79, amb les concentracions absolutes més altes registrades en els conreessis més tolerants a la sal. Aquestes troballes indiquen que P. lunatus és moderadament tolerant a la sal i que els seus principals mecanismes per adaptar-se a l'estrès salí són el manteniment d'altes concentracions de K + i l'acumulació de prolina en les fulles. D'altra banda, es van analitzar en hivernacle 24 genotips locals de P. vulgaris d'Espanya durant dues temporades consecutives. De cada genotip, es van conrear cinc plantes i es van caracteritzar (17 trets quantitatius i 15 qualitatius) utilitzant els descriptors de l'IBPGR. Els resultats obtinguts indiquen una alta variabilitat per a la majoria dels trets, especialment els relacionats amb el rendiment i els seus components. A més, es van analitzar les respostes als tractaments per dèficit hídric i estrès salí, pel que fa a inhibició de l'creixement i contingut de prolina foliar (Pro), en 47 genotips de Phaseolus vulgaris de diferents orígens. Per a la majoria de les variables de creixement analitzades i Pro, els efectes de l'cultiu, el tractament i les seves interaccions van ser altament significatius (p <0.001); els trets morfològics de les arrels, el diàmetre de la tija i el nombre de fulls es van deure principalment a una variació incontrolada, mentre que la variació de l'pes fresc i el contingut d'aigua de les tiges i les fulles va ser induïda clarament per l'estrès. Sota les condicions experimentals, els efectes mitjana de l'estrès salí sobre el creixement de les plantes van ser relativament més febles que els de el dèficit hídric. . Pro, per la seva banda, va ser l'única variable que va mostrar una correlació negativa amb tots els paràmetres de creixement, però particularment amb els de tiges i fulles esmentats anteriorment, com ho indiquen els coeficients de correlació de Pearson i els PCA. Es proposa l'ús de Pro com un marcador bioquímic adequat per a exàmens simples, ràpids i a gran escala de genotips de mongeta, per excloure els més sensibles, aquells que acumulen concentracions més altes de Pro en resposta a tractaments d'estrès hídric o salí. Així mateix, s'han analitzat les respostes a la salinitat en sis conreessis de mongeta comú: quatre varietats locals d'Espanya i dues línies experimentals de Cuba. La prolina va ser usada per a classificar la tolerància dels conreessis, Les concentracions de sucres solubles totals van variar amb els tractaments i entre els genotips, però va ser difícil avaluar el seu paper en la tolerància a l'estrès de les plantes analitzades. Els canvis en el contingut de malondialdehid (MDA) no van indicar peroxidació de la membrana induïda per sal com a resultat de l'estrès oxidatiu secundari; en conseqüència, no es va detectar acumulació de compostos fenòlics totals i flavonoides, com a mecanisme de defensa antioxidant. Aquests resultats destaquen la fiabilitat de l'ús de prolina com a marcador bioquímic de l'estrès salí en jueva i la importància de l'mecanisme relacionat amb el transport de potassi a les fulles per conferir tolerància a l'estrès a alguns conreessis de mongeta. / [EN] During centuries of cultivation in the Iberian Peninsula after their introduction in the 16th century, beans adapted to new environments, evolving numerous landraces.In this study was also evaluated the resistance to salinity of several local Spanish cultivars of Phaseolus lunatus L. (lima bean). Plants were subjected to various salt treatments and growth and biochemical parameters were determined. It was observed that salt stress reduced the fresh weight of aerial organs, which allowed us to classify the four genotypes according to their tolerance to salinity. In addition, proline increased in all cultivars, most notably in cv. VPH-79, with the highest absolute concentrations recorded in the most salt tolerant cultivars. These findings indicate that P. lunatus is moderately salt tolerant and that its main mechanisms for adapting to salt stress are the maintenance of high K+ concentrations and proline accumulation in leaves. In studies conducted in this research project, 24 landraces of P. vulgaris from Spain were analyzed in greenhouses during two consecutive seasons. From each genotype, five plants were grown and characterized for 17 quantitative and 15 qualitative traits using IBPGR descriptors. . The results obtained indicate high variability for most of the traits, especially those related to yield and its components. On the other hand, this study analyzed the responses to water deficit and salt stress treatments, in terms of growth inhibition and leaf proline (Pro) content, in 47 Phaseolus vulgaris genotypes of different origins. For most of the growth variables analyzed and Pro, the effects of cultivar, treatment and their interactions were highly significant (p <0.001); root morphological traits, stem diameter and number of leaves were mainly due to uncontrolled variation, whereas variation in fresh weight and water content of stems and leaves was clearly induced by stress. Under our experimental conditions, the average effects of salt stress on plant growth were relatively weaker than those of water deficit. . Pro, in turn, was the only variable that showed a negative correlation with all growth parameters, but particularly with those of stems and leaves mentioned above, as indicated by Pearson's correlation coefficients and PCAs. We propose the use of Pro as a biochemical marker suitable for simple, rapid, large-scale screening of bean genotypes to exclude the most sensitive, those that accumulate higher concentrations of Pro in response to water or salt stress treatments. In addition, responses to salinity were analyzed in six common bean cultivars: four local varieties from Spain and two experimental lines from Cuba. Proline was used to rank the relative tolerance of the cultivars. Concentrations of total soluble sugars varied with treatments and among genotypes, but it was difficult to assess their role in stress tolerance of the plants tested.. Changes in malondialdehyde (MDA) content did not indicate salt-induced membrane peroxidation as a result of secondary oxidative stress; consequently, accumulation of total phenolic compounds and flavonoids, as an antioxidant defense mechanism, was not detected. These results highlight the reliability of the use of proline as a biochemical marker of salt stress in common beans and the importance of the mechanism related to potassium transport to leaves in conferring stress tolerance to some common bean cultivars. / Arteaga Castillo, SM. (2021). Cultivos para el cambio climático: selección y caracterización de variedades de judía (Phaseolusvulgaris L.) y Phaseolus lunatus tolerantes a la sequía y salinidad [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/168450 / Compendio

The ability of plants to sense and respond to environmental and endogenous signals is essential to their growth and development. As part of these diverse cellular functions, ubiquitin-mediated proteolysis has emerged to be an important process involved in how plant signalling pathways can be regulated in response to such cues. Of the three enzymes involved in linking ubiquitin to protein targets, E3 ubiquitin ligases are of interest as they confer substrate specificity during this ubiquitination process. The overall focal point of this research is on plant U-box (PUB) E3 ubiquitin ligases, a family that has undergone a large gene expansion possibly attributable to the regulation of biological processes unique to the plant life cycle. In Arabidopsis there are 64 predicted PUBs, many for which biological roles have yet to be determined. And as research continues to uncover PUB functions, the functional diversity in the gene family will likely expand. Specifically the focus of this research is on characterizing two ARM repeat-containing PUBs – AtPUB18 and AtPUB19. General analysis of pub18 and pub19 T-DNA insertion lines for growth defects did not yield distinct altered phenotypes. Closer inspection of selected lines showed independent gene assortment phenotypes that, with further inordinately convoluted pursuit, proved to have an AtPUB18/19-unrelated outcome. The availability of Arabidopsis microarray databases provided exploratory expression profiling as a starting point to elucidate PUB function. AtPUB19 and closely related AtPUB18 are notable for their increased expression during abiotic stresses. While condition-directed germination assays showed a decreased sensitivity to salt and ABA for pub18 pub19 double insertion lines, no related change in susceptibility to these or other abiotic stress treatments were seen with condition-directed root growth assays. Thus, this preliminary work has begun to reveal insight into the complex abiotic stress-related roles AtPUB18 and AtPUB19 have during mediation of environmental stress acclimation in Arabidopsis.

The ability of plants to sense and respond to environmental and endogenous signals is essential to their growth and development. As part of these diverse cellular functions, ubiquitin-mediated proteolysis has emerged to be an important process involved in how plant signalling pathways can be regulated in response to such cues. Of the three enzymes involved in linking ubiquitin to protein targets, E3 ubiquitin ligases are of interest as they confer substrate specificity during this ubiquitination process. The overall focal point of this research is on plant U-box (PUB) E3 ubiquitin ligases, a family that has undergone a large gene expansion possibly attributable to the regulation of biological processes unique to the plant life cycle. In Arabidopsis there are 64 predicted PUBs, many for which biological roles have yet to be determined. And as research continues to uncover PUB functions, the functional diversity in the gene family will likely expand. Specifically the focus of this research is on characterizing two ARM repeat-containing PUBs – AtPUB18 and AtPUB19. General analysis of pub18 and pub19 T-DNA insertion lines for growth defects did not yield distinct altered phenotypes. Closer inspection of selected lines showed independent gene assortment phenotypes that, with further inordinately convoluted pursuit, proved to have an AtPUB18/19-unrelated outcome. The availability of Arabidopsis microarray databases provided exploratory expression profiling as a starting point to elucidate PUB function. AtPUB19 and closely related AtPUB18 are notable for their increased expression during abiotic stresses. While condition-directed germination assays showed a decreased sensitivity to salt and ABA for pub18 pub19 double insertion lines, no related change in susceptibility to these or other abiotic stress treatments were seen with condition-directed root growth assays. Thus, this preliminary work has begun to reveal insight into the complex abiotic stress-related roles AtPUB18 and AtPUB19 have during mediation of environmental stress acclimation in Arabidopsis.