<p>Flowering is a critical step in the plant life cycle. If flowering occurs too early or too late, seed production suffers. Flowering is regulated through numerous flowering repressors. As long as these repressors persist, the plant will remain in a vegetative growth stage. Some plants possess two separate genetic pathways, the autonomous pathway and the vernalization pathway, that promote the transition to flowering through stable downregulation of flowering repressors. Once the plant achieves floral competence, it will flower under inductive environmental conditions.</p> <p>In <i>Arabidopsis</i>, <i>FCA</i> is a key autonomous pathway gene, acting with <i>FY</i> to promote the floral transition. Recently, gene sequences resembling <i>FCA</i> were cloned from hexaploid wheat (<i>Triticum aestivum</i>) and designated as <i>WFCA</i>. WFCA shows numerous similarities to the FCA peptide, especially regarding three key regions: two RNA Recognition Motifs and the WW domain. This study seeks to determine if <i>WFCA</i> genes function similar to <i>FCA</i> by determining if they are able to complement the <i>fca-1</i> mutant of <i>Arabidopsis thaliana</i>.</p> <p>T1 progeny from an <i>Arabidopsis fca-1</i> plant transformed with <i>WFCA</i> were grown without vernalization and assayed for the final leaf number (FLN). The late flowering <i>fca-1</i> control plants bolted with an average FLN of 14.8 while the T1 population had an average FLN of 14.3. Although the numerical difference is slight, the results are statistically significant, and suggest that <i>WFCA</i> genes may have some degree of flowering promotion activity in <i>Arabidopsis</i>. The lack of strong complementation may be due to divergence of the <i>WFCA</i> genes from their <i>Arabidopsis</i> counterparts. With increasing evidence for divergence in flowering promotion between monocot and dicot species, the development of a robust monocot model system appears to be critical to provide a good framework to assist studies of the particular nuances of the monocot flowering process.</p>

<p>Flowering is a critical step in the plant life cycle. If flowering occurs too early or too late, seed production suffers. Flowering is regulated through numerous flowering repressors. As long as these repressors persist, the plant will remain in a vegetative growth stage. Some plants possess two separate genetic pathways, the autonomous pathway and the vernalization pathway, that promote the transition to flowering through stable downregulation of flowering repressors. Once the plant achieves floral competence, it will flower under inductive environmental conditions.</p> <p>In <i>Arabidopsis</i>, <i>FCA</i> is a key autonomous pathway gene, acting with <i>FY</i> to promote the floral transition. Recently, gene sequences resembling <i>FCA</i> were cloned from hexaploid wheat (<i>Triticum aestivum</i>) and designated as <i>WFCA</i>. WFCA shows numerous similarities to the FCA peptide, especially regarding three key regions: two RNA Recognition Motifs and the WW domain. This study seeks to determine if <i>WFCA</i> genes function similar to <i>FCA</i> by determining if they are able to complement the <i>fca-1</i> mutant of <i>Arabidopsis thaliana</i>.</p> <p>T1 progeny from an <i>Arabidopsis fca-1</i> plant transformed with <i>WFCA</i> were grown without vernalization and assayed for the final leaf number (FLN). The late flowering <i>fca-1</i> control plants bolted with an average FLN of 14.8 while the T1 population had an average FLN of 14.3. Although the numerical difference is slight, the results are statistically significant, and suggest that <i>WFCA</i> genes may have some degree of flowering promotion activity in <i>Arabidopsis</i>. The lack of strong complementation may be due to divergence of the <i>WFCA</i> genes from their <i>Arabidopsis</i> counterparts. With increasing evidence for divergence in flowering promotion between monocot and dicot species, the development of a robust monocot model system appears to be critical to provide a good framework to assist studies of the particular nuances of the monocot flowering process.</p>

Shoot morphogenesis in Eucalyptus occidentalis and Metrosideros excelsa was analysed at the morphological, physiological and molecular levels to understand the regulation of phase change and the floral transition. Study of the regulation of these developmental plant processes is limited in woody species due to their long juvenile phase. Six ecotypes of E. occidentalis were grown to two predetermined architectures (free branching or single stem). Free branching plants of ecotype 13648 displayed adult shoot phenology (lanceolate leaves) earlier than single stem counterparts. In addition, changes in leaf morphology in free branching plants were accompanied with changes in leaf anatomy and gas exchange signifying that in E. occidentalis complexity of shoot architecture had a significant effect on rate of phase change. Flowering was observed in all but one ecotype irrespective of architecture demonstrating that vegetative phase change and floral transition are temporally uncoupled in this species. To understand the floral transition at the molecular level in E. occidentalis, partial homologues of the inflorescence meristem identity gene TERMINAL FLOWER1 and floral meristem identity genes LEAFY and APETALA1 were isolated. The expression patterns of these meristem identity genes during development of free branching and single stem plants were analysed by quantitative real-time PCR. Increased levels of expression of EOLFY and EOAP 1 (relative to α -TUBULIN) were displayed at more proximal nodes in free branching plants than in single stem plants. Elevated floral meristem identity gene expression levels correlated with flower initiation. Further, effects of architecture and environment on gene expression were monitored in E. occidentalis. The overriding effect of shoot architecture on the floral transition was observed under warm long day and ambient environments. Elevated levels of EOLFY and EOAP 1 were correlated with floral bud score and EOAP1 was found to be a reliable marker of floral transition in E. occidentalis. Low levels of EOTFLI expression were detected in buds irrespective of their position on the plant leading to the suggestion that this might have contributed to the precocious flowering observed in this species. In contrast to E. occidentalis, M excelsa attained adult shoot phenology (pubescent leaves) faster when grown as single stem plants than as free branching plants. It appears that growth as height is required for vegetative phase change in this species. However, floral transition occurred only once single stem plants were allowed to branch. Vegetative phase change and the transition to flowering seem to be coordinated in this species with the former being a pre-requisite for the latter.

La transition florale résulte d’un jeu complexe d’interactions entre des signaux endogènes et environnementaux. Les feuilles jouent un rôle crucial dans ce processus en percevant les changements associés à la lumière et en produisant les photosynthétats qui participant à la signalisation de la floraison. Toutefois, notre connaissance des changements se produisant dans les feuilles lors de la transition florale reste limitée. Nous avons caractérisé les événements morphologiques, moléculaires et transcriptionnels en relation avec la floraison florale dans les feuilles matures chez Arabidopsis, en exploitant un système de transfert de conditions en jours courts vers des jours longs, transfert qui permet d’induire et synchroniser la floraison. Nous avons identifié la fenêtre temporelle de la transition florale, mesuré la croissance foliaire, et observé un accroissement de la ploïdie au cours du processus. Par une approche de RNA-seq, nous avons étudié la dynamique transcriptionnelle des réseaux de gènes dans la feuille, et comparé avec des données dans la racine et le méristème pour avoir une vue plus intégrée de la floraison dans la plante. De plus, nous avons analysé le mode d’action de LHP1 (LIKE HETEROPROTEIN 1), une sous unité du complexe PRC1, en exploitant des lignées transgéniques avec des modifications conditionnelles du dosage de LHP1 et en analysant les effets sur la chromatine et la transcription des gènes impliqués dans la floraison. Une modulation courte du dosage en LHP1 modifie le dépôt des marques H3K27me3 et H3K4me3, démontrant une interaction fonctionnelle entre LHP1 et le complexe PRC2, et suggérant aussi un nouveau rôle dans la formation de régions chromatiniennes de type bivalent. Enfin, étant donné le rôle clé de l’organisation nucléaire dans la régulation génique, nous avons recherché et identifié des déterminants de l’architecture nucléaire en utilisant de nouveaux outils de statistiques spatiales. / The transition to flowering results from a complex interplay between endogenous and environmental cues. The leaves play a key role in this process, by perceiving the light changes and producing photosynthates, which participate to the floral signalling. However, our knowledge on the changes occurring in leaves during floral transition is still limited. We characterised the morphological, molecular and transcriptional events related to floral transition in mature leaves in Arabidopsis, using a short-day to long-day shift to induce a synchronized flowering. We identified the temporal window of the floral transition, monitored the leaf growth and observed an increase in their ploidy level during the process. By RNA-seq we studied the transcriptional dynamics of the leaf gene network, and compared with events occurring in roots and meristems to get an integrated view of floral transition in the whole plant. Furthermore, we investigated the mode of action of LIKE HETEROPROTEIN 1 (LHP1), a PRC1 subunit, by exploiting transgenic lines with conditional alterations of LHP1 dosage and analysing the effects on chromatin and transcription of flowering genes. A short-term modulation of LHP1 dosage altered the deposition of H3K27me3 and H3K4me3, showing a functional interaction between LHP1 and PRC2, and also suggesting a new role in the formation of bivalent chromatin regions. Finally, since nuclear organisation plays a key role in gene regulation, we searched and identified determinants of the nuclear architecture by using innovative spatial statistical tools.

La transition florale est un évènement clef dans la vie d’une plante. Chez le fraisier, la compréhension des mécanismes génétiques de cette transition est un enjeu majeur pour mieux contrôler la production de fruits. La transition florale peut être étudiée à travers la remontée florale, qui est la capacité d’une plante à fleurir tout au long de la période végétative. Le fraisier cultivé octoploïde, F. x ananassa, comme le fraisier diploïde, F. vesca, présentent des génotypes remontants capables de fleurir en continu. L’objectif de cette thèse est de comprendre le déterminisme génétique et moléculaire de la remontée florale chez Fragaria. Ce travail a montré que chez les fraisiers diploïde et octoploïde, le caractère ‘remontée florale’ est contrôlé par deux verrous génétiques différents localisés à des positions non orthologues. Chez le fraisier diploïde, le gène FvKSN responsable de la remontée florale a été identifié et code pour un homologue du répresseur floral TFL1. Chez les génotypes remontants, ce gène présente une délétion dans la partie codante conduisant à une protéine non fonctionnelle, incapable de réprimer la floraison. Chez le fraisier octoploïde, le QTL majeur détecté contrôlant la remontée florale est lié à la production de stolons de manière antagoniste, suggérant l’existence d’une région génomique où s'exerce une compétition entre multiplication végétative et la reproduction sexuée. Cette région génomique comprend plusieurs gènes candidats intéressants dont FT, activateur de la floraison.Une hypothèse suggérée par ce travail est que chez le fraisier, l’alternance entre phase végétative et phase reproductive est liée à l’équilibre entre les gènes FvKSN, homologue de TFL1, et FvFT, homologue de FT. La remontée florale serait la conséquence d’une modification de cet équilibre entre ces deux gènes en faveur du développement reproductif. / The floral transition is a key event in plant life. In strawberry, understanding the genetic mechanisms of floral transition is a major issue for better control of fruit production. This transition is studied through the continuous flowering, which is the ability to flower throughout the growing season. Both, the octoploid cultivated strawberry, F. x ananassa, as the woody diploid strawberry, F. vesca, displayed continuous flowering genotypes. The objective of this work is to decipher the genetic and molecular mechanism of the continuous flowering in Fragaria.This work has shown that in diploid and octoploid strawberry the continuous flowering is controlled by two different genetic 'keys' located at non-orthologous position. In diploid strawberry, the gene FvKSN responsible of continuous flowering was identified and encodes a homologous to the TFL1 floral repressor. In the continuous flowering genotypes, this gene has a deletion in the coding region leading to a nonfunctional protein unable to repress flowering. In the octoploid strawberry, the major QTL controlling both the recurrent flowering and the runner production was identified. These traits were antagonist, which suggests competition between vegetative propagation and sexual reproduction in this region. This genomic region contains several interesting candidate genes whose FT, an activator of flowering.A hypothesis could be proposed. In strawberry, the switch between vegetative and reproductive phase is linked to balance between two genes, FvKSN, homologous to TFL1 and FvFT homologous to FT. Continuous flowering would be the consequence of balance modification between this two genes to the benefit of floral development.

Cyclic nucleotide-gated channels (CNGCs) are non-selective cation channels that were first identified in vertebrate photosensory and olfactory neurons. Although the physiological roles and biophysical properties of animal CNGCs have been well studied, much less is known about these channels in plants. The Arabidopsis genome encodes twenty putative CNGC subunits that are postulated to form channel complexes that mediate various physiological processes involving abiotic and biotic stress responses, ion homeostasis and development. The identification of Arabidopsis autoimmune CNGC mutants, such as defense no death class (dnd1 and dnd2), and the constitutive expressor of pathogenesis related genes 22 (cpr22) implicate AtCNGC2, 4, 11 and 12 in plant immunity. Here, I present a comprehensive study of the molecular mechanisms involved in CNGC-mediated signaling pathways with emphasis on pathogen defense. Previously, a forward genetics approach aimed to identify suppressor mutants of the rare gain-of-function autoimmune mutant, cpr22, identified key residues that are important for CNGC subunit interactions and channel function. First, I present a structure-function analysis of one of these suppressor mutants (S58) that revealed a key residue in the cyclic nucleotide binding domain involved in the stable regulation of CNGCs. Second, I present a new suppressor screen using AtCNGC2 T-DNA knockout mutants that specifically aimed to identify novel downstream components of CNGC-mediated pathogen defense signaling. In this screen, I successfully isolated and characterized the novel Arabidopsis mutant, repressor of defense no death 1 (rdd1), and expanded this study to demonstrate its involvement in AtCNGC2 and AtCNGC4-mediated signal transduction. Additionally, I demonstrated for the first time, the physical interaction of AtCNGC2 and AtCNGC4 subunits in planta. The findings presented in this thesis broaden our current knowledge of CNGCs in plants, and provide a new foundation for future elucidation of the structure-function relationships and signal transduction mediated by these channels.

Cyclic nucleotide-gated channels (CNGCs) are non-selective cation channels that were first identified in vertebrate photosensory and olfactory neurons. Although the physiological roles and biophysical properties of animal CNGCs have been well studied, much less is known about these channels in plants. The Arabidopsis genome encodes twenty putative CNGC subunits that are postulated to form channel complexes that mediate various physiological processes involving abiotic and biotic stress responses, ion homeostasis and development. The identification of Arabidopsis autoimmune CNGC mutants, such as defense no death class (dnd1 and dnd2), and the constitutive expressor of pathogenesis related genes 22 (cpr22) implicate AtCNGC2, 4, 11 and 12 in plant immunity. Here, I present a comprehensive study of the molecular mechanisms involved in CNGC-mediated signaling pathways with emphasis on pathogen defense. Previously, a forward genetics approach aimed to identify suppressor mutants of the rare gain-of-function autoimmune mutant, cpr22, identified key residues that are important for CNGC subunit interactions and channel function. First, I present a structure-function analysis of one of these suppressor mutants (S58) that revealed a key residue in the cyclic nucleotide binding domain involved in the stable regulation of CNGCs. Second, I present a new suppressor screen using AtCNGC2 T-DNA knockout mutants that specifically aimed to identify novel downstream components of CNGC-mediated pathogen defense signaling. In this screen, I successfully isolated and characterized the novel Arabidopsis mutant, repressor of defense no death 1 (rdd1), and expanded this study to demonstrate its involvement in AtCNGC2 and AtCNGC4-mediated signal transduction. Additionally, I demonstrated for the first time, the physical interaction of AtCNGC2 and AtCNGC4 subunits in planta. The findings presented in this thesis broaden our current knowledge of CNGCs in plants, and provide a new foundation for future elucidation of the structure-function relationships and signal transduction mediated by these channels.

[ES] El tiempo de floración es uno de los caracteres más importantes que influyen en la productividad y el rendimiento de los cultivos. La identificación de compuestos sintéticos que sean bioactivos en el control de la inducción floral es de gran interés. Su identificación podría permitirnos ajustar el tiempo de floración en los cultivos, adaptándolos a las condiciones ambientales más favorables. Para identificar estos compuestos, hemos tomado dos enfoques diferentes: un cribado genético químico y la caracterización del metaboloma de transición floral. En primer lugar, realizamos un rastreo de genética química para identificar moléculas pequeñas que tengan el potencial de controlar la expresión del florígeno, FLOWERING LOCUS T (FT) o la actividad o señalización de FT en Arabidopsis. Para ello, hemos utilizado plantas transgénicas que expresan el gen ß-GLUCURONIDASE (GUS) bajo el control del promotor FT para probar una librería de 360 moléculas preseleccionadas. Los resultados positivos obtenidos se volvieron a analizar mediante un cribado secundario basado en la expresión del gen reportero LUCIFERASE (LUC) bajo el control del promotor FT. Utilizando este enfoque, hemos identificado una molécula que induce con éxito la floración en condiciones de cultivo in vitro. En segundo lugar, hemos caracterizado la función del ácido pipecólico (Pip), una molécula previamente identificada como candidata a regular la floración. Hemos confirmado que las mutaciones en las enzimas responsables de la biosíntesis de Pip muestran una alteración en la respuesta del tiempo de floración. Además, hemos identificado un nuevo papel del Pip relacionado con el crecimiento y el tamaño de la roseta de Arabidopsis. Finalmente, utilizamos un sistema inducible basado en el promotor de CONSTANS (CO) que controla la expresión del gen endógeno de CO fusionado con el receptor de glucocorticoides de rata (CO::GR). De manera que con un solo tratamiento con dexametasona podemos inducir la floración. Con este sistema, realizamos un estudio del metaboloma de muestras de ápices y hojas mediante técnicas de metabolómica dirigida, lipidómica, cuantificación hormonal y transcriptómica. La integración de estos conjuntos de datos ómicos nos ha permitido identificar rutas metabólicas que se encuentran alteradas durante la transición floral. A su vez, la caracterización de mutantes de pérdida de función que codifican enzimas clave de esas vías metabólicas, reveló que algunos de estos mutantes mostraban un fenotipo afectado para el tiempo de floración. Entre ellos, nos enfocamos en la caracterización de los genes relacionados con el metabolismo de la rafinosa, un oligosacárido de reserva. Mutantes afectados en el gen RAFFINOSE SYNTHASE 5 (RS5) presentan un fenotipo de floración temprana y fertilidad reducida. En base a los resultados obtenidos, proponemos un modelo en el que, durante la transición floral, se produce una reestructuración de las ratios entre carbohidratos sencillos (monosacáridos y disacáridos) y de reserva, como la rafinosa. Estos cambios podrían ser modulados por el ácido abscísico (ABA) y por genes relacionados con la floración, desencadenando cambios en el metabolismo de la trehalosa y promoviendo una expresión temprana de FT. / [CA] El temps de floració és un dels caràcters amb més influència en la productivitat i el rendiment dels cultius. La identificació de compostos sintètics bioactius per al control de la inducció floral és de gran interés, ja que la seua identificació podria permetre ajustar el temps de floració dels cultius, aspecte que podria contribuir a l'adaptació a condicions ambientals més favorables. Per a identificar aquests compostos, hem portat a terme dues aproximacions diferents: un garbellat genètic químic i la caracterització del metaboloma de la transició floral. En primer lloc, hem realitzat un cribratge genètic-químicper a identificar xicotetes molècules amb potencial per a controlar l'expressió del florígen, FLOWERING LOCUS T (FT) o l'activitat o la senyalització de FT a Arabidopsis. Per a portar a terme aquest cribratge, hem utilitzat plantes transgèniques que expressen el gen ß-GLUCURONIDASE (GUS) sota el control del promotor de FT amb les quals hem assajat una llibreria de 360 molècules preseleccionades de manera prèvia. Els resultats positius obtinguts en aquest cribratge t s'han sotmés a un cribratge secundari basat en l'expressió del gen reporter LUCIFERASE (LUC) sota el control del promotor FT. La utilització d'aquesta primera aproximació ha permés la idenfiticació d'una molècula que indueix amb èxit la floració en condicions de cultiu in vitro. En En segon lloc, hem caracteritzat la funció de l'àcid pipecòlic (Pip), una molècula prèviament identificada com a candidata a regular la floració. Aquesta aproximació ens ha permet confirmar que mutacions als enzims responsables de la biosíntesi de Pip comporten una alteració al temps de floració. A més, en aquest treball hem identificat un nou paper del Pip relacionat amb el creixement i la grandària de la roseta d'Arabidopsis. Finalment, hem utilitzat un sistema induïble basat en el promotor de CONSTANS (CO) que controla l'expressió del gen endogen de CO fusionat al receptor de glucocorticoides de rata (CO::GR). Aquesta construcció ens proporciona una ferramenta amb la qual induir la floració amb un sol tractament amb dexametasona. A continuació, hem realitzat un estudi del metaboloma de mostres d'àpexs i fulles mitjançant tècniques de metabolòmica dirigida, lipidómica, quantificació hormonal i transcriptòmica. La integració d'aquest conjunt de dades ómiques ens ha permés identificar les rutes metabòliques que es troben alterades durant la transició floral. Al mateix temps, la caracterització de mutants de pèrdua de funció que codifiquen enzims clau per a aquestes rutes metabòliques, ha revelat que alguns d'aquests mutants mostren un fenotip afectat pel que fa al temps de floració. Dintre dels mutants analitzats, ens hem centrat en la caracterització dels gens relacionats amb el metabolisme de la rafinosa, un oligosacàrid de reserva. Els mutants del gen RAFFINOSE SYNTHASE 5 (RS5) presenten un fenotip de floració primerenca i fertilitat reduïda. Sobre la base dels resultats obtinguts, proposem un model en el qual, durant la transició floral, es produeix una reestructuració de les ràtios entre carbohidrats senzills (monosacàrids i disacàrids) i de reserva, com la rafinosa. Aquests canvis podrien ser modulats per l'àcid abscísic (ABA) i per gens relacionats amb la floració, i desencadenariencanvis al metabolisme de la trehalosa, així com la generació de l'expressió primerenca de FT. / [EN] Flowering time is one of the most important traits affecting crop productivity and yield. The identification of natural or synthetic bioactive compounds for the control of flowering induction is of great interest. The identification of compounds with the potential to regulate flowering could allow us to fine-tune flowering responses in crops and adapt them to the changing environmental conditions. To identify these compounds, we have taken two different approaches: a chemical genetic screening and the characterization of the metabolome of floral transition. First, we performed a chemical genetic screening to identify small molecules that have the potential to control the expression of the florigen FLOWERING LOCUS T (FT) or FT activity or signaling in Arabidopsis. We used transgenic plants expressing the ß-GLUCURONIDASE gene (GUS) under the control of the FT promoter to test a preselected library of 360 molecules. Positive hits were retested by a secondary screening based on the expression of the LUCIFERASE (LUC) reporter gene under the control of the FT promoter. Using this approach, we have identified one molecule that successfully induces flowering under in vitro culture conditions. Secondly, we have characterized the function of pipecolic acid (Pip), a molecule previously identified as a candidate to regulate flowering time. We have confirmed that mutations in enzymes responsible for Pip biosynthesis display an altered flowering response. A new role for Pip in rosette growth is also revealed in this work. Finally, we used an inducible system based on the promoter of CONSTANS (CO) driving the expression of CO fused to the rat glucocorticoid receptor (CO::GR). Such a construction provides a tool to induce flowering with a single dexamethasone treatment. We then performed a comprehensive metabolomic study of the shoot apex and leaf samples that included targeted metabolomics, lipidomics, hormone quantification, and transcriptomics. Integration of these omic datasets has allowed us to point out metabolic pathways that are altered during floral induction. Characterization of loss-of-function mutants coding key enzymes of those metabolic pathways revealed that some of these mutants showed a flowering time phenotype. Among them, we focused on the characterization of the contribution of the raffinose metabolism, a storage oligosaccharide, to the determination of flowering time. Mutants affecting RAFFINOSE SYNTHASE 5 (RS5) exhibit an early flowering phenotype and reduced fertility. We propose a model in which the balance between simple and storage carbohydrates in the apex changes during floral induction. This change could be modulated by ABA and flowering-related genes, and it triggers changes in trehalose metabolism, promoting flowering by an early FT upregulation. / Praena Tamayo, J. (2022). Identification of Bioactive Molecules in the Control of Flowering Time [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/185177