Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Wheat is the main winter crop in Rio Grande do Sul State. Temperature and photoperiod are the major environmental factors that control development in wheat. Wheat plants exposed to cold, non freezing temperatures induce them to enter the reproductive phase. Temperature and photoperiod response functions are used to simulate the wheat development. Developmental models are important part of water soil balance, growth and yield crop models. Thus, the objectives of this thesis were: (i) to evaluate vernalization sensitivity of some Brazilian wheat genotypes and to fit a vernalization response function for these genotypes; (ii) to determine the best temperature, photoperiod and vernalization functions to simulate wheat development with the Wang and Engel (WE) model for some Brazilian wheat genotypes; and (iii) to improve the prediction of available soil water in the soil by modifying two mechanistic models. To achieve the first objective, a factorial experiment with eight levels of vernalization (0, 7, 14, 21, 28, 35, 42 and 49 vernalization days) and six wheat genotypes were used. Also a field experiment was carried out in Santa Maria, RS, Brazil, to provide independent data on the date of developmental stages of six Brazilian wheat genotypes for evaluating the original and the modified WE model. Soil water content was determined with the gravimetric method to evaluate water balance models during three sowing dates. For those genotypes that presented some response to vernalization, response functions are presented, which can be used in models for simulating the development of Brazilian wheat cultivars with distinct vernalization requirements. The WE model simulates better the development of the Brazilian wheat genotypes using cardinal temperatures higher than original WE model and using daily maximum and minimum temperatures in the calculation of the temperature response function. The modified Campbell; Diaz water balance model is more realistic and has a greater potential for performing well in regions others than it was developed. The modified Amir; Sinclair water balance model simulates better the available soil water than the original model. / O trigo é a principal cultura de inverno do Estado do Rio Grande do Sul. A temperatura e o fotoperíodo são os dois elementos meteorológicos que mais influenciam o desenvolvimento de plantas de trigo. Quando se expõem plantas de trigo a temperaturas baixas não congelantes, estas podem ser induzidas a entrarem no estágio reprodutivo, diminuindo o seu ciclo de desenvolvimento. Para simular o desenvolvimento do trigo são utilizadas funções de resposta a temperatura e fotoperíodo. O modelo de desenvolvimento é parte importante em modelos de simulação de balanço de água no solo, crescimento e rendimento das culturas. Assim, os objetivos desta tese foram: (i) determinar a sensibilidade à vernalização de alguns genótipos de trigo do sul do Brasil e, ajustar uma função de reposta a vernalização para aqueles que apresentaram sensibilidade; (ii) determinar a melhor função de temperatura, fotoperíodo e vernalização para simular o desenvolvimento de alguns genótipos brasileiros de trigo com o modelo de Wang e Engel (WE); e (iii) obter uma melhor predição do balanço de água no solo, modificando dois modelos mecanísticos de balanço de água no solo. Para atingir o primeiro objetivo, foi conduzido um experimento fatorial com oito níveis de vernalização (0, 7, 14, 21, 28, 35, 42 e 49 dias de vernalização) e seis genótipos de trigo. Também foi realizado um experimento com várias datas de semeadura em Santa Maria, RS, Brasil, para obtenção de dados independentes dos estágios de desenvolvimento de seis genótipos Brasileiros de trigo para avaliar o modelo WE modificado. Foi determinado o conteúdo de água no solo pelo método gravimétrico em três datas de semeadura, com a finalidade de avaliar o desempenho dos dois modelos de balanço de água no solo. Para os genótipos que apresentaram resposta à vernalização são apresentadas funções de resposta, que podem ser usadas em modelos de simulação do desenvolvimento de genótipos brasileiros de trigo. O modelo WE simula melhor o desenvolvimento do trigo quando são usadas as temperaturas cardinais maiores do que as do modelo original e usando as temperaturas mínimas e máximas diária para o cálculo da função de resposta a temperatura. O modelo de balanço de água no solo de Campbell; Diaz modificado é mais realístico e com maior possibilidade de desempenho satisfatório em regiões de clima distinto daquelas em que foi desenvolvido. O modelo de balanço de água no solo de Amir; Sinclair modificado estima melhor a água disponível no solo que o modelo original.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The dual purpose wheat has the capacity to produce forage and grain, through the expression of morphological and bromatologic traits and yield components. Thus, the overall goal was to identify biometric models to understand the interrelationships between traits, direct and indirect selection in breeding wheat for dual purposes. The specific objectives of this study were to determine the canonical correlations between groups of morphological traits and grain yield, and identify the direction and the magnitude of the relationship; and identify the phenotypic relationships of cause and effect bromatologic between forage characters in wheat genotypes under different dual purpose cutting managements. The experiments were conducted in the growing seasons 2013 and 2014 in the experimental area of the Federal University of Santa Maria Campus Frederico Westphalen - RS. A randomized complete block design was used in three trials, the first experiment was arranged in a factorial: five genotypes (BRS Tarumã, BRS Umbu, BRS Figueira, BRS Guatambu and BRS 277) x four cutting managements (uncut, a cut, two cuts and three cuts). The second experiment was arranged in a factorial: Five genotypes (BRS Tarumã, BRS Umbu, BRS Figueira, BRS Guatambu and BRS 277) x Three cutting managements (first cut, second cut and third cut). The traits evaluated were: number of tillers per plant (AF), stem diameter of tillers (DAF), diameter of the main stem (DCP), number of fertile tillers (AFF), number of ears per square meter (ESPM), number of grains per ear (NGE), grain weight per ear (MGE), thousand grain weight (MMG), grain yield (RG), weight hectolitre (PH), green matter per hectare (MV), dry matter per hectare (MS), percentage of hemicellulose (HEM), cellulose (CEL), mineral matter (MM), neutral detergent fiber (FDN), acid detergent fiber (FDA), lignin (LIG), total carbohydrates (CT), carbohydrates no fiber carbohydrates (CNF), crude protein (PTN), and lipids (LIP). Groups of morphological traits and grain yield in wheat dual purpose reveal highly significant relationships. In the management at uncut and one cut wheat, associations are similarly established for both groups, by increasing the DCP, and determining the ESPM the increase, NGE and MGE, MMG, PH and RG. With two cuts the associations are established through the DAF, which influences an increase in MMG, PH and RG. Three cuts showed that the increase in AF increment the ESPM, NGE and MGE, MMG, PH and RG. The indirect selection aimed at increasing the PTN in the first cut can be based on CT, CNF and MV. The second cut provides indirect selection with LIG, CNF, MV and MS. The increase of PTN in the third cut can be obtained by indirect selection to the FDA, CEL, LIG, MM, MV and MS. Indirect selection through forage characters and bromatologic can be successful, since it considers the effect assigned to each cutting management. / O trigo duplo propósito apresenta capacidade de produzir forragem e grãos, através da expressão de caracteres morfológicos, bromatológicos e componentes do rendimento. Desta maneira, o objetivo geral foi identificar modelos biométricos que permitam compreender as inter-relações entre caracteres, e direcionar a seleção indireta no melhoramento genético de trigo duplo propósito. Os objetivos específicos deste trabalho foram: determinar as correlações canônicas entre grupos de caracteres morfológicos e do rendimento de grãos, e identificar o sentido e a magnitude das relações; e identificar as associações fenotípicas de causa e efeito entre caracteres forrageiros e bromatológicos em genótipos de trigo duplo propósito submetidos a diferentes manejos de corte.Os experimentos foram realizados nas safras agrícolas 2013 e 2014 na área experimental da Universidade Federal de Santa Maria Campus de Frederico Westphalen RS. Utilizou-se o delineamento de blocos ao acaso em três repetições, o primeiro experimento foi organizado em fatorial: Cinco genótipos (BRS Tarumã, BRS Umbu, BRS Figueira, BRS Guatambu e BRS 277) x Quatro manejos de corte (sem corte, um corte, dois cortes e três cortes). O segundo experimento foi organizado em fatorial: Cinco genótipos (BRS Tarumã, BRS Umbu, BRS Figueira, BRS Guatambu e BRS 277) x Três manejos de corte (primeiro corte, segundo corte e terceiro corte). Os caracteres avaliados foram: número de afilhos por planta (AF), diâmetro do colmo dos afilhos (DAF), diâmetro do colmo principal (DCP), número de afilhos férteis (AFF), número de espigas por metro quadrado (ESPM), número de grãos por espiga (NGE), massa de grãos por espiga (MGE), massa de mil grãos (MMG), rendimento de grãos (RG), peso hectolitro (PH), massa verde por hectare (MV), massa seca por hectare (MS), percentual de hemicelulose (HEM), celulose (CEL), material mineral (MM), fibras em detergente neutro (FDN), fibras em detergente ácido (FDA), lignina (LIG), carboidratos totais (CT), carboidratos não fibrosos (CNF), proteína bruta (PTN), e lipídios (LIP). Os grupos de caracteres morfológicos e de rendimento de grãos em trigo duplo propósito revelam relações altamente significativas. No manejo sem cortes e com um corte, associações são estabelecidas similarmente para ambos os grupos, através do aumento do DCP, sendo determinante ao acréscimo de ESPM, NGE e MGE, MMG, PH e RG. Com dois cortes as associações são estabelecidas através do DAF, que influencia o aumento da MMG, PH e RG. Com três cortes evidencia-se que o aumento do AF incrementam ESPM,NGE e MGE, MMG, PH e RG.A seleção indireta visando incrementar PTN no primeiro corte pode ser baseada nos CT,CNF e MV. O segundo corte proporciona a seleção indireta com a LIG, CNF, MV e MS. O incremento de PTN no terceiro corte poderá ser obtido através da seleção indireta com FDA, CEL, LIG, MM, MV e MS. A seleção indireta através dos caracteres forrageiros e bromatológicos pode ser realizada com sucesso, desde que se considere o efeito atribuído a cada manejo de corte.

Mieux connaitre les facteurs qui gouvernent l’apparition des évènements de recombinaison (crossing-overs ; CO) chez le blé tendre (Triticum aestivum L.) est primordial car ce processus est l’outil principal du sélectionneur pour permettre le brassage de la diversité génétique et l’introgression de régions d’intérêt dans des variétés agronomiques. L’utilisation de techniques de cytogénétique développées sur l’orge a permis de comparer la mise en place de la synapse lors de la méiose chez des lignées de blé tendre délétées de tout ou partie du bras long du chromosome 3B et qui avaient été préalablement montrées comme présentant un nombre de chiasmas réduit par rapport à la variété euploïde. Les analyses cytogénétiques couplées à des études bioinformatiques de la séquence montrent que le synapsis a lieu quasiment normalement chez les mutants et que la délétion de certains gènes connus comme impactant le déroulement de la méiose pourrait expliquer le phénotype observé. De plus, le développement de ressources génomiques (SNP, séquence) à destination des sélectionneurs a permis la réalisation de cartes génétiques haute densité des 21 chromosomes ancrées sur la séquence du génome. Tous les chromosomes montrent le même profil de recombinaison avec un accroissement dans les parties distales et une réduction drastique dans les parties centromériques et péri-centromériques. L’exploitation de plus de 250 CO localisés dans des fenêtres de moins de 25 kb sur le chromosome 3B utilisé comme modèle pour l’étude de l’impact de la séquence sur la recombinaison, montre que les profils de recombinaison ancestrale et actuelle sont conservés et que les CO ont lieu préférentiellement dans les parties promotrices des gènes exprimés en méiose ce qui suggère que la conformation chromatinienne influence la recombinaison. Finalement, ces données ont aussi été l’opportunité de détecter des motifs liés à la recombinaison qui présentent des similarités avec celui ciblé par la protéine PRDM9 qui conduit à la recombinaison chez l’humain. Cela suggère que les mécanismes de contrôle de la recombinaison sont conservés chez les eucaryotes. / Better knowledge of the factors that drive recombination (crossovers; COs) in bread wheat (Triticum aestivum L.) is of main interest since this process is the main tool allowing breeders to admix the genetic diversity and to introgress regions of interest in agronomic varieties. We used cytogenetic techniques previously developed on barley to compare the establishment of synapsis during meiosis in deletion lines missing part or whole of the long arm of chromosome 3B of bread wheat and which were previously shown as having a reduced chiasmata number compared to euploid varieties. Cytogenetic analysis combined with bioinformatics studies showed that the synapsis occurs almost normally in mutants and that deletion of some genes known to impact meiosis behavior may explain the observed phenotype. In addition, development of genomic resources (SNPs, sequence) for wheat breeders allowed simultaneous elaboration of high density genetic maps for the 21 chromosomes anchored on genome sequence. All chromosomes present the same recombination pattern with an increase of recombination in the distal parts and reduction in centromeric/pericentromeric regions of the chromosomes. Analysis of more than 250 COs mapped in windows lower than 25kb located on chromosome 3B used as model to study the impact of sequence features on recombination showed that current and ancestral recombination patterns are conserved and that COs preferentially occur in the promoter part of gene expressed in meiosis suggesting that chromatin conformation impacts recombination. Finally, these data were the opportunity to detect recombination-associated motif which presents similarities with the motif targeted by the PRDM9 protein driving recombination in human. This suggests that the control of recombination mechanisms is conserved among eukaryotes.

La teneur et la composition en protéines de réserve du grain de blé tendre (Triticum aestivum L.) sont les principaux déterminants de sa valeur d’usage et de sa qualité nutritionnelle. La composition en protéines de réserve du grain est déterminée par la teneur en assimilâts azotés et soufrés par grain via des lois d’échelle qui pourraient être les propriétés émergentes de réseaux de régulation. Plusieurs facteurs de transcription intervenant dans cette régulation ont été mis en évidence, mais les voies et mécanismes impliqués sont encore très peu connus. Le constat est identique en ce qui concerne l’impact de la nutrition azotée et soufrée sur ce réseau de régulation. Le développement des outils de génomique fonctionnelle et de bioinformatique permet aujourd’hui d’aborder ces régulations de manière globale via une approche systémique mettant en relation plusieurs niveaux de régulation. L’objectif du travail présenté est d’explorer les réseaux de régulation –omiques impliqués dans le contrôle de l’accumulation des protéines de réserve dans le grain de blé tendre et leur réponse à l’approvisionnement en azote et en soufre. Une approche d’inférence de réseaux basée sur la découverte de règles a été étendue, implémentée sous la forme d’une plateforme web. L’utilisation de cette plateforme a permis de définir des sémantiques multiples afin d’inférer dans un cadre global, des règles possédant différentes significations biologiques. Des facteurs de transcription spécifiques de certains organes et certaines phases de développement ont été mis en évidence et un intérêt particulier a été apporté à leur position dans les réseaux de règles inférés, notamment en relation avec les protéines de réserve. Les travaux initiés dans cette thèse ouvrent un champ d’investigation innovant pour l’identification de nouvelles cibles de sélection variétale pour l’amélioration de la valeur technologique et de la qualité nutritionnelle du blé. Ils devraient ainsi permettre de mieux maîtriser la composition en protéines de réserve et ainsi produire des blés adaptés à des utilisations ciblées ou carencé en certaines fractions protéiques impliquées dans des phénomènes d’allergénicité et d’intolérance du gluten, ce dans un contexte d’agriculture durable et plus économe en intrants. / Grain storage protein content and composition are the main determinants of bread wheat (Triticum aestivum L.) end-use value. Scaling laws governing grain protein composition according to grain nitrogen and sulfur content could be the outcome of a finely tuned regulation network. Although it was demonstrated that the main regulation of grain storage proteins accumulation occurs at the transcriptomic level in cereals, knowledge of the underlying molecular mechanisms is elusive. Moreover, the effects of nitrogen and sulfur on these mechanisms are unknown. The issue of skyrocketing data generation in research projects is addressed by developing high-throughput bioinformatics approaches. Extracting knowledge on from such massive amounts of data is therefore an important challenge. The work presented herein aims at elucidating regulatory networks involved in grain storage protein synthesis and their response to nitrogen and sulfur supply using a rule discovery approach. This approach was extended, implemented in the form of a web-oriented platform dedicated to the inference and analysis of regulatory networks from qualitative and quantitative –omics data. This platform allowed us to define different semantics in a comprehensive framework; each semantic having its own biological meaning, thus providing us with global informative networks. Spatiotemporal specificity of transcription factors expression was observed and particular attention was paid to their relationship with grain storage proteins in the inferred networks. The work initiated here opens up a field of innovative investigation to identify new targets for plant breeding and for an improved end-use value and nutritional quality of wheat in the context of inputs limitation. Further analyses should enhance the understanding of the control of grain protein composition and allow providing wheat adapted to specific uses or deficient in protein fractions responsible for gluten allergenicity and intolerance.

Dans un contexte de réduction des intrants agricoles, la création de variétés de blé qui utilisent l’azote de manière plus efficiente est aujourd’hui nécessaire. Cette thèse, issue d'un partenariat public-privé entre l'Institut National de la Recherche Agronomique et Biogemma, avait pour but d'apporter des outils nécessaires à la création de variétés répondant à cette exigence. Pour ce faire, nous avons analysé 225 variétés commerciales génotypées avec 24K SNP et testées dans huit combinaisons d’année, lieu et régime azoté. Nous avons montré que même si la sélection a amélioré l’efficience d’utilisation de l’azote en condition optimale et sub-optimale, ce progrès génétique doit être accéléré et mieux réparti entre les différents traits. Nous proposons pour cela de mixer sélection phénotypique et sélection assistée par marqueurs. Dans ce sens, nous avons développé une méthode pour définir les régions chromosomiques associées à nos 28 traits. Parmi les 333 régions identifiées, nous avons notamment localisé le gène NAM-A1 et avons pu caractériser ses variants naturels. Nous avons aussi montré que la sélection génomique pourrait être plus efficace si les SNP étaient présélectionnés en fonction de leurs significativités en génétique d’association multi-environnementale. Les réseaux d’interactions épistatiques furent aussi étudiés, mettant en évidence un sous-réseau particulièrement intéressant. Nos résultats et méthodes sont discutés au regard des stratégies d’amélioration variétale et de découverte de gènes. Des pistes de recherche complémentaires et des améliorations ont aussi été suggérées. / In a context of fertiliser reduction, breeding for enhanced nitrogen use efficiency in bread wheat is necessary. This PhD thesis resulting from private-public collaboration between the French National Institute for Agricultural Research and Biogemma aimed providing necessary tools. Analyses were conducted using a dataset of 225 commercial varieties genotyped with 24K SNP and tested in eight combinations of year, location, and nitrogen regimes. We showed that even if past selection increased nitrogen use efficiency at high and moderate nitrogen regimes, genetic progresses need to be accelerated and better balanced between traits. This could be achieved by mixing phenotypic and marker assisted selections. In this sense, we developed a method to define quantitative trait locus from genome-wide association study: 333 chromosomal regions involved in 28 NUE-related traits have been identified. The NAM-A1 gene was located in one of these regions and its natural variants were characterized. We also showed that genomic selection could be improved by pre-selecting SNP based on their significance in a multi-environmental genome-wide association study. Networks of epistasis interactions were also studied and an interesting sub-network was identified. Results and methods are discussed regarding breeding and gene discovery strategy. Further investigations and improvements are suggested.

La concentration en protéines des grains est un critère qualitatif majeur qui conditionne la valeur économique et technologique du blé tendre (Triticum aestivum L.). Cependant, la forte relation négative existant entre concentration en protéines et rendement en grains implique que l’amélioration de la concentration en protéines par une approche génétique soit complexe à atteindre sans impacter négativement le rendement. Pour contourner cette difficulté, il a été proposé qu’une sélection variétale basée sur l’écart à cette relation négative (nommé Grain Protein Deviation ; GPD) permette d’améliorer la concentration en protéines indépendamment du rendement. Au niveau physiologique, le GPD est fortement corrélé à la capacité des génotypes à absorber de l’azote après floraison indépendamment de la quantité d’azote déjà absorbée à floraison, suggérant que la satiété en azote soit à la base de son établissement. Envisager une sélection sur la base du GPD nécessite cependant d’acquérir des connaissances approfondies des mécanismes impliqués dans la régulation de l’absorption d’azote par la satiété en azote, qui permettraient de cibler précisément des traits simples à quantifier et robustement associés à cette capacité accrue d’accumulation de protéines dans les grains.Cette étude se base sur deux expérimentations conduites en conditions contrôlées et une expérimentation au champ. Dans chacune de ces expérimentations, différents niveaux de fertilisation ont été appliqués en pré-floraison afin d’obtenir des statuts azotés contrastés à floraison. L’effet du statut azoté à floraison sur l’absorption post-floraison a ensuite été observé dans différentes conditions de disponibilités d’azote après floraison. Des mesures physiologiques et moléculaires ont été réalisées en parallèle des mesures d’absorption d’azote.Nous avons mis en évidence que l’absorption d’azote post-floraison présente une dynamique élaborée qui suppose qu’elle est soumise à des régulations complexes. Parmi celles-ci, le statut azoté des plantes à floraison conditionne en grande part la quantité d’azote absorbée dans les jours qui suivent la floraison (PANUprécoce , de floraison à floraison + 250 degrés-jour). La quantité de PANUprécoce se présente comme un déterminant fort de la concentration en protéines des grains du fait de la forte corrélation positive observée entre ces deux traits en conditions contrôlées et au champ, et ce indépendamment du niveau de rendement. L’étude de deux génotypes robustement contrastés pour le GPD a montré qu’à statuts azotés équivalents, la quantité de PANUprécoce est sujette à des effets génétiques qui tendent à confirmer l’impact de la variabilité génétique de satiété en azote sur l’établissement du GPD.Ces travaux ont permis de proposer des marqueurs du GPD potentiellement valorisables en sélection. Au niveau physiologique, la croissance des tiges après floraison se présente comme un marqueur prometteur du GPD car ce trait est fortement corrélé à la PANUprécoce. Au niveau moléculaire, la concentration en nitrates des racines, également soumise à des effets génétiques, est proposée comme marqueur potentiel du fait de son rôle probable dans la régulation expressionnelle des gènes impliqués dans l’absorption et l’assimilation d’azote. / Grain protein concentration is one of the major qualitative criteria of bread wheat (Triticum aestivum L.) economic and technological value. However, the negative relationship existing between protein concentration and grain yield implies that grain protein concentration improvement is complex to achieve without detrimental effect on grain yield. Breeding programs based on the deviation to this negative relationship (Grain protein deviation of GPD) have been proposed to be a suitable strategy to improve grain nitrogen concentration without detrimental effects on yield. At a physiological level, GPD is strongly correlated with genotypes aptitude to uptake nitrogen after flowering independently of the nitrogen amount already taken up before this stage, suggesting that satiety for nitrogen could be involved in its establishment. Breeding for GPD implies however a more detailed knowledge of the processes implied in nitrogen uptake regulation by nitrogen plant satiety. This would allow targeting traits both simple to measure and robustly associated with this increased capacity to accumulate proteins in grains.The present study is based on two experiments carried on under controlled conditions and a third led under field conditions. In all experiments, various levels of pre-flowering fertilization were applied in order to obtain contrasted plant nitrogen status at flowering. Nitrogen status effect on post-flowering nitrogen uptake was observed under various post-flowering N availability conditions. Physiological and molecular measurements were carried out in parallel with uptake measurements.We highlighted that post-flowering nitrogen uptake has an elaborate dynamic, suggesting the involvement of complex regulations. Among these, plant nitrogen status at flowering determines to a great extent the amount of nitrogen taken up during the days following flowering (early PANU, from flowering to flowering +250 °C.days-1). Early PANU appears to be a strong determinant of grain protein concentration, as strong positive correlations were observed between these two traits both under controlled conditions and field conditions, independently of grain yield level. The study of two genotypes strongly contrasted for GPD highlighted that, despite comparable N status, early PANU is subjected to strong genetic variations which tend to identify N satiety as a determinant of GPD.The present study identified robust markers of GPD of potential use in plant breeding. At a physiological level, post flowering stem elongation appears to be a promising marker of GPD since this trait is strongly correlated with early PANU. At a molecular level, root nitrate concentration, a trait submitted to genetic variations, is also proposed as a marker of GPD because of its role in the expression regulation of the genes governing nitrogen uptake and assimilation.

La fusariose des épis des céréales est due à un champignon pathogène (Fusarium spp.) qui entraine non seulement une perte directe de rendement en interrompant le remplissage des grains, mais également une perte indirecte par la production de mycotoxines, responsables de perturbations de procédés industriels et d'intoxications alimentaires. Parmi les différents moyens de lutte, la création de variétés résistantes semble la stratégie la plus efficace et la plus durable. Plusieurs variétés exotiques ont ainsi été identifiées comme résistantes mais présentent la particularité d'être difficilement cultivables sous nos latitudes. L'obtention de variétés résistantes adaptées à nos climats passe donc par une meilleure connaissance des mécanismes de résistance disponibles. La détection de QTL (Quantitative Trait Loci) chez le blé tendre a déjà permis de localiser certains des facteurs génétiques impliqués dans des mécanismes de résistance. Cependant l'utilisation de ces résultats en amélioration des plantes se heurte à deux contraintes majeures : la position des QTL reste le plus souvent imprécise et ces QTL, dérivant de populations biparentales, ne représentent qu'une fraction de la diversité génétique potentiellement intéressante pour ce caractère. L'objectif de la thèse était d'étudier la résistance du blé à la fusariose en réalisant une approche de génétique d'association. L'utilisation de génotypes faiblement apparentés et d'une densité élevée de marqueurs a permis de détecter des associations entre le polymorphisme génétique et des variations phénotypiques. Après avoir réalisé une synthèse sur le pathogène et sur l'approche par génétique d'association, le premier travail a été de réaliser une carte génétique fiable afin de pouvoir localiser les associations mises en évidence. Un panel de 195 variétés de blé tendre élites a été évalué pour leur résistance globale à la fusariose, pour leur résistance à la progression des symptômes et pour leur résistance à l'accumulation des mycotoxines. Des notations morphologiques (précocité, taille, aristation, nombre d'épillets par épi et extrusion des anthères) ont également été réalisées afin d'évaluer leur influence dans l'infestation. Ces variétés ont été génotypées avec 3016 marqueurs SNP, 200 marqueurs SSR et 1400 marqueurs DArT. Préalablement à la réalisation des tests d'association, l'étude de la structure a mis en évidence trois origines géographiques (française, anglaise et allemande) des variétés du panel. De même, l'étude du déséquilibre de liaison a montré que celui-ci était conservé sur une distance comprise entre 2 et 6 cM. L'étude d'association réalisée sur les notations d'infestation a permis d'identifier plusieurs zones associées, dont plusieurs sont colocalisées avec des Meta-QTL et/ou avec des zones identifiées avec les notations morphologiques. La densification en marqueurs de 6 zones associées avec les différentes notations d'infestation, localisées sur les chromosomes 1A, 1D, 2A, 2B, 5A et 7A, ont permis de confirmer ces régions, de restreindre fortement l'intervalle d'intérêt et de mettre en évidence de potentiels gènes candidats. Cette analyse a ainsi permis de mieux comprendre les mécanismes génétiques et morphologiques impliqués dans la résistance à la fusariose des épis. La décomposition en trois partie de cette résistance (résistance globale, résistance à la progression des symptômes, et résistance à l'accumulation des mycotoxines) montre l'existence de mécanismes génétiques indépendants et donc complémentaire à prendre en compte dans une stratégie de création de variétés résistantes à la fusariose des épis. / Fusarium head blight (FHB), caused by the fungal pathogen Fusarium spp., is a major cereals disease that not only cause direct yield losses, by interrupting grain filling, but also indirect quality losses by the production of mycotoxins, responsible of industrial processes disturbance and food poisoning. Most wheat breeding programs in FHB-affected areas of the world have been screening germplasm to identify sources of improved tolerance. Unfortunately, these sources of genetic resistance are often of exotic origin and not adapted to West European growing conditions. The selection of adapted varieties with improved tolerance therefore needs a better characterization of resistance mechanisms. Several QTL for FHB resistance in wheat have been identified in European germplasm, but the use of these information in marker-assisted selection is constrained by the precision of the QTL and the low diversity tested by using biparental population.The aim of the present study is to use association mapping, also called linkage disequilibrium mapping, to identify loci involved in the resistance to FHB. This method refers to the analysis of statistical associations between genotypes determined in a collection of individuals, and the phenotypes of the same individuals. A dense genetic map was compiled to localize precisely the association results. Resistance to F. graminearum was studied in a panel of 195 elite wheat varieties by the evaluation of three components: resistance to global infection, resistance to symptom progression and resistance to accumulation of mycotoxins. Morphological factors (plant height, heading date, awnedness, spikelets per ears, anther extrusion), known to influence resistance to FHB, were also recorded. All the varieties have been genotyped with around 3300 SNP markers, 200 SSR markers and 1400 DArT markers. We first investigated the structure of the panel, which could generate bias in the estimate of allele effects, if not included explicitly in the association models. We showed that the structure is based on geographical origin (French, German and UK). Study of the linkage disequilibrium (LD) showed an extent of LD between 2 and 6 cM. Results of association studies permitted to identify several loci for each of the evaluated components of resistance. Some of these loci colocalized with the results of the MetaQTL analysis and/or with loci associated with morphological traits. We selected more specifically 6 loci, located on chromosome 1A, 1D, 2A, 2B, 5A and 7A. Marker saturation of the regions, allowed to confirm the genome wide association results and to increase the accuracy of the loci of interest. This analysis allowed to better understand the many factors that influenced FHB resistance, whether genetic or morphological. Results show that the genetic mechanisms are independent between the three components and therefore, information obtained for each component are to be used complementary to create varieties with increased resistance to FHB.

Doctor of Philosophy / Department of Plant Pathology / John P. Fellers / Harold Trick / In Kansas, wheat (Triticum aestivum L.) is severely affected by the biotrophic fungus Puccinia triticina (leaf rust). Although resistant varieties have been developed, the fungus tends to overcome new sources resistance very quickly. Plants have evolved a single gene (R genes) defense network that can recognize specific pathogen effectors (Avr), in a gene-for-gene manor. In rusts, effectors are secreted proteins responsible for inducing the uptake of nutrients and inhibit host defense responses. Identification of secreted proteins during the infection may help to understand the mode of infection of P. triticina. Little is known about molecular interactions in the pathosystem wheat-leaf rust and no Avr genes from cereal rusts have been cloned. In order to understand pathogenicity in leaf rust and generate new alternatives for disease control, the goal of this research is identify P. triticina secreted proteins from a collection of expressed genes during the infection, and to characterize putative Avr function for three candidates. From 432 EST’s derived from haustoria and infected plants, fifteen secreted proteins were identified and 10 were selected as potential avirulence candidates. Pt3 and Pt 51 are two P. triticina (Pt) candidates expressed specifically in the haustoria and encode small cysteine-rich secreted proteins. Eight candidates are expressed at early stages of infection, during spore germination and 6 days after inoculation. They are small-secreted proteins. None are repetitive elements or have nuclear localization signals. They also do not share a conserved motif with known filamentous fungus Avr proteins. Five candidates are novel proteins, two have similarity with predicted proteins, one is homologous with Hesp-379-like protein, one is homologous with superoxide dismutase, and one has a cell glucanase predicted function. Pt3, Pt12 and Pt27 were tested by transient expression experiments using co-bombardment with GUS into leaf rust resistant isogenic lines. Reduction in the expression of reporter gene GUS co-expressed with Pt27 indicates a potential avirulence factor for Lr26 in wheat.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: In order to test the effect of different plant growth-promoting strategies on Triticum aestivum L. (wheat), we investigated the ability of biochar and a grain-associated soil yeast, to improve the growth of this crop. Our first goal was to study the effect of biochar amendments to sandy soil on the growth and nutrition of wheat in the presence of mycorrhizal fungi. This was accomplished by amending soil with 0%, 1%, 2.5%, 5% and 10% (w/w) biochar and cultivating wheat plants in these soil-biochar mixtures. After harvesting, plant growth and mycorrhizal colonization of roots were measured. In addition, we studied the nutritional physiology of these plants with regards to nitrogen (N), phosphorous (P) and potassium (K) concentrations, as well as the growth efficiencies and uptake rates of these nutrients. We found that wheat growth was improved by biochar amendments to soil, probably as a result of elevated K levels in the plant tissues supplied by the biochar amendments. The second goal of this study was to obtain a soil yeast from the rhizosphere of another monocot in the family Poaceae, i.e. Themeda triandra Forssk. (red grass), and then evaluate this isolate for its ability to improve wheat performance. Three different Cryptococcus species were isolated from the rhizosphere of wild grass, i.e. Cryptococcus zeae, Cryptococcus luteolus and Cryptococcus rajasthanensis. Since C. zeae was previously isolated from maize, an isolate representing this species was selected to be used in further experimentation. With the ultimate goal of testing the ability of this yeast to improve wheat growth, its effect on wheat germination was investigated and compared to that of two other soil yeasts, i.e. Cryptococcus podzolicus CAB 978 and Rhodotorula mucilaginosa CAB 826. These three yeasts were subsequently tested for their ability to improve wheat growth in pot cultures in a greenhouse. After one and two months of growth, the culturable yeasts present in the rhizosphere and bulk soil were enumerated. The effects of these yeasts were elucidated by measuring wheat growth in terms of dry weight, as well as root and shoot relative growth rates (RGR). Changes in wheat nutrition were evaluated by determining the concentrations, growth efficiencies and uptake rates for P, K, zinc (Zn) and iron (Fe). During this study, it was found that only C. zeae CAB 1119 and C. podzolicus CAB 978 were able to enhance seed germination. Similarly, it was shown that C. zeae CAB 1119 was able to improve wheat growth during the first and second month of cultivation, whereas C. podzolicus CAB 978 only improved growth during the first month, and R. mucilaginosa CAB 826 had no effect on growth. This improved growth could be attributed to C. zeae CAB 1119 improving the P, K, Zn and Fe growth efficiency of wheat, which positively influenced the root and shoot RGR, and subsequently wheat growth. Our final goal was to test whether C. zeae CAB 1119 could affect wheat growth and nutrition when cultivated in sandy soil, which contained natural microbial consortia and 10% (w/w) biochar. Plants treated with viable or autoclaved cells of C. zeae CAB 1119, were subsequently cultivated in soil only or soil amended with biochar. After one month, plants were harvested and growth was measured with regards to dry weight, root RGR and shoot RGR. In addition, the concentrations of P, K, Zn and Fe were analyzed for these plants, where after the growth efficiencies and uptake rates were calculated for these four nutrients. Results indicated that plants growing in soil amended with biochar, and treated with viable C. zeae CAB 1119, showed the best growth. The increased root and shoot RGR witnessed in these plants was probably due to increased concentrations of P and K in the plants. This study opens new avenues of research with regards to the bio-fertilizers of wheat. / AFRIKAANSE OPSOMMING: Die uiteindelike doel van die studie was om die effek van verskillende plantgroei bevorderende metodes op die groei van Triticum aestivum L. (koring) te ondersoek. Dus het ons die vermoë van houtskool en ‘n graan-geassosieerde grondgis getoets om die groei van dié plant te bevorder. Die eerste doel van die studie was om die effek van houtskool toedienings tot sanderige grond te evalueer. Dit is bewerkstellig deur 0%, 1%, 2.5%, 5% en 10% (w/w) van die houtskool by die sand toe te voeg en koring in die houtskool-sand mengsels te kweek. Na die verlangde groei tydperk is die koring geoes en die mikorrizale kolonisasie op en in die koring wortels bepaal. Gedurende hierdie studie is die effek van bogenoemde toedienings op die fisiologie van die plante ondersoek deur die konsentrasies, opname tempo’s, en groei ekonomie van die plante vir stikstof (N), fosfaat (P) en kalium (K) te bepaal. Ons het gevind dat die groei van koring deur die toediening van houtskool bevorder is en dit blyk dat dié effek weens die teenwoordigheid van hoë K vlakke in die plantweefsel is. Die tweede doel van ons studie was om ‘n gis vanuit die risosfeer van ‘n monokotiel wat aan die familie Poacea behoort, naamlik Themeda triandra Forssk. (rooigras) te isoleer. Die vermoë van die isolaat om die groei van koring te bevorder was daarna getoets. Drie verskillende Cryptococcus spesies was vanuit die risosfeer van rooigras geïsoleer, nl. Cryptococcus zeae, Cryptococcus luteolus en Cryptococcus rajasthanensis. Omdat C. zeae in ‘n vorige studie vanaf mielies geisoleer was, is ‘n isolaat van hierdie spesie gebruik in verdere eksperimente. Met die doel om te bepaal of dié gisspesie koringgroei kan bevorder, was die effek van C. zeae op die ontkieming van koring bestudeer en vergelyk met dié van twee ander grond giste, nl. Cryptococcus podzolicus CAB 978 en Rhodotorula mucilaginosa CAB 826. Hierdie drie giste is ook ondersoek om die groei van koring in ‘n glashuis te bevorder. Na een en twee maande se groei was die getalle van giste teenwoordig in die risosfeer en grond verder weg van die wortels bepaal. Die effek van dié giste op die groei van koring is bepaal in terme van droë gewig asook die relatiewe wortel en halm groei tempos. Veranderinge in die nutrient status van koring is ondersoek deur die konsentrasies, groei-ekonomie en tempo van opname vir P, K, sink (Zn) en yster (Fe) te bepaal. Ons het gedurende dié studie gevind dat C. zeae CAB 1119 en C. podzolicus CAB 978 die ontkieming van koring kon verbeter. Ons het ook gevind dat C. zeae CAB 1119 die groei van koring gedurende die eerste en tweede maand van groei kon bevorder, terwyl C. podzolicus CAB 978 dit net gedurende die eerste maand kon vermag en R. mucilaginosa CAB 826 geen effek gehad het nie. Die verbeterde groei kon aan C. zeae CAB 1119, wat die P, K, Zn en Fe groei effektiwiteit van die plante verbeter het, toegeskryf word. Die verbetering van groei effektiwiteit het ‘n positiewe invloed op die relatiewe groeisnelheid van die wortels en halms gehad, en dus op koringgroei. Die laaste doel van die studie was om te bepaal of C. zeae CAB 1119 die groei van koring kon bevorder wanneer die koring in sand wat natuurlike mikrobiese populasies bevat en met houtskool aangevul is, gekweek word. Plante is met lewensvatbare of nielewensvatbare selle van C. zeae CAB 1119 behandel en gekweek in sanderige grond, en/of grond waarby 10% (w/w) houtskool toegevoeg is. Die plante is na een maand geoes en die groei bepaal in terme van droë massa en die relatiewe wortel en halm groei tempos. Die konsentrasies van P, K, Zn en Fe in die plante, asook die fisiologie van die plante, nl. groei ekonomie en tempo van opname, met betrekking tot P, K, Zn en Fe is bepaal, Ons het gevind dat plante wat in die houtskool-grond mengsel gekweek is en met lewensvatbare selle van C. zeae CAB 1119 behandel is die beste groei getoon het. Die verbeterde relatiewe groei tempos van die wortels en halms was mees waarskynlik die gevolg van verhoogde P en K konsentrasies in die plante. Hierdie studie toon nuwe resultate in verband met die gebruik van biologiese alternatiewes tot kunsmis.

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Good quality water for agricultural use is rapidly becoming a luxury due to competition for this water among the municipal, industrial and agricultural sectors. This has often forced growers to use poor quality water for irrigation. Salinity is one of the main sources of poor water quality and high electrical conductivities (EC’s) due to salinity may become a problem. The aim of this study was to compare the response of South African spring wheat and South African spring barley at germination, seedling growth, vegetative growth, reproductive growth and maturity stage to salinity stress caused by irrigation with saline water. This study was conducted in the laboratory and under controlled glasshouse conditions at the University of Stellenbosch in the Western Cape Province of South Africa. Treatments in trial 1 (incubation trial) were made up of three wheat cultivars (SST 027, SST 056 and SST 087) and three barley cultivars (Nemesia, Erica and Hessekwa) exposed to five EC levels of NaCl solutions (4, 8, 12, 16 and 20 dS m-1) and a control (0 dS m-1) of distilled water, during the germination phase. In trial 2 (pot trial), wheat cultivar SST 027 and barley cultivar SVG 13 were also subjected to the above solutions, but plants were grown till the tillering stage. In trial 3 (pot trial) cultivars used in trial 2 were subjected to five nutrient solutions with EC levels of 1.6, 3, 6, 9 and 12 dS m-1 and allowed to grow till maturity (harvesting stage). Fully balanced nutrient solution with EC = 1.6 dS m-1 was used as a control and NaCl was added to the solutions to obtain the needed EC. In trial 1, final germination percentage (FGP), salt tolerance (ST) and germination rate (GR) were measured at 7 days after incubation. The study showed that when the EC level was increased, FGP, ST and GR of all wheat and barley cultivars tested were decreased. However, significant reduction was only observed at high EC levels with regard to FGP and ST. Wheat cultivars recorded faster GR compared to barley cultivars and tended to be less sensitive to salinity in the germination stage. Cultivars from the same species did not show significant differences. In trial 2, shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW) and root dry weight (RDW) were measured at 35 days after planting (DAP). In general, the study showed that salinity had a significant (P0.05) effect on seedling growth of all measured parameters of both wheat and barley. Mean values for most growth parameters were higher for barley cultivar SVG 13 as compared to wheat cultivar SST 027. However, little evidence was found to show that barley is more salt tolerant than wheat at the seedling stage. In trial 3, selected growth parameters were measured at tillering (28 DAP), booting (54 DAP), flowering (71 DAP) and maturity stage (150 DAP). The study showed that salinity had a significant (P0.05) effect on the vegetative growth, reproductive growth and grain yield of both wheat and barley. Although barley generally produced higher dry weights especially at the early growth stages no clear evidence was found that South African spring barley is more salt tolerant than South African spring wheat. / AFRIKAANSE OPSOMMING: Besproeiingswater met ‘n goeie kwaliteit vir landboukundige gebruik word vinning baie skaars weens kompetisie, a.g.v menslike en industriële gebruik. Produsente word dus dikwels gedwing om water met ‘n swak kwaliteit te gebruik vir besproeiing. ‘n Hoë sout inhoud (brakwater) soos gemeet deur ‘n hoë elektriese geleidingsvermoë (EC), mag dus ‘n problem wees. Die doel van hierdie studie was om te bepaal hoe Suid Afrikaanse lente koring en gars gedurende ontkieming asook saailing-, vegetatiewe-, reproduktiewe- en rypwordingstadiums reageer teenoor soutstremming wat veroorsaak is deur besproeiing met brakwater. Die studie is uitgevoer in laboratoriums en onder gekontrolleerde glashuistoestande by die Universiteit van Stellenbosch in die Weskaap Provinsie van Suid Afrika. Behandelings in die eerste proef (inkubasie studie) het bestaan uit drie koring kultivars (SST 027, SST 056 en SST 087) en drie gars kultivars (Nemesia, Erica en Hessekwa) wat tydens ontkieming benat is met vyf NaCl-oplossings met EC waardes van 4, 8, 12, 16 en 20 dS m-1 onderskeidelik, asook ‘n kontrole met gedistilleerde water (0 dS m-1). In die tweede proef is die koring kultivar, SST 027 en die gars kultivar SVG 13 in ‘n potproef ook aan bogenoemde oplossings blootgestel maar toegelaat om tot die stoelstadium te ontwikkel. In die derde proef is genoemde twee kultivars besproei met vyf voedingsoplossings met EC-waardes van 1.6, 3, 6, 9 en 12 dS m-1 en toegelaat om tot oesstadium te ontwikkel. ‘n Volledig gebalanseerde voedingsoplossing met EC = 1.6 dS m-1 is as kontrole gebruik en NaCl is by ander oplossings gevoeg om die verlangde EC te verkry. In die eerste proef waar die finale ontkiemingspersentasie (FOP), sout toleransie (ST) en ontkiemingstempo (OT) na 7 dae gemeet is, is gevind dat FOP, ST en OT van al die koring en gars kultivars wat getoets is, met toenemende EC gedaal het. Statisties betekenisvolle afnames in FOP en ST is egter slegs by hoë EC waardes waargeneem. Koring kultivars het vinniger ontkiem as gars kultivars en was geneig om meer tolerant teenooor sout stremming te wees vergeleke met gars. Verskille tussen kultivars van dieselfde spesie was egter weglaatbaar klein. In die tweede proef waar plante toegelaat is om te groei tot die stoelstadium (35 dae na plant) is al die gemete planteienskappe (stingel- en wortellengte, asook vars en droë massas van stingels en wortels) van beide gars kultivar, SVG 13 en koring kultivar, SST 027, betekenisvol verlaag deur ‘n toename in EC van die besproeiingswater. Hoewel gars ten opsigte van die meeste gemete eienskappe groter gemiddeldes as koring getoon het, is weinig bewys gevind wat daarop dui dat die getoetsde gars kultivar SVG 13 meer souttolerant is as die koring kultivar SST 027. In die derde proef waar dieselfde koring en gars kultivars vanaf plant tot oestyd besproei is met genoemde voedingsoplossings en metings tydens stoelstadium (28 dae na plant), stamverlenging (54 dae na plant), blomstadium (71 dae na plant) en oesrypstadium (150 dae na plant) gedoen is, is alle gemete vegetatiewe-, reproduktiewe- en opbrengskomponente van beide spesies verlaag deur die soutstremming. Hoewel gars ook in hierdie proef veral gedurende vroeë groeistadiums groter droë massas as koring geproduseer het, is geen konkrete bewyse gevind wat daarop dui dat die getoetsde Suid Afrikaanse lente gars kultivar SVG 13 meer sout tolerant is as die koring kultivar SST 027.