Submitted by (lucia.rodrigues@ufrpe.br) on 2017-02-20T14:08:02Z No. of bitstreams: 1 Domingos Eduardo Guimaraes Tavares de Andrade.pdf: 2752116 bytes, checksum: f1548d1f41182d089565eefd683ee4ff (MD5) / Made available in DSpace on 2017-02-20T14:08:02Z (GMT). No. of bitstreams: 1 Domingos Eduardo Guimaraes Tavares de Andrade.pdf: 2752116 bytes, checksum: f1548d1f41182d089565eefd683ee4ff (MD5) Previous issue date: 1999-02-24 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Fresh tomato is very important in the Agreste Region of Pernambuco State, Brazil. However its production is impaired by the occurrence of Fusarium wilt caused by Fusarium oxysporum f.sp. lycopersyci. This study aimed to survey the disease intensity in planting areas of Camocim de São Félix county, Agreste of Pernambuco and to determine the ideal sample size for disease assessment, to analyze the disease spatial pattern in field, to characterize the variability of Fusarium oxysporum f.sp. lycopersyci populations and to select the resistance of tomato cultivars to races 1 and 2 of the pathogen. The disease survey in 50 planting areas showed high disease prevalence (72%) and average incidence of 17,15%. Using the incidence data from 36 areas as pilot-samples, the sample size for disease assessment was determined accordimg to the mean variability coefficient. The number of rows to be sampled was inversely related to disease incidence and acceptable error. To quantify the disease in future surveys, considering 10% error, each area should have 130rows and 12 plants/row sampled. The disease spatial pattern was studied in 11 planting areas in plots with 480 plants, using mapping, ordinary runs, fitting of β-binomial distribution and spatial autocorrelation analyses. Seven areas showed agregation of diseased plants and four areas presented the randomized pattern suggesting that there is not a single spatial pattern of the diasease in field.Thirty-six pathogen isolates were characterized in relation to epidemiological components, races and isoenzymatic patterns. The disease incidence separated isolates into two similarity groups but based upon the area under the disease progress curve (AUPDC) and progress rate there was three groups. Only one isolate belonged to race 1 while all the others were race 2 suggesting a small population variability regarding to races. The relative mobility of bands indicated six similarity groups for esterases and eight groups for fosfatase. There were no significant correlations among the relative mobility values for isozymes and the values for epidemiological components. In the resistance assay the disease temporal progress was analysed in 25 tomato cultivars inoculated with isolates of races 1 and 2. Race 2 isolates induced disease symptoms in all cultivars but race 1 isolates only induced symptoms in cultivars Santa clara I-5300, Jumbo AG-592, Barão Vermelho AG-591, Débora Plus AF-799, Débora and Viradouro. The cultivars Seculus and Rio Grande showedlonger incubation periods and smaller incidence values, progress rate and AUPDC, suggesting their use in programs of Fusarium wilt integrated management in Agreste of Pernambuco. / A cultura do tomateiro estaqueado apresenta expressiva importância na região Agreste do Estado de Pernambuco tendo, contudo, sua produção é limitada devido à ocorrência de murcha-de-fusário, causada por Fusarium oxysporum f.sp. lycopersici. Este estudo objetivou realizar o levantamento da intensidade da murcha-de-fusário em áreas de plantio no município de Camocim de São Félix, Agreste do Estado de Pernambuco, determinar o tamanho ideal da amostra para quantificação da doença, analisar o arranjo espacial da doença no campo, caracterizar a variabilidade de populações de F. oxysporum f.sp. lycopersici e selecionar cultivares de tomateiro resistentes às raças 1 e 2 do patógeno. No levantamento da intensidade da murcha-de-fusário em 50 áreas de plantio, foi constatada uma alta prevalência da doença (72%), com incidência média de 17,15%. Utilizando os dados de incidência de 36 áreas como amostragens-piloto o tamanho de amostras para quantificação da doença foi determinado com base no coeficiente de variação da média. O número de linhas por área, a ser amostrado, reduziu com a elevação da incidência da doença e do erro aceitável. Considerando o nível de erro de 10%, a amostragem em cada área de 130 linhas com 12 plantas/linha é apropriada para quantificar a incidência da doença em levantamentos futuros. O arranjo espacial da doença foi investigado em 11 áreas de plantio, numa parcela de 480 plantas/área, utilizando-se as análises de mapeamento, “ordinary runs”,ajuste à distribuição beta-binomial e autocorrrelação espacial. Em sete áreas ficou evidenciada a agregação de plantas doentes, enquanto que em quatro, ficou evidente o arranjo aleatório, indicando não haver um padrão único de arranjo espacial da doença no campo. Na caracterização da variabilidade de F. oxysporum f.sp. lycopersici, 36 isolados foram avaliados em relação a componentes epidemiológicos, a raças e a padrões isoenzimáticos. Com base na incidência da doença foi possível a separação dos isolados em dois grupos de similaridade, elevando-se para três quando consideradas a área abaixo da curva de progresso da doença e a taxa de progresso. Apenas um isolado foi caracterizado como pertencente à raça 1, enquanto os demais foram pertencentes à raça 2, indicando uma pequena variabilidade na população quanto à raça. O padrão isoenzimático possibilitou a separação dos isolados em seis grupos de similaridade para esterase e oito grupos para fosfatase. Não foram constatadas correlações significativas entre os valores da mobilidade relativa para as isoenzimas e os obtidos nos componentes epidemiológicos. Na avaliação da resistência ao patógeno, foi analisado o progresso temporal da murcha-de-fusário em 25 cultivares de tomateiro inoculadas com isolados das raças 1 e 2. Todas as cultivares apresentaram plantas com sintomas da doença, quando inoculadas com os isolados da raça 2, enquanto apenas as cultivares Santa Clara I-5300, Jumbo AG-592, Barão Vermelho AG-591, Híbrido Débora Plus AF-799, H. Débora e Viradoro evidenciaram suscetibilidade ao isolado da raça 1. As cultivares H. Seculus e Rio Grande destacaram-se das demais ao propiciarem os maiores períodos de incubação e os menores valores de incidência, de taxa de progresso e de área abaixo da curva de progresso da doença, indicando o potencial para utilização em programas de manejo integrado da murcha-de-fusário no Agreste de Pernambuco.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-03-16T12:53:24Z No. of bitstreams: 1 Eddy Enrique Barraza Andrion (1).pdf: 947495 bytes, checksum: aa5e0f6002d19bd71d54a71eae9dc237 (MD5) / Made available in DSpace on 2017-03-16T12:53:24Z (GMT). No. of bitstreams: 1 Eddy Enrique Barraza Andrion (1).pdf: 947495 bytes, checksum: aa5e0f6002d19bd71d54a71eae9dc237 (MD5) Previous issue date: 2009-07-31 / The cowpea (Vigna unguiculata L.) is one of the main crops in the Northeast of Brazil especially for the small farmers. The Fusarium wilt and Rhizoctonia canker caused by Fusarium oxysporum f.sp. tracheiphilum and Rhizoctonia solani, respectively are the cowpea diseases showing more frequency and intensity in the Northeast of Brazil. This work aimed to evaluate the natural suppressiveness of 66 soils of this region to the Fusarium wilt and Rhizoctonia canker, and to analyze the physical, chemical and biological characteristics of this soils associated with disease suppressiveness or conducivity. The evaluated soils were grouped from highly suppressive to highly conducive in relation to Fusarium wilt and Rhizoctonia canker severities. The main variables involved in Fusarium wilt suppressiveness were high levels of phosphorus and potassium, basal respiration (CO2 evolution) and indexes of microbial diversity and equitability. For Rhizoctonia canker important correlations were determined with levels of phosphorus, potassium and sodium, basal respiration and enzymatic activity of fluorescein diacetate. There was no correlation between physical factors and suppressiveness to Fusarium wilt, but it was possible to correlate the levels of sand, clay and silt with suppressiveness and/or conducivity of Rhizoctonia canker. Three soils previously classified as highly supressive to Rhizoctonia canker were evaluated in relation to eight strains and three inoculum densities of R. solani. There was significant difference among soils and strains in relation to levels of disease severity. In the three soils the severity levels induced by the strain CMM-1053 were similar to those observed in former studies. Most of the strains showed different behavior in relation to soils, except for CMM-1064 and CMM-1066. There was significant difference among disease severity levels and different inoculum densities. The three soils presented good stability in relation to the different R. solani strains, but the inoculum density may be a limiting factor in the implementation of the natural soil suppressiveness or the supressivity induction in conducive soils. / O caupi (Vigna unguiculata L.) é uma das culturas mais importantes da região Nordeste do Brasil, principalmente na economia de pequenos produtores rurais. A murcha-de-fusário e a rizoctoniose, causadas pelos fungos Fusarium oxysporum f.sp. tracheiphilum e Rhizoctonia solani, respectivamente, são as doenças mais freqüentes e de maior intensidade em caupi no Nordeste brasileiro. Esta tese teve como objetivos avaliar a supressividade natural de 66 solos do Nordeste brasileiro à murcha-de-fusário e rizotoniose do caupi, analisar as características físicas, químicas e biológicas dos solos associadas com a supressividade ou conducividade às doenças, bem como avaliar a estabilidade da supressividade de três solos à rizoctonose do caupi, considerando diferentes isolados e densidades de inóculo de R. solani. Em relação à severidade da murcha-de-fusário e da rizoctoniose do caupi, os solos avaliados foram agrupados desde fortemente supressivos a altamente conducivos. As principais variáveis envolvidas na supressividade da murcha-de-fusário foram elevados teores de fósforo e potássio, respiração basal (CO2 evoluído) e os índices de diversidade e eqüitabilidade microbiana. Para a rizoctoniose, foram determinadas correlações importantes com os níveis de fósforo, potássio e sódio, respiração basal e atividade enzimática de diacetato de fluoresceína. Não foram correlacionados fatores físicos com a supressividade à murcha-de-fusário, porém foi possível correlacionar os teores de areia, argila e silte com asupressividade e/ou conducividade da rizoctoniose. Três solos classificados como fortemente supressivos à rizoctoniose foram avaliados em relação a oito isolados e três densidades de inoculo de R. solani. Houve diferença significativa entre os solos e os isolados quanto aos níveis de severidade da doença. Nos três solos os níveis de severidade induzidos pelo isolado CMM-1053 foram similares aos verificados nos estudos prévios. A maioria dos isolados apresentou comportamentos diferente em função dos solos, com exceção dos isolados CMM-1064 e CMM-1066. Foi verificada diferença significativa entre os níveis de severidade da doença e as diferentes densidades de inoculo. Os três solos evidenciaram estabilidade em relação aos diferentes isolados de R. solani, porém a densidade de inóculo pode ser um fator limitante na implementação da supressividade natural dos solos ou da indução da supressividade em solos conducivos.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-03-16T15:49:19Z No. of bitstreams: 1 Erick Farias Couto.pdf: 519238 bytes, checksum: 39bbbff610acf377a744dada09f340cf (MD5) / Made available in DSpace on 2017-03-16T15:49:19Z (GMT). No. of bitstreams: 1 Erick Farias Couto.pdf: 519238 bytes, checksum: 39bbbff610acf377a744dada09f340cf (MD5) Previous issue date: 2008-03-03 / The cotton has been in the human history for ages; it is used to the confection of clothes and its subproducts are an important source of protein to the domestic animals. Because of its wide distribution in the Brazil, the ocurrence of disease has become more frequently. Among the diseases, great importance is given to the fusarium wilt of cotton (Fusarium oxysporum f. sp. vasinfectum) because of its potential to cause severe losses and its hard control. The present work aimed to develop alternatives to be offered to the cotton producers. The first experiment refers to the evaluation of the planting methods of cotton and the reaction of 106 cultivars in relation to the vascular wilt of fusarium. Among the methods of planting, the plastic cups was chosen because in this method the roots of the seedlings can grow more vigorously. In the water restricion method there was no ocurrence of typical simptoms of the vascular wilt. The paper towel method resulted in anormal seedlings or the seedlings were contaminated with parasites. It was possible to determinated a group with a high level of resistance among the cultivars tested. In this group, its important to say that the cultivar SP 2473-A also exhibit resistance to the ramulosis. The second experiment is reffered to the resistance induction with the abiotic inducers (acibenzolar-S-metil, metil jasmonato e fosfato de potássio) in seedlings of the cotton cultivar ‘BRS Cedro’ and the evaluation of the enzymatic activity elicited (in samples of leaves and stem) in seedlings induced (once and twice) and seedlings without the induction, inoculatedand not inoculated with Fusarium oxysporum f. sp. vasinfectum. The infection index was also evaluated in this treatments. The treatment with methyl jasmonate (two inoculations) in the stem showed the minor infection index (45,00). It was possible to correlate this treatment with the minor infection index and the high level of the enzyme superoxide dismutase in the stem. / O algodão tem acompanhado a história do homem desde tempos remotos, serve como matéria prima para a confecção de vestuário e ainda apresenta como subprodutos uma rica fonte de proteína para o consumo de animais domésticos. Devido a sua ampla distribuição em todo o Brasil, a ocorrência de doenças tem se tornado cada vez mais freqüente. Dentre as doenças, um grande destaque é dado a murcha de fusário (Fusarium oxysporum f. sp. vasinfectum), devido ao seu potencial em causar sérios prejuízos e seu difícil controle. Diante do exposto, o presente trabalho refere-se as atividades realizadas visando desenvolver uma alternativa para a cadeia produtiva do algodoeiro. O primeiro experimento refere-se a avaliação de métodos de plantio de algodoeiro e avaliação de 106 cultivares de algodoeiro em relação a murcha de fusário. Dentre os métodos de plantio avaliados, o plantio em copo plástico foi o escolhido por ter proporcionado um melhor desenvolvimento do sistema radicular das plântulas de algodoeiro. No método da restrição hídrica não ocorreu o aparecimento de sintomas característicos da murcha de fusário. O método do papel toalha resultou em plântulas anormais ou as sementes foram parasitadas com contaminantes. Entre as cultivares testadas quanto a reação a murcha de fusário foi possível estabelecer um grupo com um alto nível de resistência com destaque para a cultivar SP 2473-A, que também possui resistência contra a ramulose. O segundo experimento refere-se a indução de resistência com os indutores abióticos (acibenzolar-S-metil, metiljasmonato e fosfato de potássio) em plântulas da cultivar BRS Cedro de algodoeiro e avaliação da atividade enzimática elicitada (amostras de folhas e caule) em plantas induzidas (com uma e duas induções) e não induzidas, inoculadas e não inoculadas com Fusarium oxysporum f. sp. vasinfectum, sendo ainda realizada a avaliação do índice de infecção. O menor índice de infecção (45,00) foi obtido pelo tratamento com metil jasmonato (duas inoculações) no caule. Neste tratamento foi possível estabelecer a provável conexão entre o menor índice de infecção e um alto nível da enzima peroxidase nas folhas e da enzima superóxido dismutase no caule.

<p>Microorganisms, including two fungi, <i>Phytophthora cryptogea</i> and <i>Fusarium oxysporum</i> strain Fo-(IMI 386351), and one bacterium, <i>Pesudomonas</i> sp. strain MF30, were tested for their abilities to stimulate plant defence responses in tomato (<i>Lycopersicon esculentum</i> –L.) and to serve as effective biocontrol agents (<b>Bs</b>). The study included <i>in vivo</i> and <i>in vitro</i> characterization of biological attributes of the microorganisms, pertaining to their abilities to stimulate plant immunity against a fungal pathogen, <i>Fusarium oxysporum</i> f. sp. <i>lycopersici</i> (Fol), the causal agent of tomato wilt disease. Using <i>Lycopersicon esculentum</i> –L. as a model plant for examining some fundamental elements of the plant-microorganism interaction, the study reveals and clarifies some aspects of the close association and the complexity of such systems.</p><p>For each <b>B</b>, the results revealed a <b>B</b>-distinct plant-microorganism interaction, which included systemic induced resistance (SIR). A phylogenetic analyses of the partial sequences of two Fo-(IMI 386351) genes, a mitochondrial small subunit ribosomal DNA (mtSSU rDNA) and the nuclear translation elongation factor 1α (EF-1α), provided phylogenetic trees confirming that Fo-(IMI 386351) might be a member of Fol or of <i>F. oxysporum</i> f. sp. <i>melonis</i>, which have polyphyletic evolutionary origins. RFLP analysis (mtDNA), suggested that Fo-(IMI 386351) probably belongs to Fol. For routine and accurate differentiation between two morphologically indistinguishable <i>F. oxysporum formae speciales</i> strains, <i>F. oxysporum</i> f. sp. <i>lycopersici</i> and <i>F. oxysporum</i> f. sp. <i>radicis-lycopersici</i>, a molecular method (mtDNA RFLP analysis) was developed, and its usefulness for such differentiation was compared with that of two other methods: isozyme analysis and an osmotic method, revealed with high performance liquid chromatography (HPLC). The HPLC-spectra of Fo-(IMI 386351) had an extra peak for the two tested fractions, indicating that activation of the observed plant defence mechanism could have been at least partially the result of one of the products of the eliciting microbe. Preliminary results obtained by nuclear magnetic resonance spectrometry of those fractions suggest that the extra peak probably represents an oligosaccharide, which may have acted as a mobile signal and triggered the plant defence mechanisms.</p><p>We concluded that (1) our three tested microorganisms are able to stimulate plant defence mechanisms by triggering SIR (plant immunity), (2) the complexity and elaborateness of evolved plant-microbe interactions involving plant defence can, at least in some cases, be observed and studied in the laboratory, and (3) molecular tools can be a powerful means for identifying fungal strains and for clarifying their taxonomical relationships.</p>

The investigation was designed to explore the structure, composition and activity of a biological soil crust on an acidic, sandy soil from a temperate climate. The crust covers several hundreds of square meters on the hilltop of a large terminal moraine. The conjugate alga <i>Zygogonium ericetorum</i> forms the essential matrix for the crust, a dense web of algal filaments with interspersed lichens and mosses. The crust is composed of three layers, with an uppermost layer consisting nearly entirely of a dense algal mat. In lower layers, a parasitic fungus, penetrating the algal cells, is another important component of the crust community. In this soil crust, photosynthetic and respiratory activity is stabilized at low water activities.

Microorganisms, including two fungi, Phytophthora cryptogea and Fusarium oxysporum strain Fo-(IMI 386351), and one bacterium, Pesudomonas sp. strain MF30, were tested for their abilities to stimulate plant defence responses in tomato (Lycopersicon esculentum –L.) and to serve as effective biocontrol agents (Bs). The study included in vivo and in vitro characterization of biological attributes of the microorganisms, pertaining to their abilities to stimulate plant immunity against a fungal pathogen, Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease. Using Lycopersicon esculentum –L. as a model plant for examining some fundamental elements of the plant-microorganism interaction, the study reveals and clarifies some aspects of the close association and the complexity of such systems. For each B, the results revealed a B-distinct plant-microorganism interaction, which included systemic induced resistance (SIR). A phylogenetic analyses of the partial sequences of two Fo-(IMI 386351) genes, a mitochondrial small subunit ribosomal DNA (mtSSU rDNA) and the nuclear translation elongation factor 1α (EF-1α), provided phylogenetic trees confirming that Fo-(IMI 386351) might be a member of Fol or of F. oxysporum f. sp. melonis, which have polyphyletic evolutionary origins. RFLP analysis (mtDNA), suggested that Fo-(IMI 386351) probably belongs to Fol. For routine and accurate differentiation between two morphologically indistinguishable F. oxysporum formae speciales strains, F. oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici, a molecular method (mtDNA RFLP analysis) was developed, and its usefulness for such differentiation was compared with that of two other methods: isozyme analysis and an osmotic method, revealed with high performance liquid chromatography (HPLC). The HPLC-spectra of Fo-(IMI 386351) had an extra peak for the two tested fractions, indicating that activation of the observed plant defence mechanism could have been at least partially the result of one of the products of the eliciting microbe. Preliminary results obtained by nuclear magnetic resonance spectrometry of those fractions suggest that the extra peak probably represents an oligosaccharide, which may have acted as a mobile signal and triggered the plant defence mechanisms. We concluded that (1) our three tested microorganisms are able to stimulate plant defence mechanisms by triggering SIR (plant immunity), (2) the complexity and elaborateness of evolved plant-microbe interactions involving plant defence can, at least in some cases, be observed and studied in the laboratory, and (3) molecular tools can be a powerful means for identifying fungal strains and for clarifying their taxonomical relationships.

Sorghum [Sorghum bicolor (L.) Moench] is a major food security crop for millions of people in sub-Saharan Africa and the fourth most important crop in Africa. The potential sorghum yields are limited due to a number of abiotic, biotic and socio-economic constraints. Among the biotic stresses is the parasitic weed, Striga hermonthica, which inflicts yield losses ranging from 30-100%. Various control options have been recommended to reduce levels of Striga damage. However, these techniques need to be integrated for effective control and to boost sorghum productivity. A series of experiments was conducted to integrate host resistance improvement and the use of a biological control agent, Fusarium oxysporum f.sp. strigae to control Striga hermonthica. These studies were also focused on improving breeders‟ awareness of the traits that farmers‟ desire, on the assumption that farmers‟ variety preference traits are the missing link in technology development and adoption process for S. hermonthica management. The objectives of the study were to: 1) determine farmers‟ views on sorghum production opportunities; threats; indigenous knowledge and perceptions; breeding priorities; Striga infestation; and the coping mechanisms of farmers in the north eastern and north western Ethiopia, 2) evaluate sorghum genotypes for compatibility to F. oxysporum inoculation where grown in Striga infested soil in controlled environments, 3) determine field responses of sorghum genotypes and F. oxysporum compatibility for integrated Striga management (ISM), 4) determine the variability present among selected sorghum genotypes exhibiting S. hermonthica resistance, and compatibility with the biological control agent using phenotypic and simple sequence repeat (SSR) markers, 5) identify F. oxysporum compatible sorghum parents and hybrids with high combining ability for grain yield, yield components, and Striga resistance for ISM, and 6) undertake farmers‟ participatory assessment, and identify their preferred traits for sorghum genotypes under ISM, simultaneously with the breeders‟ evaluation. A participatory rural appraisal (PRA) research was conducted involving 315 farmers in nine districts of three administrative zones within two provinces in Ethiopia. Sorghum landraces were preferred by >85% of participants rather than previously improved released varieties. The participating farmers listed and prioritized their sorghum production constraints. In the North Shewa and North Wello zones drought was the most important constraint, followed by Striga. In the Metekel zone Striga was the number one constraint followed by a lack of genotypes with high grain quality. Controlled environment experiments were conducted involving greenhouse and laboratory tests in order to evaluate 50 sorghum genotypes for their compatibility with F. oxysporum and for possible deployment of the bio-control agent to control Striga. Striga population was reduced by 92% through the application of F. oxysporum, resulting in yield increment of 144%. Twelve sorghum genotypes were identified as promising parents for breeding and to control Striga through integration of host resistance and F. oxysporum seed treatment. During field and sick plot plot evaluations differential responses to F. oxysporum application among the sorghum genotypes were observed for various attributes including Striga plant height. Most traits showed highly significant (p<0.001) genotype X site interactions. Similarly, the main effects of F.oxysporum application were highly significant (p<0.001) across sites for most of the traits. The genotype and genotype X environment biplot identified 13 genotypes that consistently performed well following Fusarium application. The variability present among 14 selected sorghum genotypes exhibiting S. hermonthica resistance, and compatibility with a biological control agent, Fusarium oxysporum, were determined using phenotypic and 20 polymorphic simple sequence repeat (SSR) markers. Highly significant (p<0.001) differences were detected among genotypes for phenotypic traits. Principal component analysis showed three components that accounted for 73.99% of the total variability exhibited among genotypes. Cluster analysis allocated the genotypes into two major groups, one with a further two subgroups based on morphological traits, showing clear demarcations between the genotypes. The SSR markers revealed high levels of polymorphisms among genotypes, with the mean number of alleles per locus being 6.95 and the mean polymorphic information content being 0.80. The observed genetic diversity was relatively wide, with the allele sizes ranging from 203.6-334 bp. The SSR markers allocated genotypes into two distinct clusters close to the phenotypic markers. Forty sorghum hybrids were developed through a line by tester mating design involving 10 lines selected for their compatibility with F. oxysporum and high agronomic performances and four Striga resistant tester parents. The F1s and their parents were field evaluated with complementary in-vitro tests. Field evaluations were conducted at two locations: Kobo and Shewa Robit in Ethiopia, which are well known for their severe Striga infestation. Significant (p<0.05) general combining ability (GCA) effects were observed among testers and lines at both sites for days to 50% flowering and maturity, plant height, biomass, number of Striga plants and Striga plant height. Furthermore, significant (p<0.05) specific combining ability (SCA) effects were detected for days to 50% flowering, biomass, grain yield and number of Striga plants. From the complementary in-vitro experiment, highly significant variation (p<0.01) was exhibited due to line x tester interaction for maximum Striga germination distance. The study identified paternal parents with high GCA effects including SRN-39 and Birhan and maternals 235761, 2384443, IC9830, 235466, 237289,235763, and 235929 to be useful for breeding for ISM in sorghum. At Kobo, cross 235763 x N-13 and Shewa Robit IC9830 x SRN-39 had significantly negative SCA effects for the numbers of Striga plants. Progenies of these crosses will be selected in the Striga resistance breeding program. In the participatory sorghum genotypes assessment, farmers were invited to assess and select the genotypes based on their preferences at maturity and harvesting. The standard agronomic traits and Striga parameters relevant for breeding were collected by the breeders. Earliness, Striga resistance, high yield and high grain quality and threshability were the most important farmers‟-preferred traits for sorghum genotypes. Comparative analyses between farmers‟ and breeders‟ evaluations revealed highly significant correlations (p<0.01) except between Striga resistance and Striga damage and pest resistance and insect damage. Repeatability of scoring genotypes among farmers was consistent (>0.80) for all traits except Striga and pest resistance. The prioritized traits through farmers‟ participation are important for further breeding program. Overall, the study established farmers‟ preferred traits, the effectiveness of ISM to boost sorghum productivity, and identified useful parents and crosses for effective sorghum breeding to control Striga in Ethiopia. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Banana is the most important fruit crop in the world but ironically one of the crops least studied. This fruit constitutes a major staple food for millions of people in developing countries and also it is considered the highest selling fruit in the world market making this crop a very important export commodity for the producing countries. At the present time, one of the most significant constraints of banana production that causes significant economical losses are fungal diseases. Among these, Panama disease, also known as Fusarium wilt has been the most catastrophic. Panama disease is caused by the soil-borne fungus Fusarium oxysporum formae specialis (f.sp) cubense (FOC), which infects susceptible bananas through the roots causing a lethal vascular wilt. To date, the race 4 of this pathogen represents the most serious threat to banana production worldwide since most of the commercial cultivars are highly susceptible to this pathogen. Introduction of FOC resistance into commercial cultivars by conventional breeding has been difficult because edible bananas are sterile polyploids without seeds. Genetic transformation of banana, which has already been established in various laboratories around the world has the potential to solve this problem by transferring a FOC race 4 resistance gene into susceptible banana cultivars (eg. Cavendish cultivars). However, a FOC resistant (R) gene has not been isolated. Genes that confer resistance to Fusarium oxysporum have been isolated from tomato and melon using a map-based positional cloning approach. The tomato I2 and melon Fom-2 genes belong to the non-Toll/interleukin like receptors (TIR) subclass of nucleotide-binding site and leucine-rich repeat (NBS-LRR) R genes. These genes confer resistance only to certain races of F. oxysporum in their corresponding plant families limiting their use in other plant families. The fact that these two Fusarium resistance genes share the same basic non-TIR-NBS-LRR structure suggests a similar Fusarium resistance mechanism is shared between the families Solanaceae and Cucurbitaceae. This observation opens the possibility to find similar Fusarium resistance genes in other plant families including the Musaceae. A remarkable discovery of a population of the wild banana Musa acuminata subspecies (ssp.) malaccensis segregating for FOC race 4 resistance was made by Dr. Ivan Buddenhagen (University of California, Davis) in Southeast Asia. Research carried out at Queensland Department of Primary Industries (Australia) using this plant material has demonstrated that a single dominant gene is involved in FOC race 4 resistance (Dr. Mike Smith, unpublished results). Tissue-culture plantlets of this FOC race 4 segregating population were kindly provided to the Plant Biotechnology Program (Queensland University of Technology) by Dr. Mike Smith to be used in our research. This population holds the potential to assist in the isolation of a FOC race 4 resistance gene and other potential Fusarium resistance genes. The overall aims of this research were to isolate and characterise resistance gene candidates of the NBS-type from M. acuminata ssp. malaccensis and to identify and characterise potential Fusarium resistance genes using a combination of bioinformatics and gene expression analysis. Chapter 4 describes the isolation by degenerate PCR of five different classes of NBS sequences from banana (Musa acuminata ssp malaccensis) designated as resistance gene candidates (RGCs). Deduced amino acid sequences of the RGCs revealed the typical motifs present in the majority of known plant NBS-LRR resistance genes. Structural and phylogenetic analyses showed that the banana RGCs are related to non-TIR subclass of NBS sequences. The copy number of each class was estimated by Southern hybridisation and each RGC was found to be in low copy number. The expression of the RGCs was assessed by RT-PCR in leaf and root tissues of plants resistant or susceptible to Fusarium oxysporum f. sp. cubense (FOC) race 4. Four classes showed a constitutive expression profile whereas no expression was detected for one class in either tissue. Interestingly, a transcriptional polymorphism was found for RGC2 whose expression correlated with resistance to FOC race 4 suggesting a possible role of this gene in resistance to this devastating FOC race. Moreover, RGC2 along with RGC5 showed significant sequence similarity to the Fusarium resistance gene I2 from tomato and were chosen for further characterisation. The NBS sequences isolated in this study represent a valuable source of information that could be used to assist the cloning of functional R genes in banana. Chapter 5 describes the isolation and characterisation of the full open reading frame (ORF) of RGC2 and RGC5 cDNAs. The ORFs of these two banana RGCs were predicted to encode proteins that showed the typical structure of non-TIR-NBS-LRR resistance proteins. Homology searches using the entire ORF of RGC2 and RGC5 revealed significant sequence similarity to the Fusarium resistance gene I2 from tomato. Interestingly, the phylogenetic analysis showed that RGC2 and RGC5 were grouped within the same phylogenetic clade, along with the Fusarium resistance genes l2 and Fom-2. These findings suggest that the banana RGC2 and RGC5 are potential resistance gene candidates that could be associated with Fusarium resistance. The case of RGC2 is more remarkable because its expression was correlated to FOC race 4 resistance (Chapter 4). As a first step to test whether RGC2 has a role in FOC race 4 resistance, different expression constructs were made with the ORF of this sequence. One of the constructs contains a RGC2 putative promoter region that was successfully cloned in this work. These constructs will be used to transform susceptible banana plants that can then be challenged with FOC race 4 to assess whether resistance has been acquired by genetic complementation. The results of this thesis provide interesting insights about the structure, expression and phylogeny of two potential Fusarium resistance genes in banana, and provide a rational starting point for their functional characterisation. The information generated in this thesis may lead to the identification of a Fusarium resistance gene in banana in further studies and may also assist the cloning of Fusarium resistance genes in other plant species.

In previous studies silicon has been associated with reduced disease severity and incidence, the enhanced accumulation of phenolic compounds and lignin, and with changes in the defence-related enzyme activity and transcript abundance of defence and stress related genes. All of these aspects of plant defence were considered in this study on cotton infected with Fusarium oxysporum f. sp. vasinfectum (Fov), and the results obtained have greatly enhanced our understanding of the effects of silicon on this interaction. In all experiments conducted, defence responses were only significantly enhanced by silicon treatment following inoculation with Fov, strongly suggesting that silicon can prime defence responses in cotton infected with Fov. Sicot F-1 was the cultivar most resistant to Fov infection at the commencement of this research, whilst Sicot 189 was considered to have moderate resistance to the pathogen. Vascular discolouration was significantly reduced in the more resistant cultivar, Sicot F-1 following treatment with potassium silicate, compared to mock inoculated plants and inoculated plants treated with potassium sulphate or calcium sulphate. No significant differences between treatments were observed in the moderately resistant cultivar, Sicot 189, though further trials may need to be conducted to confirm this result. In both cultivars, silicon content was significantly greater in plants which had been treated regularly with liquid potassium silicate, rather than with calcium silicate powder. Histological investigation of cotton infected with Fov, with and without silicon treatment, was conducted to ascertain the effects of this element on the accumulation of fungitoxic phenolic compounds, cell ultrastructural changes and fungal infection structures. Fov proliferated through the cortex and stele of plants from both the resistant (Sicot F-1), and moderately resistant (Sicot 189) cultivars, regardless of silicon treatment. However, defences were more rapidly and intensely induced in endodermal and vascular regions of inoculated, potassium silicate treated Sicot F-1 plants. Significantly more phenolic compounds were present at seven days post infection (dpi) in root extracts of inoculated, potassium silicate treated Sicot F-1 plants. Phenolic compounds were not significantly increased in inoculated, potassium silicate treated root extracts of Sicot 189 plants at three or seven dpi. Lignin assays demonstrated that the dry weight percentage of lignin in root material from inoculated, potassium silicate treated Sicot F-1 plants was significantly higher than that of extracts from inoculated plants not receiving silicon treatment at three dpi. This trend was also observed at seven dpi; however lignin content was not significantly different in this case. Percentage lignin content in the roots of Sicot 189 plants was not significantly different between inoculated potassium silicate treated plants and those not treated with silicon. Histological alterations were not observed in mock inoculated water or potassium silicate treated plants, nor were any significant increases in phenolic compounds or lignin accumulation detected in control treatments not inoculated with the pathogen. The expression of several defence related genes was assessed with quantitative reverse transcriptase real-time polymerase chain reaction. The results obtained verify that potassium silicate can enhance defence responses in Sicot 189 and Sicot F-1 plants inoculated with Fov, with silicon having a more pronounced effect on the more resistant cultivar, Sicot F-1. Genes upregulated at three and four dpi in potassium silicate treated, Fov inoculated Sicot F-1 plants included peroxidase, cadinene synthase and polygalacturonase inhibiting protein (PGIP), with peroxidase associated with phenol oxidation and lignification and cadinene synthase with phytoalexin biosynthesis. Osmotin-like protein and chitinase class I were consistently upregulated in potassium silicate treated, inoculated Sicot 189 plants; both genes coding for pathogenesis related (PR) proteins, with chitinase also classified as an antifungal protein. In both cultivars, silicon treatment without Fov inoculation did not result in the significant up-regulation of any of the defence genes assessed, providing further evidence for the role of silicon in priming in this interaction. The activities of three defence related enzymes, peroxidase, chitinase and β-1, 3- glucanase was assessed in root and shoot material by colourimetric assays. Regular application of potassium silicate significantly increased the activity of peroxidase in root extracts from the highly resistant cultivar Sicot F-1, at three, four and seven dpi with Fov, and in root extracts from the moderately resistant Sicot 189 at three and four dpi. Significant increases in chitinase activity in inoculated, silicon treated Sicot 189 plants were observed in root extracts at three dpi, and in shoot extracts at four dpi. Soluble potassium silicate treatment resulted in significant increases in β-1, 3- glucanase activity in Sicot 189 root extracts at four dpi. Few significant differences between treatments in terms of chitinase and β-1, 3- glucanase activity were detected in Sicot F-1 plants, though higher levels of each of these enzymes were present in root and shoot extracts from this cultivar. In this study the effects of acibenzolar-S-methyl, applied in the form of Bion®, on defence gene expression and enzyme activity in cotton infected with Fov were more pronounced in plants cultivated from treated seed, rather than in plants treated via foliar spray; a finding which is particularly relevant to the industry presently. Significant up-regulation of chitinase class I, peroxidase, and β-1, 3-glucanase transcripts and enzyme activities occurred in the Bion® seed soak treatment with Fov inoculation compared to all other treatments. It was possible to compare the actions of silicon with those of Bion® in this study. Bion® primed defence responses in cotton infected with Fov, in a manner similar to that observed in silicon treated cotton. The use of silicon and Bion® treatments, both alone and in combination as part of integrated disease management programmes, may potentially contribute to increased protection against this pathogen in Australian cotton fields in the future.

The following contains two projects focused on the fungal pathogen, Fusarium oxysporum. The first project was purely computational in the examination of transposable elements (TEs), which are mobile sequences with the ability to multiply and move in their host genome. In F. oxysporum, TEs such as miniature impala elements are associated with the secreted in xylem gene that are related to its virulence over its host. The F. oxysporum species complex can be utilized as a model system for the examination of TE content and TE expression during the infection cycle. To find whether TEs play a role in the infection process and if their expression changes when fungi are in planta, a comparison was made using RNA-seq data from a pathogenic (Fo5176) and a non-pathogenic strain (Fo47) of F. oxysporum interacting with the model plant Arabidopsis thaliana. Complementary to this, the copy numbers of the same TEs were calculated in the two aforementioned strains and in F. oxysporum f.sp. lycopersici 4287 (Fo4287) to find if there was a correlation between expression and copy number. Using these two different datasets together showed that TE expression and copy number are lower in the non-pathogenic strain and unlinked in the infection course. The second project examined the growth inhibition of Fusarium oxysporum isolates Fo32931 (the isolate pathogenic to immunocompromised humans) and Fo4287 with the use of extracts from chilies of Capsicum chinense. Pepper plants were grown from seed and the peppers were harvested for an ethanol (100%) extraction. After preparation, the optical density of growth of the F. oxysporum isolates was measured for a 48-hour period with 96-well plate containing varying concentrations of the extracts and controls. Growth curves were analyzed and normalized to a growth control. After doing High Performance Liquid Chromatography, an estimated concentration of capsaicin (the causal agent of the burning sensation from hot chilis) was established. A correlation between the amount of growth inhibition and the concentration of capsaicin was made. Taken together, the data suggests that an increase of capsaicin concentration in extracts is correlated with reduced growth for the two tested isolates of F. oxysporum.