L’avènement du génotypage à haut débit permet aujourd’hui de mieux exploiter le phénomène d’association, appelé déséquilibre de liaison (LD), qui existe entre les allèles de différents loci sur le génome. Dans ce contexte, l’utilité de certains modèles utilisés en cartographie de locus à effets quantitatifs (QTL) est remise en question. Les objectifs de ce travail étaient de discriminer entre des modèles utilisés en routine en cartographie et d’apporter des éclaircissements sur la meilleure façon d’exploiter le LD, par l’utilisation d’haplotypes, afin d’optimiser les modèles basés sur ce concept. On montre que les modèles uni-marqueur de liaison, développés en génétique il y a vingtaine d’années, comportent peu d’intérêts aujourd’hui avec le génotypage à haut débit. Dans ce contexte, on montre que les modèles uni-marqueur d’association comportent plus d’avantages que les modèles uni-marqueur de liaison, surtout pour des QTL ayant un effet petit ou modéré sur le phénotype, à condition de bien maîtriser la structure génétique entre individus. Les puissances et les robustesses statistiques de ces modèles ont été étudiées, à la fois sur le plan théorique et par simulations, afin de valider les résultats obtenus pour la comparaison de l’association avec la liaison. Toutefois, les modèles uni-marqueur ne sont pas aussi efficaces que les modèles utilisant des haplotypes dans la prise en compte du LD pour une cartographie fine de QTL. Des propriétés mathématiques reliées à la cartographie de QTL par l’exploitation du LD multiallélique capté par les modèles haplotypiques ont été explicitées et étudiées à l’aide d’une distance matricielle définie entre deux positions sur le génome. Cette distance a été exprimée algébriquement comme une fonction des coefficients du LD multiallélique. Les propriétés mathématiques liées à cette fonction montrent qu’il est difficile de bien exploiter le LD multiallélique, pour un génotypage à haut débit, si l’on ne tient pas compte uniquement de la similarité totale entre des haplotypes. Des études sur données réelles et simulées ont illustré ces propriétés et montrent une corrélation supérieure à 0.9 entre une statistique basée sur la distance matricielle et des résultats de cartographie. Cette forte corrélation a donné lieu à la proposition d’une méthode, basée sur la distance matricielle, qui aide à discriminer entre les modèles utilisés en cartographie.

Doctor of Philosophy / Department of Agronomy / Guihua Bai / Growing resistant cultivars is an economically effective method to control wheat disease Fusarium head blight (FHB) caused by Fusarium graminearum. Ninety-five wheat lines mainly from China and Japan were evaluated for resistance to initial infection (type I), spread of symptoms within a spike (type II), and deoxynivalenol (DON) accumulation in infected grains (type III). Most of lines were resistant or moderately resistant, 15 lines had DON content lower than 2 ppm and six lines showed a high level of resistance for all the three types. Deoxynivalenol content was significantly correlated with type II, but not type I resistance. Fifty-nine of the ninety-five lines were evaluated for genetic diversity on the basis of amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs). Genetic relationships among these lines were consistent with pedigrees and their geographic distribution. Chinese lines had broader genetic diversity than Japanese lines. Sumai 3 is a widely used Chinese variety for FHB-resistant breeding in the US and elsewhere. Haplotype patterns of the SSR markers linked to FHB resistance quantitative trait loci (QTL) on chromosomes 3BS, 5AS and 6BS of Sumai 3 indicated that only a few Sumai 3 derivatives carry all of these Sumai 3 QTL. SSR data also suggested that these QTL in Sumai 3 were derived from Chinese landrace Taiwan Xiaomai. Some highly resistant lines may carry novel QTL for FHB-resistance QTL, and need further investigation. A mapping population of 139 recombinant inbred lines derived from the cross of Wangshuibai (resistant Chinese landrace)/Wheaton (susceptible cultivar) was genotyped with more than 1300 SSR and AFLP markers. Five QTL for type I resistance were detected on chromosome arms 3BS, 4BS, 5DL, 3AS, and 5AS; seven QTL for type II resistance on 3BS, 1AL, 5AS, 5DL, 7AL, and 3DL; and seven QTL for type III resistance on 3BS, 5AS, 1AS, 5DL, 1BL, and 7AL. These QTL together explained 31.7%, 64%, and 52.8% of the phenotypic variation for FHB type I, II, and III resistance, respectively. QTL on 5AS, the distal end of 3BS, and 5DL contributed to all three types of resistance. FHB resistance QTL identified in Wangshuibai can be used in developing wheat cultivars with enhanced FHB resistance by pyramiding FHB resistance QTL from other sources.

Este estudo teve por objetivo mapear QTLs para características de desempenho e de carcaça em Gallus gallus . Foram estudadas 350 aves F2 oriundas de um cruzamento, na primeira geração, de machos de corte da linhagem TT com fêmeas de postura da linhagem CC. O peso vivo com 1, 35 e 42 dias de idade; o ganho de peso, o consumo de ração e a conversão alimentar de 35 a 41 dias de idade; os pesos dos pulmões, fígado, coração, moela, peito, coxas (peso de coxas e sobre-coxas), carcaça (sem vísceras, pés e cabeça), carcaça residual (peso da carcaça sem peito, asas e coxas), asas, cabeça, pés e gordura abdominal; o comprimento do intestino e o percentual de hematócrito, foram os fenótipos analisados. Foram utilizados 79 marcadores microssatélites, os quais cobriram 1510,7 cM dos cromossomos 1, 2, 3, 4, 5, 8, 11 e 13. Primeiramente, foram realizadas análises isoladas de cada fenótipo original e de variáveis canônicas obtidas por análise de componentes principais dos fenótipos. O teste razão de verossimilhanças (LRT) entre um modelo incompleto (apenas com efeitos fixos de sexo, incubação e o efeito aleatório de valor genético infinitesimal) e um completo (todos os efeitos anteriores mais os efeitos de QTL) foi o procedimento utilizado nas análises, exceto para testar modelos com interações epistáticas, onde a metodologia de quadrados mínimos foi utilizada. Modelos com interação QTL x sexo também foram testados. Posteriormente, foram feitas análises de múltiplos fenótipos simultaneamente, onde foi possível testar a hipótese de QTL pleiotrópico x QTLs ligados, além dos testes descritos acima, com exceção de efeitos epistáticos. As análises descritivas e de componentes principais foram obtidas no SAS, enquanto o mapeamento de QTL foi realizado no programa QxPak, exceto para análise de efeitos epistáticos, em que um código em Fortran 90 foi empregado. O modelo univariado, sem interações, permitiu mapear oito QTLs altamente significativos (cinco no GGA1 para PV35, PV42, gordura abdominal, comprimento do intestino e peso da cabeça; dois QTLs no GGA2 para PV35 e PV42; e um QTL no GGA3 para gordura abdominal) seis significativos (dois no GGA1 para conversão alimentar e ganho de peso; dois no GGA3 para peso das asas e das coxas; um no GGA4 para peso da cabeça; e um no GGA8 para peso da moela), além de 13 ligações sugestivas para diversas características. Dez QTLs apresentaram interação com sexo, sendo cinco específicos para machos. O modelo com busca simultânea de dois QTLs mapeou seis QTLs anteriormente perdidos (cinco para PV35 e PV42; e um para peso da cabeça). Interações epistáticas foram observadas para PV35 e PV42 entre um QTL em 69 cM do GGA1 com QTLs em 333 cM do GGA1, 272 cM do GGA3 e 77 cM do GGA5. Dois QTLs e seis ligações sugestivas foram mapeados na análise de variáveis canônicas, os quais não haviam sido mapeados com as variáveis originais. Com o procedimento de múltiplas características foi possível mapear nove QTLs pleiotrópicos e o aumento de poder do teste foi evidenciado, principalmente, no GGA2. / This study aim to map QTL for performance and carcass traits in (Gallus gallus) . There were used 350 F2 chickens developed by crossing a broiler male line (TT) with a layer line (CC). The body weight with 1, 35 and 42 days of age, weight gain, feed intake and feed conversion from 35 to 41 days, weights of lung, liver, heart, gizzard, breast, drums and thighs, carcass (without giblets, feet and head), residual carcass (weight of carcass without breast, drums, thighs, and wings), wings, head, feet, and abdominal fat, intestine length and hematócrito value were the phenotypes analyzed. Seventy nine microssatellite markers were used, which covered 1510.7 cM of chromosomes 1, 2, 3, 4, 5, 8, 11, and 13. Firstly, QTL analysis was carried out for each original trait and for canonical variables, obtained from principal components analysis of the phenotypes. The likelihood ratio test (LRT) between a reduced model (only fixed effects of sex, hatch and random effect of infinitesimal genetic value) and a full model (all anterior effects and QTL effects) was applied to map QTL, but mean square approach was used for mapping QTL with epistatic effect. Besides, models with QTL by sex interaction were also tested. Finally, multi-trait analysis was used to test the hypothesis of pleiotropic x linkage QTLs, besides of the tests previously described, except models with epistatic effects. For descriptive and principal components analysis the SAS software was used. QTL mapping was carried out with QxPak software and a fortran 90 source code to test models with epistatic effect. The univariate model, without interactions, allowed to map eight highly significant QTLs (five in the GGA1, for PV35, PV42, abdominal fat, intestine length, and head weight; two QTLs in the GGA2, for PV35 and PV42; and one QTL in the GGA3 for abdominal fat), six significant QTLs (two in the GGA1 for feed conversion and weight gain; two in the GGA3 for wings and drums and thighs weights; one in the GGA4 for head weight; and one in the GGA8 for gizzard weight), besides 13 suggestive linkages for several traits. Ten QTLs interacted with sex, being five of them male specific QTLs. The model with simultaneous search for two QTLs was important to map six QTLs previously lost (five for body weight at 35 and 42 days; and one for head weight). Epistatic Interactions were observed for body weight among a QTL in 69 cM of GGA1 with QTLs in 333 cM of GGA1, 272 cM of GGA3 and 77 cM of GGA5. Two QTLs and six suggestive linkages were mapped with the analysis on canonical variables, which have not been mapped with the original variables. With the multi-trait approach nine pleiotropic QTLs were mapped and an increase in the test power was observed mainly in the GGA2 chromosome.

Los objetivos de esta tesis son estudiar el comportamiento y el control genético de diferentes caracteres relacionados con la resistencia al encamado del arroz, así como parámetros de calidad del grano, en dos poblaciones que comparten el mismo parental femenino, y en dos condiciones de cultivo: las balsetas en que generalmente se realiza la selección de las primeras generaciones segregantes, y parcelas de campo; y analizar si es posible aumentar la eficiencia en la selección de estos caracteres: idoneidad de la selección en F2 e identificación de las regiones cromosómicas más importantes en la determinación de estos caracteres, y que puedan ser apropiadas para un programa de selección asistida por marcadores (M.A.S.). Para ello se ha realizado un análisis cuantitativo (estimas de heredabilidad, correlación entre caracteres y eficacia de selección), y un análisis de QTLs (loci que controlan los caracteres cuantitativos). En el genotipado de las poblaciones se han utilizado marcadores de tipo SSR. Se han identificado y caracterizado los loci implicados en el control genético de cada uno de los caracteres, y se han comparado su estabilidad y efectos en los diversos genotipos y ambientes. En muchos casos, se detectaron QTLs que afectan simultáneamente a varios caracteres, en coincidencia con las correlaciones encontradas entre los mismos caracteres. Se han localizado zonas de especial interés que podrían ser utilizadas para M.A.S. (selección asistida por marcadores). La selección fue efectiva para reducir la altura y aumentar el grosor y la longitud de los entrenudos basales en las dos poblaciones, y para incrementar del número de panículas y la resistencia al doblado en una de las poblaciones. / Torró Torró, I. (2010). Análisis de los factores que determinan la resistencia al encamado y características de grano en arroz (Oryza sativa L.), y su asociación con otros caracteres, en varias poblaciones y ambientes: bases genéticas y QTLs implicados [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/9317 / Palancia

La culture de Légumineuses présente le double intérêt de permettre une production de graines à haute valeur nutritionnelle sans nécessité d’un apport d’engrais azoté. La nutrition azotée des légumineuses dépend en effet majoritairement de la fixation symbiotique de l’azote atmosphérique réalisée par des bactéries du sol, les rhizobia, au sein des nodosités, et dans une moindre mesure, de l’assimilation de l’azote minéral du sol par les racines.Une meilleure compréhension a été acquise sur le contrôle génétique de la mise en place des racines et des nodosités et sur leur impact sur la nutrition azotée. Une grande variabilité génétique pour ces caractères a été mise en évidence, ainsi que l’existence de corrélations génétiques entre eux. Une approche de génétique quantitative a permis d’identifier des régions génomiques pouvant être impliquées dans leurs variations. Deux pistes d’amélioration de la nutrition azotée ont aussi été étudiées : l’amélioration de l’acquisition d’azote par les racines à partir d’une étude détaillée d’un mutant de développement racinaire, et l’amélioration de la symbiose via l’étude de la capacité des pois à favoriser les associations symbiotiques avec les rhizobia les plus performants.Les résultats obtenus apportent des bases de réflexion concernant la conception d’un idéotype de nutrition azotée. Au-delà de la complémentarité indispensable entre les deux voies d’acquisition d’azote, il convient d’optimiser l’interaction entre les deux partenaires symbiotiques, mécanisme complexe mettant en jeu la formation et le fonctionnement des nodosités, en lien avec une signalétique et des interactions trophiques entre partenaires et intra-plante. / Grain legume pulse crops are of great interest to allow a production of seeds high nutritional value without any contribution of nitrate fertilizer. The nitrogen nutrition of legumes depends indeed mainly on the fixation in nodules of atmospheric dinitrogen through the plant-rhizobium symbiosis, and to a lesser extent, absorption by roots of soil mineral nitrogen.A better understanding has been obtained on the genetic control of the development of roots and nodules and on their impact on nitrogen nutrition. High genetic variability of these characters has been detected, and the existence of genetic correlations between them demonstrated. A quantitative genetic approach has identified several genomic regions that may be involved in their variations. The two different ways to improve nitrogen nutrition were also studied: the improvement of nitrogen acquisition by roots through a detailed study of a root architecture mutant, and the improvement of symbiosis via the study of the ability of peas to promote symbiotic associations with the most effective rhizobia.The results provide interesting bases for the design of a pea nitrogen-nutrition ‘ideotype’. Beyond the essential complementarity between the two pathways of nitrogen acquisition, it is necessary to optimize the interaction between the two symbiotic partners, which is a complex mechanism involving nodules formation and functioning in connection with complex signaling and trophic interactions between the partners and intra-plant.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21805号 / 農博第2318号 / 新制||農||1065(附属図書館) / 学位論文||H31||N5177(農学部図書室) / 京都大学大学院農学研究科農学専攻 / (主査)教授 白岩 立彦, 教授 奥本 裕, 教授 稲村 達也 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第13342号 / 論農博第2885号 / 新制||農||1079(附属図書館) / 学位論文||R2||N5249(農学部図書室) / (主査)教授 奥本 裕, 教授 白岩 立彦, 教授 丸山 伸之 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of tightly linked markers. GWAS of virulence and fungicide sensitivity using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for virulence, and two for fungicide sensitivity. The genes associated with virulence that were detected in this study were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB.

This dissertation contains three research chapters conducted on Sclerotinia stem rot (SSR) of canola (Brassica napus L.). This disease is caused by the fungus Sclerotinia sclerotiorum and is considered endemic in canola-producing areas of North Dakota. The first research chapter presents results of a study that evaluated the role of eight phenotyping scoring systems and nine variant calling and filtering methods in detection of QTL associated with response to SSR. The study, conducted on two doubled-haploid mapping populations, showed that using multiple phenotypic data sets derived from lesion length and plant mortality and imputing missing genotypic data increased the number of QTL detected without negatively affecting the effect (R2) of QTL. Nineteen QTL were detected on chromosomes A02, A07, A09, C01, and C03 in this study. The second research chapter presents results of a work that assessed the role of temperature regimes and wetness duration on S. sclerotiorum ascospore germination and ascosporic infection efficiency. This study showed that optimum ascospore germination occurred at 21 °C while it significantly decreased at 10 and 30 °C. Infection efficacy experiments indicated that extreme temperatures and interrupting wet periods were detrimental for the disease development. A logistic regression model with 75% accuracy was developed for the disease perdition. The third research chapter presents results of a study that evaluated the role of temperature on mycelial growth of 19 S. sclerotiorum isolates collected from different geographical regions and on SSR development on plant introduction (PI) lines with different levels of resistance. Mycelial growth and disease development peaked at 25 °C. While lesion expansion on resistant cultivars and the susceptible check was negatively affected at 30 °C, the disease developed significantly on the PI with a high level of susceptibility. Results of these studies provide insights into integrated management strategies of SSR.

Bovine mastitis, or inflammation of the mammary gland, has substantial economic and animal welfare implications. A genetic basis for mastitis resistance traits is recognized and can be used to guide selective breeding programs. The discovery of regions of the genome associated with mastitis resistance, and knowledge of the underlying molecular mechanisms responsible, can facilitate development of efficient mastitis control and therapeutic strategies. The objectives of this dissertation research were to identify sites of genetic variation associated with mastitis resistance, and to define the contributions of the milk-secreting epithelial cells to mammary gland immune responses and mastitis resistance. Twenty seven regions of the bovine genome potentially involved in mastitis resistance were identified in Holstein dairy cattle. Additionally, this research demonstrates a role of bovine mammary epithelial cells in mastitis resistance, and provides guidance for the use of an in vitro model for mastitis studies. Primary bovine mammary epithelial cells from mastitis-resistant cows have differential expression of 42 inflammatory genes compared with cells from mastitis-susceptible cows, highlighting the importance of epithelial cells in mastitis resistance. Bovine mammary epithelial cells display both similarities and differences in pro-inflammatory gene expression compared to fibroblasts, and their expression of inflammatory genes is influenced by administration of the enzyme phospholipase A2. The growth potential of milk-derived bovine mammary epithelial cells in vitro can be extended, facilitating their use in mastitis studies, by transfection with a viral protein. Collectively, this research contributes to current knowledge on bovine mastitis resistance and in vitro models.