O gênero Fusarium é um grupo de fungos de importância mundial, não só por causar patologias em plantas, mas também porque abriga espécies toxigênicas. Dentre estas, Fusarium verticillioides, Fusarium proliferatum e Fusarium subglutinans, cujos teleomorfos se agrupam no complexo Gibberella fujikuroi, estão associadas a patologias em milho. O presente estudo caracterizou uma coleção de 100 isolados de Fusarium spp. tanto do ponto de vista morfológico como molecular com vistas a identificá-los em nível de espécie. Para isto, foram usados como marcadores morfológicos a presença/ausência de clamidósporos, o tipo de célula conidiogênica e a disposição dos microconídios sobre a célula conidiogênica. Os isolados foram também identificados em espécie baseado em informações disponíveis na literatura acerca de marcadores moleculares desenvolvidos a partir da reação de PCR e primers espécie-específicos. A ausência de clamidósporo permitiu alocar a totalidade dos isolados no complexo G. fujikuroi. Os demais critérios morfológicos permitiram identificar 77 isolados como F. verticillioides, 20 como F. proliferatum, 2 como F. subglutinans. Apenas 1 isolado não foi possível identificar em espécie. Análises moleculares concordaram em 100% dos casos em que os isolados foram identificados como F. verticillioides e F. subglutinans. Porem, no caso dos 20 isolados identificados morfologicamente como F. proliferatum apenas 4 foram confirmados na análise molecular; os demais foram identificados como F. verticillioides. A diversidade genética estudada por AFLP ratificou a separação das espécies F. verticillioides e F. proliferatum, com um índice de similaridade de 0,40. Marcadores AFLP também evidenciaram alta diversidade genética de F. verticillioides. Todos os isolados causaram podridão do colmo em três híbridos comerciais de milho e não variaram em agressividade, independente do nível de resistência dos híbridos. / The genus Fusarium is an important group of fungi worldwide, not only for its capability to cause disease but because it also contains species which produce toxins. Among these, Fusarium verticillioides, Fusarium proliferatum and Fusarium subglutinans, which teleomorphs are grouped in the Gibberella fujikuroi group are associated with diseases in maize. This study characterized a collection of 100 isolates of Fusarium spp. under morphological and molecular criteria to identify them at the species level. For this purpose, morphological markers such as presence/absence of chlamydospores, conidiogenou cell type and microconidia arrangement on conidiogenou cell were assessed. The isolates were also identified at the species level based upon available information about molecular markers developed from the PCR reaction using speciesspecific primers. The absence of chlamydospores in all of the isolates placed them within the G. fujikuroi complex, and based on the other morphological criteria, 77 isolates were identified as F. verticillioides, 20 as F. proliferatum, 2 as F. subglutinans and one isolate remained unidentified at the species level. The molecular analyses agreed with the morphological identification of all F. verticillioides and F. subglutinans. However, in the case of 20 isolates identified morphologically as F. proliferatum only 4 were confirmed, the rest being identified as F. verticillioides. The genetic diversity based on AFLP confirmed the separation of F. verticillioides and F. proliferatum in two groups, with a similarity index of 0.40. AFLP markers also showed high genetic diversity within F. verticillioides. All isolates were caused stalk rot on three commercial hybrids and did not vary in aggressiveness regardless of the resistance level of the hybrids.

Nos últimos anos, o plantio mecanizado da cana-de-açúcar vem sendo cada vez mais utilizado no Brasil. Tal sistema possui menor custo sobre o convencional e viabiliza o plantio durante o ano todo. Entretanto, a maior quantidade de ferimentos nas mudas colhidas mecanicamente e a realização de plantios em períodos frios e com umidade do solo inadequada têm aumentado a incidência da podridão abacaxi, doença causada pelo fungo Thielaviopsis paradoxa. Áreas onde esta doença é problemática apresentam muitas falhas, exigindo, em alguns casos, replantio. Thielaviopsis paradoxa penetra nas mudas através de ferimentos, o que é importante em cana-de-açúcar, uma vez que os colmos são seccionados durante o plantio. Medidas que estimulem a brotação rápida ou que protejam os ferimentos das mudas produzem excelentes resultados no controle da doença. Com o objetivo de avaliar o controle da podridão abacaxi da cana-de-açúcar por meio da pulverização de fungicidas em mudas no sulco de plantio, foram instalados quatro experimentos, sendo dois em casa de vegetação e dois no campo. Para os ensaios em casa de vegetação, utilizou-se um substrato esterilizado, composto por uma mistura de solo, areia e esterco de gado. Uma suspensão de T. paradoxa na concentração de 103 esporos/g de substrato foi incorporada dois dias antes do plantio. As avaliações foram realizadas em um período de 45 dias, determinando-se o número de plantas, a velocidade de brotação, a biomassa da parte aérea e de raízes, e a severidade da doença. No campo, um dos experimentos foi realizado sem a inoculação do patógeno, com a colheita das mudas e plantio mecanizados. No outro experimento, uma suspensão do fungo foi inoculada com pulverizador costal manual na concentração de 9 x 104 esporos/m2, e o plantio foi realizado manualmente. As avaliações foram realizadas em um período de 13 meses, determinando-se o número de plantas, a velocidade de brotação, a biomassa da parte aérea, o teor de açúcares totais recuperáveis e o rendimento. Nos quatro experimentos, os fungicidas foram pulverizados sobre as mudas imediatamente após o plantio, com pulverizador costal pressurizado com CO2. Os dados das avaliações foram submetidos à análise de variância e à análise de contrastes ortogonais. Além disso, os tratamentos foram comparados com a testemunha através do Teste de Dunnett a 5% de significância. Os resultados mostraram que a pulverização de fungicidas nas mudas controlou a podridão abacaxi da cana-de-açúcar, sendo que os efeitos dessa prática foram mais positivos em condições mais favoráveis à manifestação da doença. Os fungicidas Azoxistrobina + Ciproconazol; Azoxistrobina + Fluodioxonil + Metalaxil- M; Propiconazol; Piraclostrobina e Piraclostrobina + Epoxiconazol foram eficientes no controle da podridão abacaxi da cana-de-açúcar. Por outro lado, Carboxina + Tiram, comercialmente utilizado com essa finalidade, não foi efetivo em controlar a doença, tanto em casa de vegetação como no campo. / In the last few years, mechanized planting of sugarcane has been frequently used in Brazil. This system has a lower cost than the conventional system and enables planting throughout the year. However, the higher quantity of injuries in seedpieces harvested mechanically and the planting at low temperatures and with inadequate soil humidity have increased the incidence of pineapple disease, caused by the fungus Thielaviopsis paradoxa. Areas where this disease is problematic present stand reduction, requiring, in some cases, replanting. Thielaviopsis paradoxa penetrates the seedpieces through wounds caused due to stalk sectioning during planting. Measures which increase shoot emergence or which protect seedpieces wounds produce excellent results in the disease control. In order to assess control of pineapple disease of sugarcane through in-furrow fungicide spray application on seedpieces, four experiments were installed, two in greenhouse and two under field conditions. For the experiments in the greenhouse, substrate consisting of a mixture of soil, sand and cattle manure was used. Suspension of T. paradoxa at the concentration of 103 spores/g of substrate was incorporated two days before planting. Evaluations were done in a period of 45 days assessing number of shoots, germination speed, biomass of shoots and roots, and disease severity. In the field, one of the experiments was performed with no inoculation of the pathogen, and the seedpieces harvesting and planting were mechanized. For the other experiment, a suspension of T. paradoxa spores at the concentration of 9 x 104 spores/m2 was sprayed in the plots and the planting was performed manually. Evaluations were done in a period of 13 months assessing number of shoots, germination speed, biomass of shoots, total recoverable sugar content and yield. In the four experiments, fungicides were sprayed on seedpieces immediately after the planting with a CO2 pressurized sprayer. Data were submitted to analysis of variance and to analysis of orthogonal contrasts. Moreover, treatments were compared to control by Dunnett´s Test at 5% of significance. Results showed that in-furrow spray application on seedpieces controlled pineapple disease of sugarcane, and the effects of this practice were more positive under more favorable conditions for the disease manifestation. The fungicides Azoxystrobin + Cyproconazole; Azoxystrobin + Fluodioxonil + Metalaxyl-M; Propiconazole; Pyraclostrobin and Pyraclostrobin + Epoxiconazole were efficient for controlling pineapple disease of sugarcane. On the other hand, Carboxin + Thiram, commercially used for this purpose, was neither effective in the greenhouse nor in the field to control the disease.

Esse trabalho teve dois objetivos distintos, quantificar e caracterizar os danos pós-colheita em frutos de ameixa e nectarina na Companhia de Entrepostos e Armazéns Gerais de São Paulo (CEAGESP) e testar produtos que possam ser utilizados no controle das doenças pós-colheita podridão parda (Monilinia fructicola) e podridão mole (Rhizopus stolonifer) nestes dois frutos. Durante a safra 2003 e 2004, foram realizados 20 levantamentos de quantificação de danos em frutos de nectarina e 11 em frutos de ameixa. Em cada levantamento foram avaliados 1% do total de caixas comercializados em cinco permissionários da CEAGESP. A amostragem foi estratificada por variedade, calibre e procedência dos frutos, sendo quantificados danos mecânicos, fisiológicos e doenças pós-colheita. Para o controle da podridão parda e mole, o efeito curativo e protetor do CaCl2, cera e luz UV-C, em diferentes concentrações e o efeito curativo do tratamento com ozônio foram avaliados. A incidência de danos na CEAGESP em frutos de ameixa variou de 5 a 47%, e em nectarina entre 14 e 54%, considerando as safras 2003 e 2004. Tanto em ameixa como em nectarina os danos mais freqüentes foram os mecânicos, com variação de 2 a 25% em frutos de ameixa e de 7 a 30% em frutos de nectarina. Danos fisiológicos variaram de 1 a 22% e de 2 a 18% em frutos de ameixa e nectarina, respectivamente. Danos provocados por doenças variaram de 0 a 13% em frutos de ameixa e de 1 a 9% em frutos de nectarina. Entre os patógenos mais constatados figuraram fungos do gênero Rhizopus, Monilinia, Geotrichum, Cladosporium, Fusarium e Alternaria, além de bactérias. Correlação entre a incidência de frutos com dano mecânico e a incidência de frutos doentes foi constatada na safra 2004, nos dois frutos. Em ameixa, a variedade Gulfblazer apresentou maior incidência a danos mecânicos e fisiológicos. Não foi observada diferença na incidência de danos mecânicos e de doenças, entre as variedades de nectarina avaliadas na safra 2003. Na safra 2004, a incidência de danos mecânicos e fisiológicos foi superior na variedade Sunraycer comparada às demais variedades. Em relação aos produtos testados, no geral, CaCl2 a 1%, mostrou potencial de controle das duas doenças nos dois frutos, aplicado como protetor ou curativo. A cera ECF 124 a base de carnaúba foi o produto mais eficiente, com redução de até 70% das duas doenças em ambos os frutos, principalmente quando aplicada de maneira protetora, a 9%. As doses (1,4 e 5,2 kJm-2) de UV-C testadas não controlaram as doenças com resultados praticamente iguais à testemunha (dose 0,0 kJm-2). A presença de ozônio não reduziu nenhuma das doenças em nenhum dos dois frutos avaliados. / This study had two distinct objectives, to quantify and characterize the postharvest damages in plums and nectarines in the wholesale market of São Paulo (CEAGESP), and to test products that can be used in the control of the postharvest diseases such as the brown rot (Monilinia fructicola) and soft rot (Rhizopus stolonifer) in these two fruits species. Twenty assessments in nectarine and eleven in plums were carried out in 2003 and 2004. In each year 1% of the total of boxes commercialized in five outlets of CEAGESP was assessed, considering mechanical and physiological damages and postharvest diseases. The selection of samples was conducted through stratified sampling, taking fruit cultivar, place of origin and fruit size as the stratification criteria. Curative and protective control measures of brown and soft rot were analyzed testing CaCl2, wax and UV-C light, in different concentrations. The ozone was studied only as curative treatment. The incidence of damages in plums at CEAGESP ranged from 5 to 47%, and in nectarines from 14 to 54%. Either in plums or in nectarines, postharvest mechanical injuries were the most frequent damages, varying from 2 to 25% in plums and from 7 to 30% in nectarines. Physiological damages ranged from 1 to 22% and from 2 to 18% in plums and nectarines, respectively. Postharvest diseases ranged from 0 to 13% in plums and from 1 to 9% in nectarines. The most frequent postarvest pathogens were Rhizopus, Monilinia, Geotrichum, Cladosporium, Fusarium and Alternaria, besides bacteria. A correlation between the incidence of mechanical damages and the incidence of postharvest diseases in 2004 in both fruits was noticed. Cultivar Gulfblazer (plum) showed more incidence of mechanical and physiological damages than Reubennel. No differences were observed in the incidence of mechanical and physiological damages among the cultivars of nectarines assessed in 2003. No difference in the susceptibility to postharvest diseases among the nectarine cultivars Sunred, Sunripe, Sunraycer and Colombina in 2003 was verified. In 2004 cv. Sunraycer showed incidence of mechanical damages significantly higher than the other varieties. Regarding the products tested, as a whole, CaCl2 at 1% showed potential of controlling the two diseases in both kind of fruits, applied as a protective or curative measure. The carnauba wax (ECF 124) was the most efficient product, with a reduction of up to 70% of both diseases in both kind of fruits, mainly when applied as a protective agent, at 9%. The doses (1,4 e 5,2 kJm-2) of UV-C tested did not control the diseases with results practically similar to the reference dose (0,0 kJm-2). The presence of ozone did not reduce either of the diseases in any of the fruits evaluated.

Chez S. tuberosum, les pathogènes bactériens Pectobacterium et Dickeya causent les maladies de la jambe noire et de la pourriture molle au champ et lors du stockage des tubercules. Outre les méthodes de prophylaxie, aucune méthode de lutte n’est efficace contre ces bactéries. La FN3PT/RD3PT mène des projets de recherche en phytopathologie et épidémiologie pour mieux comprendre les traits de vie et la physiologie de ces pathogènes, et proposer des solutions de lutte adaptées. L’objectif de ce travail était double : comparer le pouvoir pathogène de deux bactéries émergentes D. dianthicola et D. solani et étudier des stratégies de lutte biologique contre Pectobacterium et Dickeya. D’abord, deux souches isolées au champ, D. dianthicola RNS04.9 et D. solani 3337 ont été comparées au niveau de leur pouvoir pathogène sur tubercules et sur plante entière. Cette étape a nécessité la mise au point de pathosystèmes appropriés. D. dianthicola RNS04.9 apparait plus virulente que D. solani 3337 sur plante entière, alors que le contraire est observé sur tubercules. Une comparaison génomique complétée d’études fonctionnelles ont révélé l’exsitence de certains traits propres à chaque souche, notamment, le catabolisme de l’arabinose et de l’urée chez D. solani 3337 et celui du rhamnose chez D. dianthicola RNS04.9. Ensuite, un criblage d’isolats bactériens a été réalisé pour identifier des agents de lutte biologique capables d’inhiber la croissance de Dickeya et Pectobacterium. Six bactéries, des genres Pseudomonas ou Bacillus, ont été retenues. Les essais menés en serre ont montré l’efficacité d’une combinaison de trois Pseudomonas pour diminuer les symptômes de jambe noire causées par D. dianthicola et sa transmission à la descendance. La séquence du génome de ces agents de lutte biologique a été déterminée. Avec ces données, par qPCR, un maintien des agents de phytoprotection dans le sol a été observé. Enfin, un criblage de molécules chimiques a été réalisé sur la base de leur capacité anti-quorum-sensing pour réduire l’expression des facteurs de virulence chez Pectobacterium. Deux inhibiteurs du quorum-sensing ont été identifiés. En conclusion de ce travail, la possibilité de coupler différentes stratégies de lutte contre ces pathogènes pectinolytiques est discutée. / Pectobacterium and Dickeya phytopathogens are the causative agents of the blackleg and soft rot diseases on S. tuberosum, in the field or during tuber-storage. Today, no effective method permits to control these bacteria. The FN3PT / RD3PT conducts plant pathology and epidemiology researches to understand the life traits and physiology of these pathogens and propose adapted control solutions. The aim of this study was dual: to compare the virulence of two emerging pathogens D. dianthicola and D. solani, and to study biocontrol strategies directed at Pectobacterium and Dickeya. First, two strains were isolated from field samples, D. dianthicola RNS04.9 and D. solani 3337. The virulence of these strains was compared in tuber and whole plant-assays. This step required the development of appropriate pathosystems. D. dianthicola RNS04.9 appeared more virulent than D. solani 3337 on whole plant tests, while the opposite was observed on tubers tests. Genome comparisons and functional studies led to the dientifiation of some genetic traits unique to each strain such as the catabolism of arabinose and urea in D. solani 3337 and that of rhamnose in D. dianthicola RNS04.9. A screening of bacterial isolates was also performed to identify biocontrol agents capable of inhibiting the growth of Dickeya and Pectobacterium strains. Six isolates, belonging to the Pseudomonas or Bacillus genera were selected. The greenhouse trials have shown the efficacy of a combination of 3 Pseudomonas to reduce blackleg symptoms caused by D. dianthicola and its transmission to the offspring. The sequence of the genome of each biocontrol agents has been determined. With these data, the survival of biocontrol agents in the soil has been investigated by qPCR. Finally, a screening of chemical compounds was carried out on the basis of their anti-quorum sensing, i.e. their ability to quench the expression of Pectobacterium virulence factors. Two quorum-sensing inhibitors have been identified. As a conclusion to this work, opportunities to mix the various biocontrol strategies directed at pectinolytic pathogens is discussed.

O objetivo desta dissertação de mestrado foi avaliar a eficácia de uma vacina autógena no controle do footrot (FR) dos ovinos, para tanto foram desenvolvidos dois experimentos em duas propriedades rurais distintas, no Estado do Rio Grande do Sul (RS). O primeiro experimento foi conduzido em uma propriedade rural do município de Santiago, com um extenso histórico de surtos de footrot no rebanho ovino. Inicialmente foi colhido material infeccioso presente no rebanho para a produção de uma vacina autógena, posteriormente 347 ovelhas foram vacinadas (grupo V) com duas doses da vacina com 30 dias de intervalo, a dose foi 2 ml por via subcutânea. Desse grupo, 150 animais receberam a vacina na região axilar (grupo Va) e 197 animais receberam a vacina na região inguinal (grupo Vb). Um grupo de 75 ovelhas formou o grupo controle (grupo C) sem vacinação. Os dados mostraram que a prevalência do FR no grupo V que inicialmente era de 4%, sofreu uma redução para 2% na semana 23, chegando à zero na semana 30. No grupo C a prevalência de animais infectados foi de 6,7% no início do experimento, teve uma redução para 5,3% na semana 23 e ao final estava em 3,7%. Observou-se uma redução gradativa no número de ovinos infectados nos dois grupos, entretanto a eliminação seletiva ocorrida no grupo controle prejudicou a análise estatística dos dados. Amostras de sangue foram colhidas da jugular dos animais para verificar títulos de anticorpos aglutinantes contra o antígeno presente na propriedade em cinco ocasiões durante o experimento. Os resultados mostraram diferenças significativas (p<0,001) entre os títulos de anticorpos aglutinantes contra Dichelobacter nodosus no soro de ovinos vacinados e não vacinados durante o experimento. A análise das reações vacinais locais apontou a região inguinal como o melhor local para a aplicação da vacina com adjuvante oleoso por via subcutânea e também demonstrou uma relação direta entre a idade dos ovinos e o percentual de reações vacinais locais e a severidade dessas reações. Os resultados sugerem que a vacina autógena com adjuvante oleoso obteve sucesso no controle da doença. O segundo experimento foi conduzido em uma propriedade rural do município de Glorinha, com o objetivo de avaliar a resposta imunológica provocada por uma vacina monovalente e por uma vacina polivalente (7 sorogrupos) contra o FR. Trinta fêmeas ovinas, com idades variadas, foram divididas aleatoriamente em 3 grupos de 10 animais: grupo controle (C) que não foi vacinado, grupo vacinado com vacina monovalente (Vm) e grupo vacinado com vacina polivalente (Vp). Os ovinos vacinados receberam duas doses com quatro semanas de intervalo, a dose foi de 2 ml por via subcutânea na região inguinal. Amostras de sangue foram colhidas da jugular dos animais para verificar títulos de anticorpos aglutinantes contra o D. nodosus em quatro ocasiões durante o experimento. Os resultados mostraram diferenças significativas (p<0,001) entre os títulos médios geométricos (GMT) de anticorpos aglutinantes contra D. nodosus no soro de ovinos dos grupos Vm, Vp e C na quarta, sétima e 12ª semanas do experimento. Em relação aos títulos médios geométricos (GMT) entre os grupos Vm e Vp houve diferenças estatisticamente significativas na quarta e sétima semanas. A vacina monovalente induziu títulos de aglutininas superiores contra o D.nodosus em comparação com a vacina polivalente. / The objective of this work was to evaluate the efficacy of an autogenous vaccine in the control of footrot (FR) in sheep. Two field experimental works were carried on two different farms located in the State of Rio Grande do Sul (RS), Brazil. The first experiment was conducted on a farm in the municipality of Santiago, with a long history of FR outbreaks in their sheep flock. At beginning of the trail samples from FR infected sheep were collected for the production of an autogenous vaccine. Following 347 sheep were vaccinated (group V) with two doses of 2 ml subcutaneously vaccine 30 days apart. Of this group, 150 animals received the vaccine in the axillary region (group Va) and 197 animals received the vaccine in the inguinal region (group Vb). A group of 75 sheep formed the control group (group C) without vaccination. The data showed that the prevalence of FR in the group V initially 4%, was reduced to 2% at 23 weeks, reaching to zero at week 30. In the group C the prevalence of infected animals of 6.7% at the beginning of the experiment, was reduced to 5.3% at week 23, decreasing to 3.7%, at the end. There was a gradual reduction in the number of infected sheep in both groups, however the selective elimination occurred in the group C affected the statistical analysis. Blood samples were collected from the jugular vein of the animals to see evidence of agglutinating antibodies against the antigen present on the property on five occasions during the experiment. The results showed significant differences (p<0,001) between antibody titers against Dichelobacter nodosus in the serum of sheep vaccinated and not vaccinated during the experiment. The analysis of local vaccine reactions showed the inguinal region as the best place for the application subcutaneously oil-adjuvant vaccine and also demonstrated a direct relationship between the age of the sheep and the percentage of local vaccine reactions and the severity of these reactions. The results suggest that autogenous oil-adjuvant vaccine succeeded in controlling the disease. The second experiment was conducted on a farm in the municipality of Glorinha, in order to evaluate the immune response elicited by a monovalent and a polyvalent vaccine against FR, containing seven serogroups. Thirty ewes, of various ages were randomly divided into 3 groups of 10 animals each: control group (C) was not vaccinated, group vaccinated with monovalent vaccine (Vm) and the group vaccinated with polyvalent vaccine (Vp). The sheep were vaccinated with two doses of 2 ml subcutaneously in the inguinal region, four weeks apart. Blood samples were collected from the jugular vein of the animals to determine agglutination titers against D. nodosus in the beginning of the experiment (day zero) and in other three occasions, weeks 4, 7 and 12. The results showed significant differences (p<0,001) between the geometric mean titers (GMT) of antibodies against D. nodosus in the serum of sheep of groups Vm, Vp and group C in the fourth, seventh and 12th weeks of the experiment. For the geometric mean titers (GMT) between the groups Vm and Vp there was statistically significant differences in the fourth and the seventh weeks. The monovalent vaccine induced titers of higher against D. nodosus compared with the polyvalent vaccine.

Made available in DSpace on 2017-07-10T17:36:49Z (GMT). No. of bitstreams: 1 2013_Laline_Broetto.pdf: 1586357 bytes, checksum: 1ec5db5ff1f6efea61394595db367816 (MD5) Previous issue date: 2013-03-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Charcoal rot caused by Macrophomina phaseolina is a disease that occurs in a large number of plant species and besides not being economically controlled by fungicides, no genetic resistance has been found. On the other hand, there is a growing awareness of the proper handling of pesticides or of the search for new and environmentally safer technologies for handling of plant diseases. Therefore this study aimed to select isolates of Trichoderma sp. for biological control of M. phaseolina and to evaluate their mechanisms of antagonism, as well as its effect as growth promoter of common bean. Seventeen isolates of Trichoderma sp. were used, in two in vitro tests: direct confrontation with the pathogen and production of volatile compounds. After the in vitro tests, six isolates that showed increased aggressiveness to the pathogen were selected and tested in vivo for effectiveness in controlling M. phaseolina and capacity of promoting common bean growth. The isolates TI1, TM3, TM4, TLB2, TLB3, TLB9, TLB15 and TLB17 showed antagonism against M. phaseolina in direct confrontation, and the isolates TM2, TLB2, TLB12, TLB15 and TLB17 reduced the mycelial growth of the pathogen in the volatile compounds test. Regarding microsclerotia of the pathogen, all the isolates were capable of reducing their production. The isolates TI1, TM3, TLB3, TLB12 and TLB17 were good growth promoters of common bean and the isolates TI1, TM3, TLB2, TLB3, TLB12 and TLB17 increased production per plant, especially the isolate TLB12. Regarding the protection of common bean against M. phaseolina, the isolates TLB2, TLB3, TLB12 and TLB17 were efficient. Fungi of the genus Trichoderma show effectiveness in controlling M. phaseolina and stimulate growth and increase the production of common bean / Podridão de carvão causada por Macrophomina phaseolina é uma doença que ocorre em muitas espécies de plantas e, além de não ser controlada economicamente por fungicidas, nenhuma resistência genética foi encontrada. Por outro lado, existe uma crescente conscientização no manejo correto do uso de defensivos agrícolas ou na busca por novas tecnologias de manejo de doenças de plantas ambientalmente mais seguros. Sendo assim, este trabalho teve como objetivo selecionar isolados de Trichoderma sp. para controle biológico de M. phaseolina e avaliar seus mecanismos de antagonismo, bem como, seu efeito como promotor de crescimento do feijoeiro. Foram utilizados dezessete isolados de Trichoderma sp., em dois testes in vitro: confronto direto com o patógeno e produção de compostos voláteis. Após os testes in vitro, seis isolados que apresentaram maior agressividade ao patógeno foram selecionados e testados in vivo quanto à eficiência no controle de M. phaseolina e capacidade de promoção do crescimento do feijoeiro. Os isolados TI1, TM3, TM4, TLB2, TLB3, TLB9, TLB15 e TLB17 apresentaram antagonismo contra M. phaseolina no confronto direto, sendo que os isolados TM2, TLB2, TLB12, TLB15 e TLB17 reduziram o crescimento micelial do patógeno no teste dos compostos voláteis. Em relação aos microescleródios do patógeno, todos os isolados foram capazes de reduzir sua produção. Os isolados TI1, TM3, TLB3, TLB12 e TLB17 foram bons promotores de crescimento do feijoeiro, e os isolados TI1, TM3, TLB2, TLB3, TLB12 e TLB17 aumentaram a produção de grãos por planta, com destaque para o isolado TLB12. Em relação à proteção do feijoeiro contra M. phaseolina, os isolados TLB2, TLB3, TLB12 e TLB17 foram eficientes. Fungos do gênero Trichoderma apresentam eficiência no controle de M. phaseolina e estimulam o crescimento e aumento da produção do feijoeiro

Thesis (PhD. (Geography)) --University of Limpopo, 2019 / Of late climate change and consequently, the spread of crop diseases has been identified as one of the major threat to crop production and food security in subSaharan Africa. This research, therefore, aims to evaluate the role of in situ hyperspectral and new generation multispectral data in detecting maize crop viral and fungal diseases, that is maize streak virus and grey leaf spot respectively. To accomplish this objective; a comparison of two variable selection techniques (Random Forest’s Forward Variable, (FVS) and Guided Regularized Random Forest: (GRRF) was done in selecting the optimal variables that can be used in detecting maize streak virus disease using in-situ resampled hyperspectral data. The findings indicated that the GRRF model produced high classification accuracy (91.67%) whereas the FVS had a slightly lower accuracy (87.60%) based on Hymap when compared to the AISA. The results have shown that the GRRF algorithm has the potential to select compact feature sub sets, and the accuracy performance is better than that of RF’s variable selection method. Secondly, the utility of remote sensing techniques in detecting the geminivirus infected maize was evaluated in this study based on experiments in Ofcolaco, Tzaneen in South Africa. Specifically, the potential of hyperspectral data in detecting different levels of maize infected by maize streak virus (MSV) was tested based on Guided Regularized Random Forest (GRRF). The findings illustrate the strength of hyperspectral data in detecting different levels of MSV infections. Specifically, the GRRF model was able to identify the optimal bands for detecting different levels of maize streak disease in maize. These bands were allocated at 552 nm, 603 nm, 683 nm, 881 nm, and 2338 nm. This study underscores the potential of using remotely sensed data in the accurate detection of maize crop diseases such as MSV and its severity which is critical in crop monitoring to foster food security, especially in the resource-limited subSaharan Africa. The study then investigated the possibility to upscale the previous findings to space borne sensor. RapidEye data and derived vegetation indices were tested in detecting and mapping the maize streak virus. The results revealed that the use of RapidEye spectral bands in detection and mapping of maize streak virus disease yielded good classification results with an overall accuracy of 82.75%. The inclusion of RapidEye derived vegetation indices improved the classification accuracies by 3.4%. Due to the cost involved in acquiring commercial images, like xviii RapidEye, a freely available Landsat-8 data can offer a new data source that is useful for maize diseases estimation, in environments which have limited resources. This study investigated the use of Landsat 8 and vegetation indices in estimating and predicting maize infected with maize streak virus. Landsat 8 data produced an overall accuracy of 50.32%. The inclusion of vegetation indices computed from Landsat 8 sensor improved the classification accuracies by 1.29%. Overally, the findings of this study provide the necessary insight and motivation to the remote sensing community, particularly in resource-constrained regions, to shift towards embracing various indices obtained from the readily-available and affordable multispectral Landsat-8 OLI sensor. The results of the study show that the mediumresolution multispectral Landsat 8-OLI data set can be used to detect and map maize streak virus disease. This study demonstrates the invaluable potential and strength of applying the readily-available medium-resolution, Landsat-8 OLI data set, with a large swath width (185 km) in precisely detecting and mapping maize streak virus disease. The study then examined the influence of climatic, environmental and remotely sensed variables on the spread of MSV disease on the Ofcolaco maize farms in Tzaneen, South Africa. Environmental and climatic variables were integrated together with Landsat 8 derived vegetation indices to predict the probability of MSV occurrence within the Ofcolaco maize farms in Limpopo, South Africa. Correlation analysis was used to relate vegetation indices, environmental and climatic variables to incidences of maize streak virus disease. The variables used to predict the distribution of MSV were elevation, rainfall, slope, temperature, and vegetation indices. It was found that MSV disease infestation is more likely to occur on low-lying altitudes and areas with high Normalised Difference Vegetation Index (NDVI) located at an altitude ranging of 350 and 450 m.a.s.l. The suitable areas are characterized by temperatures ranging from 24°C to 25°C. The results indicate the potential of integrating Landsat 8 derived vegetation indices, environmental and climatic variables to improve the prediction of areas that are likely to be affected by MSV disease outbreaks in maize fields in semi-arid environments. After realizing the potential of remote sensing in detecting and predicting the occurrence of maize streak virus disease, the study further examined its potential in mapping the most complex disease; Grey Leaf Spot (GLS) in maize fields using WorldView-2, Quickbird, RapidEye, and Sentinel-2 resampled from hyperspectral data. To accomplish this objective, field spectra were acquired from healthy, moderate and xix severely infected maize leaves during the 2013 and 2014 growing seasons. The spectra were then resampled to four sensor spectral resolutions – namely WorldView-2, Quickbird, RapidEye, and Sentinel-2. In each case, the Random Forest algorithm was used to classify the 2013 resampled spectra to represent the three identified disease severity categories. Classification accuracy was evaluated using an independent test dataset obtained during the 2014 growing season. Results showed that Sentinel-2 achieved the highest overall accuracy (84%) and kappa value (0.76), while the WorldView-2, produced slightly lower accuracies. The 608 nm and 705nm were selected as the most valuable bands in detecting the GLS for Worldview 2, and Sentinel-2. Overall, the results imply that opportunities exist for developing operational remote sensing systems for detection of maize disease. Adoption of such remote sensing techniques is particularly valuable for minimizing crop damage, improving yield and ensuring food security.

This study evaluated the applicability of remote sensing instrumentation for site- specific management of abiotic and biotic stress on cotton grown under a center pivot. Three different irrigation regimes (100%, 75%, and 50% ETc) were imposed on a cotton field to 1) monitor canopy temperatures of cotton with infrared thermometers (IRTs) in order to pinpoint areas of biotic and abiotic stress, 2) compare aerial infrared photography to IRTs mounted on center pivots to correlate areas of biotic and abiotic stress, and 3) relate yield to canopy temperatures. Pivot-mounted IRTs and IR camera were able to differentiate water stress between the irrigation regimes, however, only the IR camera was effectively able to distinguish between biotic (cotton root rot) and abiotic (drought) stress with the assistance of groundtruthing. The 50% ETc regime had significantly higher canopy temperatures, which were reflected in significantly lower lint yields when compared to the 75% and 100% ETc regimes. Deficit irrigation up to 75% ETc had no impact on yield, indicating that water savings were possible without yield depletion.

Fusarium verticillioides è responsabile della fusariosi della spiga in mais e della contaminazione della granella con micotossine. Sono state individuate le regioni geniche e i geni candidati per la resistenza a Fusarium dal confronto tra una linea di mais resistente (CO441) e una suscettibile (CO354), impiegando tre diversi approcci: analisi QTL, analisi trascrittomica (RNASeq) e analisi metabolomica. 184 famiglie F2:3 (CO441xCO354) sono state valutate in due diversi ambienti nell’anno 2011 e inoculate artificialmente con due diverse tecniche (forchetta e stuzzicadente). E’ stata rilevata una significativa variazione genotipica in risposta all’infezione. Sulla base di una mappa preliminare di linkage molecolare contenente 74 marcatori microsatelliti polimorfici, sono stati determinati 8 QTLs comuni alla resistenza alla fusariosi della spiga e alla riduzione della contaminazione da fumonisine. Sono stati considerati geni candidati per la resistenza i geni differenzialmente espressi, risultanti dall’ RNASeq, in semi di mais CO441 prima e 72 ore dopo l’infezione. I metaboliti putativi correlati alla resistenza sono stati rilevati tramite high resolution LC-MS in entrambe le linee di mais. I geni candidati e i metaboliti mappano in pathway coinvolti nei meccanismi di difesa: fenilalanina, tirosina e triptofano biosintesi, fenilpropanoidi e flavonoidi biosintesi, metabolismo dell’acido linoleico e α-linolenico. Abbondanti trascritti derivano dalla biosintesi dei terpenoidi e dei diterpenoidi. Nei geni candidati verranno ricercati polimorfismi fra le due linee di mais e che andranno ad arricchire la mappa di linkage molecolare. / Fusarium verticillioides is responsible for Fusarium ear rot in maize and mycotoxin contamination of grain. Genomic regions and candidate genes for resistance to Fusarium were detected through the comparison of resistant (CO441) and susceptible (CO354) maize lines, by following three different approaches: Quantitative Trait Locus (QTL), transcriptomic (RNASeq) and metabolomic analyses. 184 F2:3 families (CO441xCO354) were evaluated in two different environments in 2011 and artificially infected with two side-needle inoculation methods (pin-bar and toothpick). Significant genotypic variation in response to infection was detected. On the basis of a genetic draft map containing 74 polymorphic SSRs markers, 8 common QTLs for Fusarium ear rot resistance and fumonisin contamination reduction were revealed. Candidate genes for resistance resulted from differentially expressed genes before and 72 hours post infection of CO441 kernels through RNASeq technology. Putative metabolites related to resistance were detected through high resolution LC-MS in both maize lines. Candidate genes and metabolites mapped in pathways involved in defense mechanism: phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid and flavonoid biosynthesis, linoleic and α-linolenic acid metabolism. Abundant genic transcripts derived from terpenoid and diterpenoid biosynthesis. Candidate genes will be screened for polymorphisms between the two maize lines in order to enrich the linkage map.

Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus Phanerochaete carnosa has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by P. carnosa, its genome was sequenced and transcriptomes were evaluated after growth on wood compared to liquid medium. Results indicate that P. carnosa differs from P. chrysosporium in the number and expression levels of genes that encode lignin peroxidase (LiP) and manganese peroxidase (MnP), two enzymes that modify lignin present in wood. P. carnosa has more genes for MnP with higher expression levels than LiP, while the reverse has been observed for P. chrysosporium. The abundances of transcripts predicted to encode lignocellulose-modifying enzymes were then measured over the course of P. carnosa cultivation on four wood species. Profiles were consistent with decay of lignin before carbohydrates. Transcripts encoding MnP were highly abundant, and those encoding MnP and LiP featured significant substrate-dependent response. Since differences in modes of lignin degradation catalyzed by MnP and LiP could affect the ability of each to degrade lignin from different types of wood, their activity on various hardwoods and softwoods were tested. Results suggest that MnP degrades softwood lignin more effectively than hardwood lignin, consistent with high levels of this enzyme in P. carnosa.