Made available in DSpace on 2016-12-23T14:37:31Z (GMT). No. of bitstreams: 1 Rodolfo Ferreira de Mendonca.pdf: 887040 bytes, checksum: 634504ee1a6e6bcb495cae2c0feeafe0 (MD5) Previous issue date: 2013-02-20 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The Espírito Santo state is the larger producer of conilon coffee in Brazil, and the leaf rust disease is considered the main disease of this culture. Genotypes of conilon coffee may have different behavior in relation to leaf rust. Within this approach, accurate characterization of genetic materials in search for superior leaf rust resistance is of fundamental importance, in order to assist the direct selection in the breeding program of conilon coffee being executed by Incaper (Instituto Capixaba de Assistência Técnica, Pesquisa e Extensão Rural). Therefore, this study aims to evaluate the reaction to Hemileia vastatrix of 54 genotypes of Coffea canephora selected in the referred breeding program of Incaper. The vegetal material and the fungus were collected in the Experimental Farm of Bananal do Norte, directed by Incaper, in Cachoeiro do Itapemirim, ES. The experiment was conducted in the laboratory of plant pathology of the Centro de Ciências Agrárias da Universidade Federal do Espírito Santo (CCA-UFES), Alegre, ES. A completely randomized experimental design was used, with three repetitions, and each plot was composed of 16 leaf discs, which were placed in gerbox and inoculated with 104 spores.mL-1 of H. vastatrix, using a brush. The gerboxes were placed in the dark at 22 °C for 48 hours and then at photoperiod of 12 hours until the end of the experiment. Five days later the inoculation, the discs were cleaned with cotton to prevent the growth of hyperparasites. From the tenth day, the appearance of symptoms was observed and were evaluated, until the 37th day, the incubation period, the latent period, the incidence, the percentage of discs with sporulation, the spore numbers and the severity. The data were analyzed in the software R, for Pearson correlation and STEPWISE, and in the software GENES, for variance analysis, Scott-Knott test and multivariate analysis. Based on the results, three groups of genotypes of conilon coffee were formed: Resistant, Intermediate and Susceptible. In the Resistant group, 19 genotypes were allocated: 05, 09, 11, 12, 13, 15, 16, 17, 20, 21, 22, 23, 24, 30, 33, 35, 37, 39 and 44; in the Intermediate were allocated 29 genotypes: 01, 02, 04, 06, 07, 08, 10, 14, 18, 19, 25, 26, 27, 28, 31, 34, 42, 45 and 50; and in the Susceptible group were allocated 16 genotypes: 03, 29, 32, 36, 38, 40, 41, 43, 46, 47, 48, 49, 51, 52, 53 and 54. Therefore, based on the results, it is concluded that there is variation in the resistance level of the genotypes of C. canephora to H. vastatrix. Such information should be considered in the decision about which genotypes will integrate the new cultivars to be released by the breeding program of conilon coffee / O Estado do Espírito Santo é o maior produtor nacional de café conilon e a ferrugem é considerada a principal doença da cultura. Os genótipos de conilon podem apresentar comportamento diferenciado em relação à ferrugem. Dentro desta abordagem, é de fundamental relevância a caracterização dos materiais genéticos superiores para resistência à ferrugem, no sentido de direcionar a seleção no programa de melhoramento de café conilon em execução pelo Incaper (Instituto Capixaba de Assistência Técnica, Pesquisa e Extensão Rural). Portanto, este trabalho objetiva avaliar a reação à Hemileia vastatrix de 54 genótipos de Coffea canephora selecionados no referido programa de melhoramento. A coleta do material vegetal e do fungo foi feita na Fazenda Experimental de Bananal do Norte, pertencente ao Incaper, em Cachoeiro de Itapemirim, ES. O experimento foi conduzido no laboratório de Fitopatologia do Centro de Ciências Agrárias da Universidade Federal do Espírito Santo (CCA-UFES), Alegre, ES. Foi utilizado o delineamento experimental inteiramente casualizado com três repetições, onde cada repetição foi composta por 16 discos de folha, que foram acondicionados em gerbox e inoculados com 104 esporos.mL-1 de H. vastatrix, com o auxílio de um pincel. Os gerbox foram colocados sob ausência de luz e 22ºC por 48 horas e então em fotoperíodo de 12 horas até o término do experimento. Cinco dias após a inoculação, os discos foram limpos com algodão para evitar o aparecimento de hiperparasitas. A partir do décimo dia foi observado o aparecimento de sintomas e foram avaliados, até o 37º dia, o período de incubação, o período latente, a incidência, a porcentagem de discos esporulados, o número de esporos, e a severidade. Os dados foram analisados no programa R, através da correlação de Pearson e STEPWISE e no programa Genes para a análise de variância, Scott-Knott e análise multivariada. Com base nos resultados verificou-se a formação de três grupos de genótipos de café conilon: Resistentes, Intermediários e Suscetíveis. No grupo Resistente foram alocados 19 genótipos: 05, 09, 11, 12, 13, 15, 16, 17, 20, 21, 22, 23, 24, 30, 33, 35, 37, 39 e 44; no grupo Intermediário foram alocados 19 genótipos: 01, 02, 04, 06, 07, 08, 10, 14, 18, 19, 25, 26, 27, 28, 31, 34, 42, 45 e 50; e no grupo Suscetível foram alocados 16 genótipos: 03, 29, 32, 36, 38, 40, 41, 43, 46, 47, 48, 49, 51, 52, 53 e 54. Assim, com base nos resultados, conclui-se que há variação no nível de resistência dos genótipos de C. canephora à H. vastatrix. Tal informação deve ser considerada no momento da decisão de quais genótipos integrarão as novas cultivares a serem lançadas pelo Programa de Melhoramento de Café Conilon

Disease resistance is critical in soft red winter wheat (Triticum aestivum L.) cultivars. Leaf rust caused by Puccinia triticina Eriks and stripe rust caused by Puccinia striiformis Westend. f.sp. tritici Eriks. are destructive pathogens of wheat. From 2014 to 2015 phenotypic data was collected at diverse locations for resistance to leaf rust (North Carolina, Texas, and Virginia) and stripe rust (Arkansas, North Carolina, Georgia, Texas, and Virginia) in a Pioneer ‘25R47’ /‘Jamestown’ (P47/JT) population composed of 186 F5:9 recombinant inbred lines (RILs). Analysis of the P47/JT population identified two quantitative trait loci (QTL) for leaf rust resistance on chromosome 5B and two QTL for stripe rust resistance on chromosomes 3B and 6A. Phenotypic variation (%) explained by the putative leaf rust resistance QTL of Jamestown on 5B was as high as 22.1%. Variation explained by the putative stripe rust resistance QTL of Jamestown on 3B and 6A was as high as 11.1 and 14.3%, respectively. Jamestown is postulated to contain gene Lr18. Seedlings of 186 F5:9 recombinant inbred lines from the P47/JT population and 200 F2 seedlings from eight other crosses including Jamestown and/or the Lr18 host differential line RL6009 (Thatcher*6/Africa 43) were screened with P. triticina race TNRJJ. Genetic analysis of the populations was conducted to validate the presence of Lr18 in Jamestown. Results of linkage analysis identified SNP maker IWB41960 linked within 5 cM of gene Lr18 in all three populations. From 2016 to 2017 phenotypic data was collected at diverse locations for resistance to leaf rust (Illinois, North Carolina, and Virginia) in a ‘2013412’ (PI 667644) / VA10W-21 (PI 676295) population (412/21) composed of 157 doubled haploid (DH) lines. The 412/21 DH lines were genotyped via genotyping by sequence (GBS). Analysis of the 412/21 population identified one quantitative trait loci (QTL) region associated with adult plant resistance to leaf rust on chromosome 1B. Phenotypic variation (%) explained by the putative leaf rust resistance QTL of 2013412 on 1B was as high as 40.1%. Kompetitive allele-specific (KASP) markers KASP_S1B_8414614 and KASP_S1B_8566239 were developed as markers for use in marker assisted selection. / Ph. D. / Disease resistance to leaf rust and stripe rust is important when growing soft red winter wheat. Genetic resistance can have a benefit to cost ratio of up to 27:1, considerably better than that of fungicide treatments. From 2013 to 2017 disease data was collected across multiple locations spanning the eastern United States (Arkansas, Georgia, Illinois, North Carolina, Texas, and Virginia). DNA molecular markers were used to identify specific chromosome regions containing genes associated with leaf and stripe rust resistance. DNA markers associated with genes conferring resistance to leaf rust resistance were identified in three chromosome regions, and genes in two regions were associated with stripe rust resistance. These genes and molecular markers associated with them can be used by scientists to further enhance resistance in wheat cultivars. Another study was conducted to determine if Lr18, a gene for leaf rust resistance that has a large effect, is present in the Virginia Tech soft red winter wheat breeding material. This gene (Lr18) is known to have been introduced from an ancestral species highly related to wheat. Wheat seedlings derived from crosses between lines postulated to carry Lr18 with susceptible lines were tested for resistance to a specific strain of leaf rust lacking virulence to Lr18. Genetic analysis of the ratio of resistant versus susceptible seedlings and association between DNA molecular markers and resistant seedlings were conducted to validate the presence of gene Lr18. A molecular marker linked tightly to gene Lr18 was identified in the study. This gene was found to be widely distributed in soft red winter wheat breeding materials and the molecular marker associated with gene Lr18 will be useful for scientists to further improve resistance in wheat cultivars.

L’optimisation de la biomasse produite par les taillis à courte rotation de peupliers représente un enjeu majeur pour la production de biocarburants de deuxième génération. Dans ce contexte, ce travail vise à faciliter le développement à court terme de nouvelles variétés clonales de peuplier permettant la production d’une ressource de qualité en s’intéressant plus particulièrement à l’architecture génétique de la résistance à la rouille foliaire et de la qualité du bois chez le peuplier noir (Populus nigra), espèce parente des hybrides cultivés. Des marqueurs SNP ont été développés à partir du séquençage de 665 fragments de gènes dans un panel de 21 individus. Ces derniers ont été associés à des marqueurs SSR et AFLP pour construire de nouvelles cartes génétiques sur une famille de 324 plein-frères clonés. Une technique de phénotypage à haut débit basée sur la spectrométrie à proche infrarouge a été développée pour prédire les teneurs en composés chimiques du bois ainsi que le rendement en saccharification. La mise en évidence d’une variabilité génétique importante pour l’ensemble des caractères a permis de cartographier les régions génomiques impliquées dans leur variation. Parmi les 11 QTL détectés pour la résistance, un QTL à effet majeur co-localise avec un QTL majeur associé à la résistance à la rouille foliaire du saule. Pour la qualité du bois, 15 QTL à effet faible à moyen ont été détectés, dont un cartographié sur le chromosome XIII qui colocalise avec des QTL précédemment identifiés chez le peuplier pour les teneurs en sucres et en lignines. Ce travail de thèse ouvre des perspectives d’identification de gènes sous-jacents aux QTL par génétique d’association. / Improvement of lignocellulosic resources from poplar short rotation coppices is a major challenge for the production of second generation biofuels. In this context, the present work aims at optimizing short term creation and deployment of improved poplar clonal varieties through the dissection of genetic control of both leaf rust resistance and wood quality in black poplar (Populus nigra), one of the parental species of cultivated hybrids. SNP markers have been developed from the resequencing of 665 gene fragments in a discovery panel of 21 individuals. These markers were combined with SSRs and AFLPs to build new genetic maps in a pedigree composed of 324 cloned full-sibs. High throughput phenotyping based on near infrared spectroscopy has been used to predict wood chemical contents and saccharification yield. High genetic variability expressed in all traits allowed the identification of genomic regions controlling this variation. Of the 11 QTL mapped for resistance, one major QTL co-localized with a major QTL previously detected for leaf rust resistance in willow. For wood quality, 15 QTL with low to moderate effect have been identified. Interestingly, one QTL mapped on chromosome XIII and colocalized with sugar and lignin contents QTL previously detected in poplar. Present results open perspectives towards the identification of candidate genes underlying the detected QTL through association genetics.

Leaf rust and stripe rust of wheat (Triticum aestivum L.) are caused by the fungal pathogens Puccinia triticina, and Puccinia striiformis f.sp. tritici, respectively. In North America, the incorporation of adult-plant resistance (APR) genes into breeding lines has been an important strategy to achieve durable resistance to both diseases. Previously, the spring wheat cultivar AC Domain was reported to express an effective level of adult-plant resistance (APR) to leaf rust under field conditions. Early gene postulation work had suggested AC Domain might carry the APR gene Lr34 due to its phenotypic similarity to other Lr34 carrying lines. However, new gene specific markers have shown that AC Domain is not a carrier of Lr34. The objective of this research was to genetically localize the resistance in AC Domain, which is important because the cultivar has frequently been used as a parent in Canadian breeding programs, primarily for its value as a source of pre-harvest sprouting resistance. A mapping population of 185 doubled haploid (DH) lines derived from the cross ‘RL4452’ by ‘AC Domain’ was used for this study. RL4452 is a known carrier of Lr34. During 2011-2012, the DH population was evaluated in field leaf rust nurseries at Saskatoon, SK and Portage, MB and at a stripe rust nursery at Lethbridge, AB. Field results indicated that rust resistance in the mapping population was variable, with lines ranging from highly resistant, to highly susceptible. DH lines carrying Lr34 showed a high level of resistance to both diseases. Thus, the non-Lr34 carriers were genotyped using select SSR markers, and by an Illumina 9k Infinium iSelect SNP assay for subsequent quantitative trait loci (QTL) analysis. QTL analysis revealed that AC Domain donated a major resistance QTL located on chromosome 2BS, that mapped 46 cM proximal to markers linked to Lr16, and explained a significant portion of the leaf and stripe rust phenotypic variance in all test environments. In addition, this QTL was significantly associated with the expression leaf tip necrosis (LTN), reduction in area under the disease progress curve (AUDPC), and coefficient of infection (CI). In certain environments the interaction between the 2B QTL and Lr34 was additive resulting in a superior level of rust resistance. Indoor rust testing showed AC Domain was susceptible to both diseases at the seedling stage. Taken together these results suggest that the identified resistance in AC Domain is likely due to the presence of an APR gene, on chromosome 2BS.

Proportional loss models commonly used in disease surveys are based on the assumption that per cent yield loss is the same in all crops, regardless of their yield potential. Estimates of regional crop loss may be inaccurate if the relationship between disease and yield loss is affected by crop yield potential. The importance of crop yield potential in disease: yield loss modelling was investigated and models for more accurate regional crop loss estimates were developed, taking crop yield potential into account. Two spring sown barley (cv. Triumph) experiments were conducted in 1987/88 and 1988/89 in Canterbury, New Zealand, to study the effect of crop yield potential on the relationship between disease and yield loss. Crop yield potentials of 323 to 806gDM/m² were generated in seven crops by varying nitrogen and water inputs, sowing date (mid-spring and early-summer) and season. Leaf rust (Puccinia hordei Otth) epidemics of different severity were generated by applying fungicides at different times, frequencies and rates to control the natural epidemics. Disease was measured as per cent disease severity (%DS), green leaf area, radiation interception and near-infrared radiation (NIR) reflectance from crop canopies. Yield was measured as total and grain dry weight. Epidemics were severe in the fully diseased plots from GS 34 and 46 to maturity in the late and early sown crops respectively. Disease reduced grain yield by 50 to 63% in 1987/88 and 24 to 38% in 1988/89 in the fully diseased plots. Disease: yield loss models were derived by regression analysis for each crop in 1987/88. Single point, multiple point and area under curve models were derived from %DS and GLAI variables, and proportional (%) and actual (gDM/m²) grain yield. The effect of yield potential was determined by comparing regression equation coefficients for each crop with crop yield potential. An area under green leaf area index curve (AUGLAIC): actual yield model was best suited to determining the effect of yield potential on yield loss. This model was selected because AUGLAIC summarised the effect of disease on plant growth over the season and actual yield represented the crop yield potential in the absence of disease and the response of actual yield to disease. Crop yield potential did not affect actual yield loss caused by leaf rust. Disease measured as AUGLAIC explained most of the variation in yield (R²adj=0.93) for all crops in both years. Assessment of GLAI is not suitable for estimation of regional crop loss because of the requirement for a rapid and low cost method. Reflectance of NIR from the crop canopy was investigated as an alternative to GLAI measurements. Reflectance was correlated significantly (P<0.001) with GLAI (r=0.66 to 0.89) and green area index (r=0.76 to 0.92). Reflectance measured at grain-filling (GS 85-87) explained most (R²adj=0.94) of the variation in yield for all crops in both years. The relationship between AUGLAIC and yield was validated with data from independent diseased and healthy barley crops. The AUGLAIC: yield model described the effects of disease on yield accurately but overestimated yield by 49 to 108% in the healthy crops. Models based on accumulated PAR (photosynthetically active radiation) intercepted by green leaves explained the observed deviations in yield of these crops from the AUGLAIC: yield model. Accumulated PAR models accounted for differences in incident radiation, canopy structure, radiation interception by green leaves, radiation use efficiency and harvest index which are important in determining dry matter production and grain yield. Accumulated PAR models described the effects of disease on crop growth which were not represented by GLAI alone. Variation in crop yield potential at the regional scale is important in disease: yield loss modelling and can be accounted for by using either separate equations for each yield potential crop or crop category, robust models, inclusion of a form function for yield potential or choice of disease and yield variables which integrate yield potential.

Leaf rust caused by Puccinia hordei is an important disease of barley (Hordeum vulgare) in many regions of the world. Yield losses up to 62% have been reported in susceptible cultivars. The Rph5 gene confers resistance to the most prevalent races (8 and 30) of barley leaf rust in the United States. Therefore, the molecular mapping of Rph5 is of great interest. Genetic studies were performed by analysis of 93 and 91 F2 plants derived from the crosses 'Bowman' (rph5) x 'Magnif 102' (Rph5) and 'Moore' (rph5) x Virginia 92-42-46 (Rph5), respectively. Linkage analysis positioned the Rph5 locus to the extreme telomeric region of the short arm of barley chromosome 3H at 0.2 cM proximal to RFLP marker VT1 and 0.5 cM distal from RFLP marker C970 in the Bowman x Magnif 102 population. Synteny between rice chromosome 1 and barley chromosome 3 was employed to saturate the region within the sub-centimorgan region around Rph5 using sequence-tagged site (STS) markers that were developed based on barley expressed sequence tags (ESTs) syntenic to the phage (P1)-derived artificial chromosome (PAC) clones comprising distal region of the rice chromosome 1S. Five rice PAC clones were used as queries to blastn 370,258 barley ESTs. Ninety four non-redundant EST sequences were identified from the EST database and used as templates to design 174 pairs of primer combinations. As a result, 10 EST-based STS markers were incorporated into the 'Bowman' x 'Magnif 102' high-resolution map of the Rph5 region. More importantly, six markers, including five EST-derived STS sequences, co-segregate with Rph5. Genes, represented by these markers, are putative candidates for Rph5. Results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley EST resources for marker saturation of targeted barley genomic region. / Ph. D.