Reproduction de : Thèse de doctorat : Biosciences végétales : Toulouse 3 : 2008. / Titre provenant de l'é215-232.

Bibliography: leaves 164-193. / x, 193 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This study aims to quantify the belowground input of organic carbon by barrel medic using techniques that account for root death and decomposition as well as root secretion and exudation. It also investigates the effect of defoliation on carbon allocation within the plant so as to determine the potential for optimising carbon input to the soil through grazing management. / Thesis (Ph.D.)--University of Adelaide, Dept. of Soil Science, 1997

The conversion of atmospheric dinitrogen (N2) into plant available nitrogen (N), by legumes and their prokaryotic microsymbionts, is an integral component of sustainable farming. A key constraint to increasing the amount of N2 fixed in agricultural systems is the prevalence of symbioses which fix little or no N. The biotic factors leading to this suboptimal N2 fixation have not been extensively analysed. Using the widely studied and cultivated perennial legume Medicago sativa and the model indeterminate annual legume Medicago truncatula with the sequenced bacterial microsymbiont Sinorhizobium meliloti 1021 (Sm1021) as a basis, the work presented in this thesis examined the effectiveness of N2 fixation in these associations and in other comparable systems and investigated factors which lead to the establishment of suboptimally effective symbioses. The ability of Sm1021, S. medicae WSM419 and the uncharacterised Sinorhizobium sp. WSM1022 to fix N with M. truncatula A17, M. sativa cv. Sceptre and a range of other Medicago spp. was evaluated in N-limited conditions. As measured by plant shoot dry weights and N-content, Sm1021 was partially effective with M. truncatula A17 whereas WSM1022 and WSM419 were both effective with this host in comparison to nitrogen-fed (N-fed) control plants. In contrast, Sm1021 and WSM1022 were effective with M. sativa while WSM419 was only partially effective. Nodules induced by Sm1021 on M. truncatula A17 were more numerous, paler, smaller in size and more widely distributed over the entire root system than in the two effective symbioses with this host. On the contrary, nodule number, size and distribution did not differ between these three strains on M. sativa. WSM1022 was effective on M. littoralis, M. tornata and two other cultivars of M. truncatula (Jemalong and Caliph) but Sm1021 was only partially effective on these hosts. These data indicate that the model indeterminate legume symbiosis between M. truncatula and Sm1021 is not optimally matched for N2 fixation and that Sm1021 possesses broader symbiotic deficiencies. In addition, the interaction of WSM1022 with M. polymorpha (small white nodules but does not fix N), M. murex (does not nodulate), M. arabica (partially effective N2 fixation) and M. sphaeorcarpus (partially effective N2 fixation), and the sequence of the 16S rDNA, are all consistent with this isolate belonging to the species S. meliloti. The colony morphology of TY, half-LA and YMA agar plate cultures of Sm1021, WSM419 and WSM1022 suggested differences in EPS profiles between these strains. Sm1021 is very dry, compared to the mucoid WSM419 and extremely mucoid WSM1022. Sm1021 is known to carry an insertion in expR rendering the gene non-functional and resulting in the dry colony phenotype. WSM419 has an intact copy of expR, while the expR status of WSM1022 is not known. Rm8530, a spontaneous mucoid derivative of Sm1021 with an intact expR, was significantly less effective with M. truncatula than Sm1021, but there was no difference in effectiveness between these strains on M. sativa. The effectiveness of Sm1021, when complemented with a plasmid-borne copy of expR from Rm8530, was significantly reduced on M. truncatula but not M. sativa, implicating a functional expR as being the cause of reduced N2 fixation observed with Rm8530 on M. truncatula. ExpR could reduce the effectiveness of Rm8530 by acting as a negative regulator of genes essential for symbiosis with M. truncatula, or by altering the quantity or structure of succinoglycan and/or galactoglucan produced. These data support the emerging view of ExpR being a central regulator of numerous cellular processes. The timing of nodulation between Sm1021 and WSM419 on M. truncatula and M. sativa was investigated. Compared to the other symbioses analysed, the appearance of nodule initials and nodules was delayed when M. truncatula was inoculated with Sm1021 by 3 and 4 days, respectively. To explore whether events during early symbiotic signalling exchange could account for these observed delays, leading to the establishment of a suboptimal N2-fixing symbiosis, a novel system was developed to compare the response of the Sm1021 transcriptome to roots and root exudates of M. truncatula A17 and M. sativa cv. Sceptre. This system consisted of a sealed 1 L polycarbonate chamber containing a stainless steel tripod with a wire mesh platform on which surface-sterilised seeds could be placed and allowed to germinate through the mesh, into a hydroponic medium below. After germination, Sm1021 cells were inoculated into the hydroponic solution, exposed to the roots and root exudates for 16 h, harvested and their RNA extracted. Comparison of Sm1021 mRNA from systems exposed to M. truncatula or M. sativa revealed marked differences in gene expression between the two. Compared to the no plant control, when M. sativa was the host plant, 23 up-regulated and 40 down-regulated Sm1021 genes were detected, while 28 up-regulated and 45 down-regulated genes were detected with M. truncatula as the host. Of these, 12 were up-regulated and 28 were down-regulated independent of whether M. truncatula or M. sativa was the host. Genes expressed differently when exposed to either M. truncatula or M. sativa included nex18, exoK, rpoE1 and a number of other genes coding for either hypothetical proteins or proteins with putative functions including electron transporters and ABC transporters. Characterisation of these differentially expressed genes along with a better understanding of the composition of M. truncatula root exudates would yield a clearer insight into the contribution of early signal exchange to N2 fixation. Comparison of the regulation of nodule number between Sm1021 and WSM419 on M. truncatula and M. sativa revealed nodule initials at 42 days post-inoculation (dpi) on M. truncatula inoculated with Sm1021. In contrast, no new nodule initials were present 21 dpi on any of the other interactions examined. Moreover, analysis of nodule sections revealed that the number of infected cells in M. truncatula-Sm1021 nodules was less than for comparable symbioses. These data suggest that nodule number is not tightly controlled in the M. truncatula-Sm1021 association, probably due to N2 fixation being insufficient to trigger the down regulation of nodulation. Quantification of N2 fixation activity in this and other more effective symbioses is required. The poor effectiveness of the M. truncatula-Sm1021 symbiosis makes these organisms unsuitable as the model indeterminate interaction and the implications for legume research are discussed. The recently sequenced WSM419 strain, revealed here to fix N2 more effectively with M. truncatula than Sm1021, may be a better model microsymbiont, although WSM419 is only partially effective for N2 fixation with M. sativa. The sequencing of S. meliloti WSM1022, a highly effective strain with both M. truncatula and M. sativa, would provide a valuable resource in indentifying factors which preclude the establishment of effective symbioses.

Bibliography: leaves 164-193. / x, 193 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This study aims to quantify the belowground input of organic carbon by barrel medic using techniques that account for root death and decomposition as well as root secretion and exudation. It also investigates the effect of defoliation on carbon allocation within the plant so as to determine the potential for optimising carbon input to the soil through grazing management. / Thesis (Ph.D.)--University of Adelaide, Dept. of Soil Science, 1997

Thesis (M.S.)--University of Delaware, 2006. / Principal faculty advisor: Darla J. Sherrier, Dept. of Plant and Soil Science. Includes bibliographical references.

Submitted by Reginaldo Soares de Freitas (reginaldo.freitas@ufv.br) on 2018-01-16T11:32:00Z No. of bitstreams: 1 texto completo.pdf: 1247418 bytes, checksum: e985fa1f1156f534c1dbec006984c2de (MD5) / Made available in DSpace on 2018-01-16T11:32:00Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1247418 bytes, checksum: e985fa1f1156f534c1dbec006984c2de (MD5) Previous issue date: 2017-07-18 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / O desenvolvimento de novos cultivares de alfafa está relacionado, além do potencial produtivo, com o valor nutritivo da forragem, ambos determinados por uma série de caracteres de controle genético complexo. Por isso, o melhoramento da cultura exige adoção de técnicas que maximizem a acurácia seletiva. Nesse contexto, a utilização das Redes Neurais Artificiais (RNAs) pode ser útil para otimizar a seleção simultânea de caracteres, que tem sido a estratégia mais utilizada no melhoramento da alfafa. Assim, o objetivo deste trabalho foi aplicar a abordagem de índices de seleção no contexto das redes neurais artificiais para auxiliar o melhoramento da cultura da alfafa, além de avaliar a eficiência das redes para realizar a seleção de caracteres complexos. Para isso, foram utilizados dados de 77 genótipos de alfafa avaliados em quatro cortes realizados ao longo das diferentes estações no ano, mensurados quanto a caracteres de produção e valor nutritivo. Primeiramente, foram estimados os ganhos por seleção direta, indireta e simultânea pelo índice de Taí para cada um dos grupos de caracteres. Para obtenção das redes para cada grupo, os genótipos foram subdivididos em classes segundo os escores do índice. A fim de garantir boa capacidade de generalização das redes, nas etapas de treinamento e validação foram utilizados dados ampliados de cada grupo de caracteres e, só então, as redes foram utilizadas para classificar os dados reais dos quatro cortes. Posteriormente, utilizou- se dados ampliados de três cortes para treinamento e validação e a rede, então estabelecida, foi empregada em dados reais, relativos a um dos cortes que não participou do processo de ampliação. De modo geral, as seleções diretas proporcionaram ganhos per se satisfatórios para os propósitos do melhoramento, mas sua utilização deve ser bastante criteriosa tendo em vista a existência de correlações desfavoráveis entre alguns caracteres estudados. Já as seleções indiretas apresentaram dificuldades para manter ganhos desejados em todos os caracteres no conjunto de genótipos. Os resultados da seleção simultânea utilizando o índice de Taí proporcionaram distribuição de ganhos mais equilibrada para os conjuntos de caracteres em todos os cortes. No contexto das redes neurais artificiais, as taxas de erros das redes de produção e valor nutritivo foram baixas, evidenciando a grande concordância destas com o índice. Entretanto, a limitação do conjunto de treinamento e teste das RNAs para ampliação de três cortes, levou tanto a altas taxas de erro ou a níveis muito baixos, indicativo de perda da habilidade de generalização. Quando se utilizou as redes no novo corte, as taxas de erro foram altas em todos os cenários. O baixo desempenho obtido pode ser explicado pela discrepância observada entre o conjunto de treinamento e o conjunto de teste. Dessa forma, percebe-se a importância da qualidade do conjunto de dados para treinamento de uma rede eficiente, pois a utilização desta é diretamente relacionada com a disponibilidade de bons exemplos e em grande número. O uso das RNAs será mais difundido à medida que haja mudança no paradigma da experimentação em que as decisões passarão a ser tomadas em bancos de dados, construídos ao longo do tempo de um programa de melhoramento, que constituirão de base para o processamento de dados. / Developing new alfalfa cultivars is related with productive potential besides to the nutritive value of the forage, which are determined by traits of complex genetic control. That is why alfalfa breeding requires adoption of techniques that maximize selective accuracy. In this context, using Artificial Neural Networks (ANNs) can be useful to optimize the simultaneous selection, which has been the strategy most used in alfalfa breeding. Thus, the aim of this work was to apply the selection index approach in the context of artificial neural networks to help in alfalfa breeding, as well as to evaluate the efficiency of the ANNs to perform the complex trait selection. The data from 77 alfalfa genotypes evaluated in four cuts were collected considering different seasons in the year. In each cut were measured production and nutritive value traits. Firstly, we estimated the gains by direct, indirect and simultaneous selection by the Taí index for each trait groups. To obtain the ANN for each group, the genotypes were subdivided into classes according to the index scores. In order to ensure good network generalization, in the training and validation stages we used amplificated data from each group of characters, later we used the ANNs to classify the real data of the four cuts. Subsequently, we used amplificated data from three cuts for training and validation, and the established ANNs were used in a new cut that did not participate in the amplification process. In general, the direct selections provided satisfactory individual gains for the breeding purposes, but their use must be very judicious since the existence of unfavorable correlations between some studied traits. Indirect selections, presented difficulties in maintaining desired gains in all traits in the genotype set. The results of simultaneous selection using the Taí index provided a more balanced distribution gains for the trait sets in all cuts. In the context of the artificial neural networks, the error rates of the production and nutritional value groups were low, evidencing the great agreement of these with the index. However, the limitation of the training set and test of ANNs for data of three cut amplification, led either to high error rates or to very low levels, indicating of loss of the generalization ability. When the networks were used in the new cut, error rates were high in all scenarios. The low performance obtained can be explained by the discrepancy between the training set and the test one. In this way, the importance of the quality of data set for training an efficient network is perceived, since its use is directly related to the availability of good examples and in large numbers. The use of ANNs will be more widespread with a change in the experimentation paradigm in which decisions will be made into databases built over time from a breeding program that will form the basis for data processing.

Angl. resumé

The study of arbuscular mycorrhizal symbiosis (AMS) - the mutualist relationship between the most of land plants and evolutionary old fungal group Glomeromycota - is becoming a prestigious topic. The prevalence of and extent of physiological action of AMS on plants is very interesting for the plant biology itself, but its importance grows, notably in time of global climate change, frequent soil degradation and ascending exhaustion of mineral fertilizer reserves. Although the flows in AMS of some minerals, like of phosphorus was enlightened, carbon exchange between the symbionts is still poorly understood. In this experimental work, I utilized the boom of molecular and bioinformatic methods in the quest for completely unexplained carbon flows. The organisms used include barrel medic (Medicago truncatula), the model legume for symbiotic relationships, biotic, and abiotic stresses; Rhizophagus irregularis, the widely used fungus for such experimental studies of AMS; and Sinorhizobium meliloti, the nodulating nitrogen-fixing bacterium compatible with the barrel medic. Two variants - mycorrhizal (M+) and non-mycorrhizal (NM) plants were subjected to several levels of analysis. I have checked the variants, did the measurements of phosphorus and nitrogen contents, as well as I probed the plants with...

Nous présentons l’étude de l’interaction entre la bactérie pathogène racinaire Ralstonia solanacearum et la légumineuse modèle Medicago truncatula. Un pathosystème avec les lignées A17 et F83005.5, respectivement sensible et résistante à la souche GMI1000, a été mis en place avec une procédure d’inoculation sur racines intactes. Ce dispositif expérimental nous a permis de suivre le processus infectieux, de la pénétration de la bactérie par l’extrémité racinaire au développement des symptômes foliaires. L’analyse des étapes précoces de l’interaction a permis de décrire l’apparition de symptômes racinaires qui se mettent en place rapidement après l’infection, que les lignées soient résistantes ou sensibles à la bactérie. Un arrêt de croissance de la racine s'observe dès 24 heures post-inoculation, ainsi qu’une mortalité de l’épiderme de l’extrémité racinaire. Ces phénotypes sont notés suite à des inoculations avec de faibles concentrations bactériennes, et ce sur plusieurs espèces hôtes ou non-hôtes testées. La mise en place des symptômes racinaires est dépendante de l’appareil de sécrétion de type III. Un crible de mutants d’effecteurs de type III de la souche GMI1000, basé sur l’apparition des symptômes racinaires, a permis de montrer que des pools différents d’effecteurs interviennent chez A17 et F83005.5. Chez la lignée sensible A17, deux effecteurs sont principalement impliqués, Gala7 et AvrA. L’étude de la colonisation de cette lignée a montré que le mutant gala7 ne pénètre pas la plante et n’induit pas de symptômes de flétrissement. Le mutant avrA s’est révélé capable d’induire la maladie chez la lignée A17 mais de manière nettement réduite par rapport à la souche sauvage. L’analyse des extrémités racinaires des lignées sensible et résistante infectées par la souche GMI1000 a révélé qu’au niveau des parois de l’endoderme, la présence de lignine est induite de manière plus précoce chez la lignée résistante. Des phénomènes de division cellulaire ont été identifiés autour du cylindre central et semblent également liés à une restriction de la propagation bactérienne. Au niveau du contenu cellulaire, une autofluorescence et une production de ROS semblent liés à une phase nécrotrophe de la bactérie lors de sa propagation dans la zone corticale de l’extrémité racinaire. L’étude de la colonisation bactérienne en s’affranchissant de l’étape de pénétration a révélé que des mécanismes de résistances peuvent intervenir au niveau de collet chez la lignée F83005.5 et lors de la colonisation racinaire des vaisseaux conducteurs suite à une inoculation avec le mutant gala7 / Manquant

Legumes play an important role in agriculture as major food sources for humans and as feed for animals. Bioavailable nitrogen is a limiting nutrient for crop growth. Legumes are important because they can form a symbiotic relationship with soil bacteria called rhizobia that results in nitrogen-fixing root nodules. In this symbiosis, rhizobia provide nitrogen to the legumes and the legumes provide carbon sources to the rhizobia. The Medicago truncatula NPF1.7/NIP/LATD gene is essential for root nodule development and also for proper development of root architecture. Work in our lab on the MtNPF1.7/MtNIP/LATD gene has established that it encodes a nitrate transporter and strongly suggests it has another function. Mtnip-1/latd mutants have pleiotropic defects, which are only partially explained by defects in nitrate transport. MtNPF1.7/NIP/LATD is a member of the large and diverse NPF/NRT1(PTR) transporter family. NPF/NRT1(PTR) members have been shown to transport other compounds in addition to nitrate: nitrite, amino acids, di- and tri-peptides, dicarboxylates, auxin, abscisic acid and glucosinolates. In Arabidopsis thaliana, the AtNPF6.3/NRT1.1( CHL1) transporter was shown to transport auxin as well as nitrate. Atchl1 mutants have defects in root architecture, which may be explained by defects in auxin transport and/or nitrate sensing. Considering the pleiotropic phenotypes observed in Mtnip-1/latd mutant plants, it is possible that MtNPF1.7/NIP/LATD could have similar activity as AtNPF6.3/NRT1.1(CHL1). Experimental evidence shows that the MtNPF1.7/NIP/LATD gene is able to restore nitrate-absent responsiveness defects of the Atchl1-5 mutant. The constitutive expression of MtNPF1.7/NIP/LATD gene was able to partially, but not fully restore the wild-type phenotype in the Atchl1-5 mutant line in response to auxin and cytokinin. The constitutive expression of MtNPF1.7/NIP/LATD gene affects the lateral root density of wild-type Col-0 plants differently in response to IAA in the presence of high (1mM) or low (0.1 mM) nitrate. MtNPF1.7/NIP/LATD gene expression is not regulated by nitrate at the concentrations tested and MtNPF1.7/NIP/LATD does not regulate the nitrate-responsive MtNRT2.1 gene. Mtnip-1 plants have an abnormal gravitropic root response implicating an auxin defect. Together with these results, MtNPF1.7/NIP/LATD is associated with nitrate and auxin; however, it does not act in a homologous fashion as AtNPF6.3/NRT1.1(CHL1) does in A. thaliana.