La fusariose des épis est l’une de maladies les plus dommageables des céréales tempérées et est principalement causée par le champignon toxinogène Fusarium graminearum (Fg). Ces dix dernières années, de nombreuses études ont rapporté l’induction transcriptionnelle de gènes de la plante codant pour des cytochromes P450 (P450) en réponse l’infection par Fg. Les P450s constituent une famille enzymatique impliquée dans de nombreuses voies métaboliques, certaines avec des intérêts potentiels dans la résistance face aux maladies. Nous avons utilisé la petite graminée modèle Brachypodium distachyon (Bd) pour caractériser fonctionnellement le premier gène codant pour un P450 induit chez la plante au cours de la fusariose des épis par l’utilisation de lignées altérées dans la séquence ou l’expression du gène Bradi1g75310 codant le P450 BdCYP711A29. Nous avons montré qu’en plus d’être un facteur de sensibilité à la maladie, le gène Bradi1g75310 est impliqué dans une voie de biosynthèse hormonale chez Bd, celle des strigolactones (SLs). En effet, en plus de complémenter génétiquement les phénotypes aériens de la lignée mutante max1-1 d’Arabidopsis thaliana altérée dans le gène homologue MAX1 (AtCYP711A1), une lignée de Bd surexprimant Bradi1g75310 (lignée OE) exsude davantage d’orobanchol, une SL spécifique, que la lignée sauvage ou mutante. Une analyse préliminaire de l’impact direct de l’orobanchol sur la croissance de Fg semble indiquer une activation des étapes précoces du développement du champignon (germination) qui pourrait être à l’origine de l’induction plus rapide de gènes de défenses observée chez une lignée OE de Bradi1g75310. Nous avons également montré que les 4 paralogues de Bradi1g75310 chez Bd, qui codent également pour des CYP711A, sont tous capable de complémenter la lignée max1-1 et avons généré du matériel végétal fondamental pour la poursuite de l’étude de la diversification des SLs chez la plante monocotylédone modèle Bd. Au global, ce projet constitue une première étape dans la caractérisation de l’implication des P450 dans la réponse de la plante face à l’infection par Fg en plus de donner de nouveaux indices concernant le rôle des SLs dans les interactions plante-pathogène. Les résultats obtenus au cours de ce travail de thèse pourront permettre l’amélioration de caractères tant développementaux que de résistance à la fusariose chez les céréales cultivées. / Fusarium Head Blight (FHB) is one of the most important diseases of temperate cereals and is mostly caused by the toxin producing-fungus Fusarium graminearum (Fg). This last decade, several studies reported the transcriptional activation of cereal cytochrome P450-encoding genes (P450s) in response to Fg infection. P450s constitute an enzymatic family participating in very diverse metabolic pathways with potential interest for disease resistance. We used the model temperate cereal Brachypodium distachyon (Bd) to functionally characterize the first FHB-induced P450- encoding gene using Bd lines altered in the locus or gene expression of the Bradi1g75310 gene encoding the BdCYP711A29 P450. We showed that in addition to be a plant susceptibility factor towards the disease, the Bradi1g75310 gene is involved in the hormonal biosynthetic pathway of strigolactones (SLs) in Bd. Indeed, in addition to genetically complement the shoot phenotypes of the Arabidopsis thaliana mutant line for the homologous gene MAX1 (AtCYP711A1, max1-1 line), a Bd linewhich overexpresses the Bradi1g75310 gene (OE) exudes more orobanchol, a specific SL, compared to wild-type or mutant lines. Preliminary analysis of the direct impact of orobanchol on Fg growth suggests an activation of early fungal development (germination) likely to induce faster induction of defense-related genes during FHB, observed in Bradi1g75310 OE line. We showed that the four paralogs of Bradi1g75310 encoding BdCYP711A P450s are all able to genetically complement max1-1 line and provide important plant material for studying SLs diversification in the model monocot B. distachyon. Overall, this project constitutes a first step in the characterization of P450s involvement in plant response towards Fg infection in addition to give new evidences about the role of SLs in plant-pathogen interactions. Results obtained during this Ph.D. project will allow the improvement of both developmental and FHB-related traits in cereal crops.

Rapid range expansion of newly invasive species provides a unique opportunity for studying patterns of dispersal and gene flow. In this thesis, I examined the effect of landscape features on gene flow in the invasive grass Brachypodium sylvaticum at the edge of its expanding range. I used genome-wide Single Nucleotide Polymorphism (SNP) surveys of individuals from 22 locations in the Clackamas Watershed in the Portland, Oregon metropolitan region to assess genetic diversity and structure, to identify putative source populations, and to conduct landscape genetic analyses. Resistance surfaces were created for each landscape feature, using ResistanceGA to optimize resistance parameters. My STRUCTURE analysis identified three distinct clusters, and diversity analyses support the existence of at least two local introductions. Multiple Regression on distance Matrices (MRM) showed no evidence that development, roads, canopy cover, or agriculture had a significant influence on genetic distance in B. sylvaticum. The effect of geographic distance was marginal and reflected geographic clustering. The model of rivers acting as a conduit explained a large portion of variation in genetic distance. Results indicate that rivers influence patterns of dispersal of B. sylvaticum by human recreational activity centering on use of rivers, and possibly due to movement of deer.

Brachypodium distachyon è stato recentemente proposto come pianta modello per le Triticeae che includono frumento e orzo. L’obbiettivo del presente studio è stato quello di identificare regioni genomiche associate con la resistenza quantitativa alla ruggine fogliare in Brachypodium. Le malattie causate dalle ruggini fogliari causano ingenti perdite in termini di produzione delle specie cerealicole. Una popolazione di 110 individui F2 è stata sviluppata incrociando due linee inbred di Brachypodium e una mappa di linkage di marcatori AFLP è stata create. La mappa di linkage consiste di 192 loci AFLP in dieci gruppi di linkage, e copre una lunghezza pari a 1,231 Kosambi cM. Allo scopo di identificare loci coinvolti nella resistenza quantitativa sulla mappa, i 110 individui F2 sono stati valutati per la loro reazione alla ruggine fogliare allo stadio di plantula e a quello adulto. Per confermare i risultati delle piante F2, le rispettive famiglie F3 sono state studiate per la loro resistenza alla ruggine fogliare in due esperimenti indipendenti. Due loci genomici sembrano essere maggiormente coinvolti nella resistenza. / Brachypodium distachyon has been proposed as a model species for the tribe of the Triticeae, which includes wheat and barley. The objective of our study was to identify the genomic regions associated with quantitative resistance to leaf rust in Brachypodium. Leaf rust diseases cause significant reductions annually in yield of cereal crops worldwide. An F2 mapping population of 110 individuals was generated between two Brachypodium inbred lines and a AFLP-based linkage map was developed. The linkage map consists of 192 AFLP loci in ten linkage groups, and spans a total genetic length of 1,231 Kosambi cM. To locate quantitative resistance loci on the map, the 110 F2 plants were evaluated for their reaction to the leaf rust at both seedling and adult plant stages. To improve QTL identification, F2-derived F3 families were studied for resistance to leaf rust in two independent experiments. Two major genomic regions involved in resistance to leaf rust were detected.

Submitted by Marco Antônio de Ramos Chagas (mchagas@ufv.br) on 2017-03-29T11:29:28Z No. of bitstreams: 1 texto completo.pdf: 890046 bytes, checksum: c64c252fc31992d05ef9ec060e3b832d (MD5) / Made available in DSpace on 2017-03-29T11:29:28Z (GMT). No. of bitstreams: 1 texto completo.pdf: 890046 bytes, checksum: c64c252fc31992d05ef9ec060e3b832d (MD5) Previous issue date: 2015-07-17 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Fontes de energia alternativas e sustentáveis têm recebido enorme atenção devido ao aumento dos preços, da esgotabilidade e dos problemas ambientais associados ao petró- leo, tornando a produção de biocombustíveis de segunda geração um objeto de grande interesse internacional. As gramíneas são as principais fontes destes biocombustíveis, e Brachypodium distachyon foi eleita um modelo para o estudo das gramíneas. Plantas em estágio juvenil foram avaliadas após o tratamento por duas semanas com metil jas- monato (MJ) ou ácido salicílico (AS) (ambos 100 μM). Os dois tratamentos reduziram o alongamento foliar, provavelmente resultante do efeito da inibição da elongação celu- lar e divisão celular associadas com o aumento do ácido ferúlico (FA), ácido p- cumárico (p-CA) e ABA, e com a redução no teor de AIA. A aplicação de MJ e AS também produziu vários efeitos na parede celular das folhas, como o aumento da celu- lose (MJ), xilose, arabinose e galactose (ambos tratamentos), aumento das razões arabi- nose/celulose (AS) e parede celular/massa seca total (MJ), e redução do teor de lignina (AS). Em paralelo a estas mudanças, houve aumento de fenóis solúveis totais, ácido cafeico e naringerina (para ambos tratamentos), e ácido sinápico (AS). Estas alterações não foram explicadas por mudanças na expressão de 12 genes da rota de biossíntese da parede estudados. A aplicação de AS reduziu em 15% a eficiência da sacarificação en- zimática. Este efeito foi fortemente correlacionado negativamente com o aumento de FA, p-CA, e arabinose, mas não se correlacionou com o teor de lignina. Embora o tra- tamento com MJ tenha aumentado os teores de FA e p-CA, este efeito foi contraposto pelo simultâneo aumento da celulose. Os resultados obtidos demonstram a importância do AS e do MJ para a regulação dos componentes e da digestibilidade da parede celu- lar, e a influência dos metabólitos secundários na recalcitrância da parede à sacarificação. / Renewable and sustainable sources of energy have received a lot of attention, due to the price fluctuations and environmental issues associated with the depletion of oil re- serves, prompting worldwide interest in the production of second generation biofuels. Grass species are the main biomass resources used in biofuel production, and Brachy- podium distachyon was described as a model species for grasses and cereals. Juvenile plants were analyzed after two weeks treatment with methyl jasmonate (MJ) or salicylic acid (SA) (both at 100 μM). Both treatments reduced leaf growth rate, probably be- cause of an inhibitory effect on cellular elongation and division, caused by an increase in ferulic acid (FA), p-coumaric acid (p-CA) and ABA, and lower levels of IAA. Modi- fications in cell wall compounds were observed mainly in leaf tissues, such as an in- crease of cellulose (MJ), xylose, arabinose and galactose (both treatments), arabi- nose/cellulose ratio (SA), and cell wall/biomass ratio (MJ), and reduction of lignin con- tent (SA). There was an increase in total phenolic content, cafeic acid and narigenin (for both treatments), and in sinapic acid (SA). Alterations of these compounds could not be related to the expression of 12 genes involved in cell wall biosynthesis. The ap- plication of SA reduced in 15% the saccharification yield. This effect was strongly neg- ative correlated with higher levels of FA, p-CA and arabinose, but was not associated with lignin content. MJ treatment also increased the levels of FA and p-CA, but chang- es in saccharification yield were not observed, possibly caused by an increase in cellu- lose content. These results show the importance of SA and MJ in the regulation of cell wall compounds and digestibility, and the influence of secondary metabolites in cell wall saccharification recalcitrance. / Dissertação enviada pela secretaria do curso por e-mail, em 28-03-17

Ultraviolet –B (UV-B) radiation is an abiotic stress that has significant effects on plant growth, development, and gene regulation. Due to the depletion of the stratospheric ozone layer over the past several decades, the amount of UV-B light that is reaching the earth’s surface has significantly increased. As a result, research over the past few decades on the effects of UV-B light on plant growth, development, and the mechanisms that regulate a plant’s protection and survival against UV-B light has grown greatly. Brachypodium distachyon is a relatively new model system and one that has not been extensively studied. The aim of this study was to determine the UV-B dose time required to elicit a significant increase in phenolic content, while subsequently assessing protein production to qualitatively implicate whether or not the experimental dosage of UV-B administered was initiating a UV-B specific or non-specific response. In addition, this research annotated the genes that encode the protein sequences for UVR8 and CHS proteins to see if B. distachyon possessed the necessary proteins to undergo a UV-B specific response similar to that of Arabidopsis. The results of the study show that in response to artificial UV-B light, the dose time of UV-B required to elicit a significant increase in total phenolic content is 2 hours. The data also shows an increase in total protein content after 4 hours of UV-B exposure. In addition to the metabolic data, computational analysis of chalcone synthase (CHS) and UV-RESISTANCE LOCUS 8 (UVR8) revealed that there are seven genes in B. distachyon that encode the protein transcripts for CHS and CHS-like proteins, and two genes that code for UVR8 proteins. The results of this study suggest that the UV-B dose regimen used in this study may be initiating the non-specific UV-B signaling pathway. In addition, the presence of UVR8 and CHS protein sequences suggest that B. distachyon has the capacity to work through the UV-B specific signaling pathway.

Understanding the biotic factors influencing invasive plant performance is essential for managing invaded land and preventing further exotic establishment and spread. I studied how competition between both conspecifics and native co-habitants and arbuscular mycorrhizal fungal (AMF) impacted the success of the invasive bunchgrass Brachypodium sylvaticumin early growth stages. I examined whether invasive plants performed and competed differently when grown in soil containing AMF from adjacent invaded and noninvaded ranges in order to determine the contribution of AMF to both monoculture stability and spread of the invasive to noninvaded territory. I also directly manipulated common mycelial network (CMN) formation by AMF to determine hyphal network contribution to competitive interactions. I found that invasive plants performed most poorly (as indicated by decreased chlorophyll content, size and shoot dry mass) in invaded range soil against conspecifics. This could be two-pronged evidence for existing biotic pressure on the invasives to expand into adjacent noninvaded ranges. I also found a negative effect of AMF colonization and invasive plant performance, potentially indicating deleterious plant-soil feedbacks which could help maintain plant biodiversity at a community level. CMN effects were found to be interactive with root competition and directly affected the performance and nutrient status of B. sylvaticum. Although no direct correlations between AMF colonization levels and competition were found, CMN presence contributed significantly to plant growth and nutrient status. Therefore AMF, through infection and CMN formation, may be able to influence invasive plant growth and spread in the field.

No description available.

Lignocellulosic biomass is one of the most abundant raw materials on earth that can be utilized to created carbon-neutral biofuels as a replacement for conventional fossil fuels. In order to create ideal energy crops, the regulation and deposition of cell wall polysaccharides must first be fully understood. Improved understanding of cell wall regulation will enable selection of traits that can optimize biofuel feedstocks. Herein, I utilize the grass model system Brachypodium distachyon in order to understand the transcriptional regulation of secondary cell wall deposition. Gene expression profiling was used to elucidate transcription factors that regulate secondary cell wall biosynthesis. Through this method, WALL REGULATOR INTERACTING bHLH (WRIB) was identified and its role as a secondary cell wall regulator was tested. Yeast-one- and yeast-two-hybrid assays showed that WRIB is capable of binding to promoters of secondary cell wall biosynthesis genes, as well as interacting with known secondary cell wall transcription factor proteins and also Phytochrome B. These results suggest that WRIB plays an important role in the secondary cell wall regulatory network and could perhaps be modulated by Phytochrome B. Discovery of this novel and interesting gene furthers the overall understanding of secondary cell wall development with the goal of improving our ability to engineer biofuel feedstocks.

La récente définition de Brachypodium distachyon comme modèle des graminées en fait un organisme de choix pour l’étude de leur paroi cellulaire, en particulier dans le cadre de leur utilisation comme matière première renouvelable pour le bioéthanol de seconde génération. Les lignines, dont les trois unités (H, G et S) proviennent de la polymérisation des monolignols, sont associées aux acides hydroxycinnamiques dans la paroi des céréales et représentent l’obstacle majeur à l’exploitation industrielle de la biomasse lignocellulosique. L’acquisition de connaissances sur les mécanismes dirigeant leur mise en place et leur organisation permettrait d’identifier des facteurs modulant les rendements de production qui y sont associés. Quatre familles de gènes ont été étudiées et l’implication dans la voie de biosynthèse des monolignols de trois gènes a été montrée : BdF5H2 possède une activité férulate-5-hydroxylase permettant la synthèse des précurseurs des unités S des lignines, BdCOMT3 est l’isoforme principale des acide cafféique O-Méthyltransférases et sa perte partielle de fonction cause une diminution de la quantité de lignine, la modification du rapport S/G et une baisse de quantité d’acide p-coumarique dans deux lignées mutantes indépendantes. Enfin, BdCAD1 est l’isoforme principale des alcools cinnamylique déshydrogénases : sa perte de fonction dans deux lignées indépendantes cause la diminution de la quantité globale de lignine et d’acide p-coumarique, une baisse du rapport S/G ainsi que l’accumulation de sinapaldéhyde. Par ailleurs ces deux lignées présentent des rendements de saccharification augmentés de plus d’un quart par rapport au sauvage. / Brachypodium distachyon was recently adopted as an experimental model for grass species. As such, it is used to study grass cell wall, in particular in the context of their use as renewable feedstock for the production of second generation bioethanol. Lignins are polymers of three main units (H, G and S) originating from the polymerization of monolignols, and are linked to hydroxycinnamic acids in grasses. They constitute the main bottleneck to industrial processes targeting lignocellulosic biomass and improving the understanding of the mechanisms directing their structure and deposition could lead to the identification of the factors modulating associated production yields. Four gene families were studied and the involvement of three genes in the monolignols biosynthetic pathway was shown: BdF5H2 displays a ferulate-5-hydroxylase activity enabling the synthesis of the S lignin units, BdCOMT3 is the main caffeic acid O-methyltransferase and its partial loss of function in two independent mutant lines leads to the reduction of lignin content, the modification of the S/G units ratio and a decrease in p-coumaric acid accumulation. BdCAD1 is the main cinnamyl alcohol dehydrogenase isoform: its loss of function in two independent mutant lines results in a decrease in lignin content and of the S/G ratio and the accumulation of sinapaldehyde. Moreover, these two lines display significatively increased saccharification yields.

No description available.