Powdery mildew caused by <i>Blumeria graminis</i> f. sp. <i>tritici</i> is one of the most devastating diseases in wheat (<i>Triticum aestivum</i>) worldwide. Hypersensitive, race specific genes primarily have been deployed to control the disease, however recent efforts have shifted to breeding for more durable resistance, such as "adult plant resistance" (APR). Molecular markers and quantitative trait loci (QTL) associated with APR to powdery mildew must first be validated and QTL effects evaluated in different genetic backgrounds and breeding populations to be useful in marker-assisted selection (MAS) programs. Eighteen simple sequence repeat (SSR) markers previously mapped near the three QTL in Massey for APR to powdery mildew were evaluated for association with APR for powdery mildew in a recombinant inbred line (RIL) breeding population derived from a cross between USG 3209 and a moderately susceptible cultivar Jaypee, wherein Massey is the resistance source for APR in USG 3209. Thirteen new SSR markers were added to the pre-existing genetic linkage maps near the three QTL associated with APR in the Becker by Massey (BM) population. Interval mapping analysis of mildew severity data collected in 2002 (F_5:6) and 2003 (F_6:7) field experiments with marker genotype data obtained in 2003 (F_6:7) confirmed the presence of three QTL for APR on chromosomes 1B, 2A, and 2B in the USG 3209 by Jaypee (UJ) population. The QTL on chromosomes 1B, 2A, and 2B explained 12% to 13%, 59% to 69%, and 22% to 48% of the phenotypic variance for powdery mildew severity in the UJ RIL populations, respectively, in the two field experiments. The efficiency of MAS was examined using powdery mildew data collected in 2002 and 2003 field experiments and also from a greenhouse experiment in 2004 (F_7:8), wherein adult plants of the 293 RILs were evaluated for disease severity using a composite of five different isolates of <i>B. graminis</i>. Selection of RILs possessing the QTL on chromosome 2A and to a lesser extent the one on chromosome 1B was effective in identifying powdery mildew resistance in both greenhouse and field experiments, whereas the effect of the QTL on chromosome 2B was insignificant in the greenhouse. Overall, selecting RILs with QTL on chromosomes 2A and 2B was most successful in identifying highly resistant RILs compared to selecting RILs having other combinations of two or three QTL combinations. The RILs possessing both QTL on chromosomes 2A and 2B had mean mildew severities of 4.4% and 3.2% in 2002 and 2003 field experiments, respectively. Breeders implementing MAS programs for APR to powdery mildew via selection of RILs containing the two QTL on chromosomes 2A and 2B likely will obtain RILs having high levels of resistance in the field. However, combining all three QTL may ensure greater durability of APR, on the basis that resistance conferred by QTL on chromosome 2A and 1B are genetically stable across all environments in this study. / Master of Science

La presente tesi intende esplorare gli effetti della resistenza parziale sulle epidemie di peronospora della vite (Plasmopara viticola). È stato sviluppato un modello di simulazione teorico che comprende lo sviluppo della pianta ospite e le fasi principali della malattia, dalla mobilizzazione dell’inoculo, alla moltiplicazione della malattia sulle foglie, all’infezione dei grappoli. Attraverso esperimenti (monociclici) di inoculazione è stata studiata la risposta alle infezioni di P. Viticola di 16 varietà parzialmente resistenti, analizzando le seguenti componenti: frequenza d’infezione, durata del periodo di latenza, dimensione delle lesioni, produzione di sporangi, durata del periodo infezioso e infettività degli sporangi prodotti sulle lesioni. Queste componenti di resistenza sono state incorporate nel modello, attraverso cui sono stati studiati i loro effetti sull’epidemia (policiclica) in diversi scenari. Le componenti di resistenza hanno mostrato diversi livelli di efficacia nel sopprimere l’epidemia: l’efficienza di infezione e la produzione di sporangi risultano avere un maggiore impatto nella resistenza espressa a livello di pieno campo. Questo approccio è utile per guidare lo studio fenotipico della resistenza dell’ospite e per anticipare le prestazioni di un genotipo a livello di pieno campo, che risulterebbe difficile e dispendioso considerando la natura perenne della vite. / The present dissertation aims to explore the effects of partial resistance on grapevine downy mildew (Plasmopara viticola) epidemics. A theoretical simulation model was developed including host dynamics and main phases of the disease, from inoculum mobilisation to disease multiplication on foliage, and to infection of clusters. The response to P. Viticola infection was studied for 16 grapevine varieties through (monocyclic) inoculation experiments, by measuring components of partial resistance: infection frequency, duration of latent period, size of lesions, production of sporangia, duration of infectious period, and infectivity of sporangia produced on lesion. Components of partial resistance were incorporated into the model and their effects on the (polycyclic) epidemic were investigated accross different scenarios. Components of partial resistance showed different effectiveness on the suppression of epidemics, infection efficiency and spore production having the strongest impact on the overall field resistance response. This approach is an useful tool for phenotyping studies on host plant resistance and for anticipating the performance of a genotype at the field scale, that otherwise is difficult and time requiring due to the perennial nature of grapevine.

La connaissance des effets et modes d’action des QTL (Quantitative Trait Loci) de résistance des plantes aux maladies est un enjeu majeur pour l’exploitation durable des résistances génétiques en agriculture. Dans le pathosystème pois/Aphanomyces euteiches, présentant une importance économique majeure, l’objectif de la thèse a consisté à valider les effets de QTL de résistance, seuls ou en combinaison, et à connaitre leurs modes d’action sur les étapes du cycle de l’agent pathogène. Un total de 157 NILs (Near Isogenic Lines) de pois issues d’un programme de Back-cross Assisté par Marqueurs, porteuses d’aucun, un, deux ou trois des sept principaux QTL de résistance préalablement identifiés, a été génotypé à l’aide d’une puce 15K SNPs et évalué pour la résistance. Les NILs porteuses de QTL à effets majeurs, seuls ou en combinaison avec des QTL à effets mineurs,ont présenté des niveaux accrus de résistance partielle en conditions contrôlées et au champ par rapport aux NILs dépourvues de QTL, dans différents fonds génétiques. Certaines NILs comportant des QTL individuels ou combinés à effets mineurs ont également montré un niveau réduit de sévérité de la maladie dans l’une ou les deux conditions de test. La plupart des QTL a présenté des effets significatifs sur le ralentissement de l’infection et/ou de la quantité d’ADN pathogène ayant colonisé la racine pendant sept jours après inoculation. Cette thèse fournit des outils et éléments de choix de QTL à combiner en sélection pour augmenter l’efficacité de la résistance partielle à A. euteiches dans les futures variétés de pois / Knowledge of the effects and action modes of resistance QTL to plant diseases is a major challenge for the durable use of genetic resistances in agriculture. In the pea/Aphanomyces euteiches pathosystem, which has a major economic importance, the aim of this study was to validate the single or combined effects of main resistance QTL, and study their action modes on steps of the pathogen life cycle. A total of 157 pea NILs (Near Isogenic Lines) created by Marker-Assisted Back-crossing and carrying no, one, two or three of the seven main resistance QTL previously identified, was genotyped using a 15K SNPs array and evaluated for resistance. The NILs carrying major-effect QTL, individually or in combination with minor-effect QTL, had increased levels of partial resistance in controlledconditions and in the field compared to NILs without QTL, in different genetic backgrounds. Several NILs carrying single or multiple minor-effect QTL also showed reduced levels of disease severity in one or the two test conditions. Most of the QTL had significant effects on slowing down infection and/or pathogen DNA quantity which had colonized the root for seven days after inoculation. This study gives tools and information for the choice of resistance QTL to use in pyramiding breeding strategies for increasing partial levels of resistance to A. euteiches in future pea varieties.

La résistance partielle aux agents pathogènes représente une source importante pour l'amélioration des plantes. Cependant les mécanismes moléculaires sous-jacents à ce type de résistance sont encore mal connus. L'interaction entre le riz et le champignon Magnaporthe oryzae est un modèle de choix pour ce type d'analyse, de nombreuses ressources génétiques et outils d'analyse fonctionnelle étant disponibles. Chez le riz, hormis le gène Pi21 qui contrôle la résistance partielle, aucune information biologique et fonctionnelle ne permet d'expliquer cette forme de résistance. En amont de ce travail de thèse, le phénomène de défense préformée a récemment été identifié ; il est défini par la corrélation entre l'expression des gènes liés à la défense avant infection et la résistance partielle à M. oryzae. L'identification de régulateurs de la résistance partielle et des défenses préformées a été l'objectif de cette thèse. Deux stratégies ont été adoptées. Une étude du transcriptome visant à sélectionner et caractériser des gènes candidats sur la base de leur profil d'expression constitutive a été réalisée. Une méthode de sélection par « guilt-by-association » s'est avérée efficace pour identifier des gènes impliqués dans la résistance de la plante. Les gènes AGO18, Z-BED, HSF23 et CaMBP ont été identifiés comme des régulateurs positifs des défenses de la plante. Les gènes HSF23 et CaMBP contrôlent l'expression constitutive des gènes liés à la défense mais leur sur-expression modifie la croissance des plantes. La sur-expression des gènes Z-BED et AGO18 n'a entraîné aucune modification de la croissance de la plante mais une augmentation de la résistance à M. oryzae, sans modification apparente de l'expression des gènes de défense testés. Le gène Z-BED code pour un facteur de transcription putatif dont on peut faire l'hypothèse qu'il contrôle un ensemble encore inconnu de l'arsenal de défense. Le gène AGO18 code pour une protéine argonaute potentiellement impliquée dans l'extinction de gène via la méthylation de la chromatine. Enfin le gène OB-fold est un régulateur négatif des défenses de la plante dont les cibles, potentiellement des ARN, restent à identifier.La deuxième approche a consisté en une détection de loci contrôlant la densité de lésions causées par M. oryzae. Une zone du génome, PRM1, contrôle ce phénotype, confère une résistance à un spectre de souches relativement large, semble contrôler l'expression de gènes de défense avant et au cours de l'infection, et enfin semble ralentir la croissance du champignon avant pénétration. Cette approche sans a priori renforce l'hypothèse que l'expression des gènes de défense avant infection est associée à la résistance partielle du riz à M. oryzae.De plus amples investigations seront nécessaires pour relier les phénotypes de résistance partielle tels que l'inhibition de la croissance pré-pénétration et la densité de lésions entre eux d'une part et d'autre part à l'expression des gènes de défenses avant infection / Partial resistance to pathogens is a major source for plant breeding. However, the molecular mechanisms underlying this type of resistance are still poorly understood. The interaction between rice and the fungus Magnaporthe oryzae is a model of choice for this type of analysis, many genetic and functional analysis tools being available. In rice, except for the Pi21 gene that controls partial resistance, no biological and functional information can explain this form of resistance. Prior to this thesis, the phenomenon of preformed defense has recently been identified; it is defined by the correlation between the expression of genes related to defense before infection and partial resistance to M. oryzae. Identification of partial resistance and preformed defense regulators has been the objective of this thesis. Two strategies were adopted.A transcriptome analysis to select and characterize candidate genes based on their constitutive expression pattern was performed. A method of selection by "guilt-by-association" has been effective in identifying genes involved in plant resistance. The genes AGO18, Z-BED, HSF23 and CaMBP were identified as positive regulators of plant defenses. The genes HSF23 and CaMBP control the constitutive expression of defense related genes, but their over-expression modifies plant growth. Over-expression of Z-BED and AGO18 genes does not affect plant growth but increases the resistance to M. oryzae, without apparent change in the expression of the defense genes tested. The Z-BED gene encodes for a putative transcription factor that likely controls an unknown set of the defense arsenal. The AGO18 gene encodes an Argonaute protein potentially involved in gene silencing via chromatin methylation. Finally the OB-fold gene is a negative plant defense regulator, and its hypothetical RNA targets remain to be identified.The second approach consisted of detection of loci controlling the lesions density caused by M. oryzae. A region of the genome, PRM1, controls this phenotype, confers resistance to a relatively wide range of isolates, appears to control the expression of defense genes before and during the infection, and finally seems to inhibit the growth of the fungus before penetration. This approach without a priori supports the hypothesis that the expression of defense genes before infection is associated with partial resistance of rice to M. oryzae.Further investigations are needed to link the resistance phenotypes such as partial inhibition of fungal growth pre-penetration and density of these lesions on the one hand, and the defense gene expression before infection on the other hand.

Dans un contexte d’agriculture durable, la création de variétés combinant des facteurs génétiques de résistance et d’architecture de la plante présente un intérêt majeur pour limiter le développement des maladies. La thèse a visé à analyser l’interdépendance des déterminants génétiques de l’architecture racinaire et de la résistance à A. euteiches, agent pathogène tellurique majeur du pois. Une analyse de génétique d’association conduite sur tout le génome, à partir d’une collection de 266 lignées de pois, a permis d’identifier 150 locus de résistance et d’architecture et de les comparer aux QTL précédemment étudiés. Une région commune à effet majeur a été associée à la résistance et à un caractère de développement racinaire intrinsèque. Plusieurs régions ont été détectées à la fois pour la résistance et des caractères de vigueur racinaire en réponse à l’infection.La combinaison de la résistance et de caractères d’architecture dans une sélection de lignées a été associée à une réduction des pertes de rendement au champ. Les résultats ont permis d’apporter des connaissances originales sur la génétique comparative de la résistance aux maladies et de l’architecture des plantes au niveau racinaire. Ils fournissent des outils, géniteurs et éléments de choix de QTL de résistance et d’architecture racinaire à combiner pour la sélection de futures variétés de pois résistantes à A. euteiches. / In a sustainable agriculture context, breeding for varieties combining genetic resistance and plant architecture is of major interest to limit diseases impacts in crops. The aim of this thesis was to analyze the interpendance of the genetic determinants of root architecture and resistance to Aphanomyces euteiches, a major soil born pathogen of peas. A genome wide association analysis among a 266-pea-line collection enabled us to pinpoint a total of 150 loci associated with resistance and plant architecture, and to compare them with QTL detected in previous studies. A common major locus was associated with resistance and an intrinsic root architecture trait.Several loci were detected for both resistance and disease-induced architecture. The combination of resistance and some architecture traits in selected pea lines was associated with reduced yield losses in infested fields. Results provide original knowledge on comparative genetics of disease resistance and plant architecture for root rot diseases. They provide tools (SNPs and marker haplotypes), parental lines and information for the choice of resistance and architecture QTL to combine in breeding strategies to improve resistance to A. euteiches in future pea varieties.

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Made available in DSpace on 2014-07-29T14:52:10Z (GMT). No. of bitstreams: 1 Adriane Reis Cruvinel.pdf: 2024865 bytes, checksum: cb2a5cadadc7153ce3d8e66b0c7c7e2c (MD5) Previous issue date: 2005-02-28 / During the last crops, the soybean rust has been appeared as one of the most important problems in the national agriculture. The direct loses on the production and in the costs with fungicides have been increased the damages on this crop. Aiming to understand better the disease epidemiology, this work searched for answers by epidemic progress in two locations, the time of planting effect, the cycle of planting, the use of fungicide, and by different cultivars. The experiments were assembled in Experimental Stations from Agência Rural in Senador Canedo and in Anápolis. For each place were used three times of planting, six cultivars on the three crop cycles (Monsoy 6101 and BRSNina premature cycle; Emgopa 315 and BRSGO Santa Cruz middle cycle; Emgopa 313 and BRSGO Paraíso late cycle), with and without fungicide action, have been evaluated on the three parts of the plant (lower, middle and upper). Each time, to each one of the places, have been considered as an experiment with spli-split-plot. After the disease symptom observations, the split under chemical control were freaked each 21 days using pyraclostrobin+epoxiconazole on 66,5 g + 25 g a.i. ha-1. The evaluations, after the first symptom observation, have been done weekly up to the complete leaves took away. With the periodic severity data the Area Under Progress Disease Curve (AUPDC) and Relative Area Under Progress Disease Curve (RAUPDC), that is the area divided by the epidemic time duration, were calculated. The parameters were productivity, thousand-grains weight (TGW) and small grains percent (%SG). The delay on the start of the disease on Anápolis, comparing with Senador Canedo, increases the discussion on the results. The previous disease occurrence in Senador Canedo and the high level inoculate presented can be associated to the fact of experimental site in Senador Canedo has soybean cultivate all over the year. The delay on the start of the disease on Anápolis, compared to Senador Canedo has been resulted on productivity increase and fungicide effect decrease. Comparing the time of planting in both planting places, the second one presented the highest level of severity, but the highest level of productivity even. The use of fungicide decrease significantly the AUPDC, increase the productivity, the TGW and decrease the %SG. The premature cycle cultivars presented lowest disease severity. The cultivar Emgopa 315 although be a medium cycle presented results equals premature cycles cultivars. On each site the time of planting were differentiated. On high pressure inoculate condition the difference between evaluated factors was lower. On lower inoculate pressure the evaluated factors expressed better the changes. As conclusion we have: a) how early the disease appears higher is your effect on productivity; b) using premature cultivars the escape effect decrease the disease damages when compared to medium and late cycle; c) the disease decrease the soybean cycle by the defoliation; d) although all the cultivars presented susceptibility to rust, related to lower severity on partial resistance; e) the fungicide utilization pyraclostrobin+epoxiconazole on de 66,5 g + 25 g a.i. ha-1, used on first symptom and in 21 on 21 days decrease the disease progress and the effects on productivity; f) the disease progress decrease by fungicide utilization is better in late planting; g) under the fungicide effect pyraclostrobin+epoxiconazole with 66,5 g + 25 g a.i. ha-1 there s no variation time planting and site; h) under high inoculate pressure the variation between time planting on disease progress and productivity is lower; i) the time of planting must be considered but not lonely, always in association with others factors of fungus action; j) the use of RAUPDC is necessarily when there is variation the time of soybean cycle, affecting the rust epidemic duration; l) the highest disease level occurs on the part of the plant near the soil and the defoliation difficult the disease evaluation on this part of the plant; m) the most effective disease occurs on the highest parts of the plant. / Durante as últimas safras a ferrugem asiática da soja tem se apresentado como um dos maiores problemas na sojicultura nacional. Os prejuízos diretos pela queda da produção e os gastos com fungicidas têm acarretado prejuízos que vêm aumentando a cada safra. Objetivando compreender melhor a epidemiologia da doença, este estudo a buscou respostas para fatores como variação do progresso da epidemia em duas localidades, o efeito da época de semeadura, do ciclo da cultivar, do uso de fungicida e da resposta de diferentes cultivares. Os experimentos foram montados, nas Estações Experimentais da Agência Rural de Senador Canedo e de Anápolis. Para cada local foram utilizadas três épocas de semeadura, com seis cultivares nos três ciclos da cultura (Monsoy 6101 e BRSNina ciclo precoce; Emgopa 315 e BRSGO Santa Cruz ciclo médio; Emgopa 313 e BRSGO Paraíso ciclo tardio), com e sem a ação de fungicida, sendo avaliados os três terços da planta (inferior, médio e superior). Cada época, para cada um dos locais, foi considerada como um experimento com parcelas sub-sub-divididas. Após a observação dos sintomas da doença, as parcelas com controle químico foram pulverizadas a cada 21 dias com pyraclostrobin+epoxiconazole na dosagem 66,5 g + 25 g i.a. ha-1. As avaliações após o aparecimento da doença foram realizadas semanalmente até a queda completa das folhas. Com os dados de severidade periódicos calculou-se a Área Abaixo da Curva de Progresso da Doença (AACPD) e a Área Abaixo da Curva de Progresso da Doença Relativa (AACPDR), que consiste na divisão da área pelo período de duração da epidemia. As variáveis de rendimento obtidas foram: produtividade, massa de mil grãos (MMG) e porcentagem de grãos chumbinho (%CH). O atraso da entrada da doença em Anápolis, quando comparado a Senador Canedo, propiciou variações nos resultados que enriqueceram a discussão dos dados. A antecipação da ocorrência da doença em Senador Canedo e a alta pressão de inóculo apresentadas podem estar associadas ao fato da estação experimental em Senador Canedo possuir soja cultivada durante todo o ano. O atraso da entrada da doença em Anápolis, quando comparada a Senador Canedo, possibilitou um incremento na produtividade e menor efeito de fungicida. Entre as épocas avaliadas nos dois locais, a segunda apresentou os maiores índices de severidade, mas também os maiores índices de produtividade, fator relacionado às condições do ambiente. O efeito da utilização do fungicida diminuiu significativamente a AACPD, aumentou a produtividade, a MMG e diminuiu a %CH. Cultivares de ciclo precoce apresentaram menor severidade da doença, seguidos pelas cultivares de ciclo médio e tardio. A cultivar Emgopa 315 apesar de ser de ciclo médio apresentou resultados semelhantes às cultivares de ciclo precoce nas avaliações como um todo. Em cada local as épocas se comportaram de forma diferenciada. Em condições de alta pressão de inóculo a diferença entre os fatores estudados é menor. Para pressão de inóculo menor os fatores avaliados expressaram melhor suas variações. Como conclusões retiradas a partir dos resultados discutidos concluiu-se que: a) quanto mais cedo a ferrugem aparece durante o ciclo da cultura, maior é o seu efeito na produtividade da soja; b) a utilização de cultivares de soja de ciclo precoce propicia um efeito escape, que reduz os efeitos da ferrugem, quando comparado às cultivares de ciclo médio e tardio; c) a ocorrência da doença diminui o ciclo da cultura, antecipando seu término devido à desfolha prematura; d) apesar de todas as cultivares apresentarem suscetibilidade à ferrugem, algumas apresentam menor severidade relacionada a variações nos níveis de resistência parcial à doença; e) a utilização do fungicida pyraclostrobin+epoxiconazole na dosagem de 66,5 g + 25 g i.a. ha-1, aplicado a partir do aparecimento dos primeiros sintomas e posteriormente a intervalos de 21 dias diminuiu expressivamente o progresso da doença e seus efeitos nas variáveis de rendimento da soja; f) a redução do progresso da doença devido à aplicação do fungicida estudado é mais evidente com a semeadura tardia; g) sob o efeito da mistura pyraclostrobin+epoxiconazole na dosagem de 66,5 g + 25 g i.a. ha-1 não há variação entre época de semeadura e local; h) sob alta pressão de inóculo, as variações entre épocas de semeadura no progresso da ferrugem e no rendimento da cultura são menos explícitas; i) o fator época de semeadura não deve ser considerado isoladamente, mas sempre em associação a outros fatores que influenciam a ação do fungo como aplicação de fungicida, ciclo e resistência da cultivar; j) a utilização do parâmetro Área Abaixo da Curva de Progresso da Doença Relativa (AACPDR) é justificada para dados nos quais existe variação da duração do ciclo da soja, interferindo na duração da epidemia de ferrugem. Esta adequação se faz necessária para que os resultados de progresso da doença não sejam comprometidos; l) a parte da planta mais afetada pelos sintomas é o terço inferior e a desfolha dificulta a avaliação da doença nesta região; m) o controle mais efetivo da doença pelo fungicida ocorre nos terços superior e médio da planta

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