The effect of serial (multiple-year) organic matter (OM) amendment on soil properties has been described in some cropping systems, although less is known about the effect of serially amended field soils on soil-borne plant diseases. The objectives of this study were to describe the effects of the third and fourth years of annual, serial amendment with dairy manure solids on 1) soil physical and biological properties and 2) severity of sweet corn root rot. Plots were amended with five rates of separated dairy manure solids annually for three years. In the fourth year, plots were split and only half of each plot was re-amended. Soil physical properties [bulk density, free and occluded particulate organic matter (POM), soil water retention, total porosity, gravimetric moisture content] and biological properties [microbial activity (as hydrolysis of fluorescein diacetate; FDA) and microbial biomass-C] were assessed each year in all treatments. Root rot severity was assessed in situ and in the greenhouse with multiple sweet corn (Zea mays L. cv Golden Jubilee) bioassays conducted in the amended field soils. Necrosis of the radicle and nodal roots was assessed when plants reached the 6- leaf stage. Amendment rate was positively associated with increases in soil properties that serve as indicators of soil quality, such as POM content, total porosity, microbial biomass, and FDA activity. In the third year after amendment, weak root rot suppression was observed in-field and was associated with FDA activity. By the fourth year of serial amendment this trend was no longer evident, however evidence from the high-rate treatment that was not re-amended (3HNRA) pointed to an emerging suppressive mechanism that persisted up to 13 months after the third amendment. Factors that may be interacting over time to generate observed disease suppression in these serially amended soils include: short-term post-amendment microbiostasis, soil moisture retention, inoculum potential, and a novel suppressive mechanism. / Graduation date: 2006

Submitted by Rosana Amâncio (rosana.amancio@ufcg.edu.br) on 2018-07-11T20:50:26Z No. of bitstreams: 1 Dissertação Thamara - Capa Dura.pdf: 2260125 bytes, checksum: 530ae87f1e4a9200aafe1cb3102cff39 (MD5) / Made available in DSpace on 2018-07-11T20:50:26Z (GMT). No. of bitstreams: 1 Dissertação Thamara - Capa Dura.pdf: 2260125 bytes, checksum: 530ae87f1e4a9200aafe1cb3102cff39 (MD5) Previous issue date: 2016-08-19 / CNPq / A gomose, provocada principalmente pelo oomiceto Phytophthora parasitica, é uma das mais graves doenças que acometem culturas de citros no âmbito mundial. Durante a interação, plantas induzem cascatas de sinalização a fim de induzir respostas de defesa. Contudo, P. parasitica secreta proteínas efetoras capazes de modular estas respostas por parte do hospedeiro, a fim de promover a infecção. No gênero Citrus, espécies comercialmente importantes são suscetíveis a infecção por este patógeno e a resistência a gomose é encontrada na espécie de citros Poncirus trifoliata. Considerando a escassez de informações acerca do patossistema citros-P. parasitica, o presente trabalho objetivou analisar, por meio de RT-qPCR, a expressão quantitativa de genes efetores apoplásticos e citoplasmáticos de P. parasitica e da cascata de defesa em citros, durante interações com espécies suscetíveis e resistentes, Citrus sunki e P. trifoliata, respectivamente. Dos 17 genes efetores estudados, 10 apresentaram expressão quantitativa relativa diferencial ao nível de significância induzida em P. parasitica após inoculação em raízes de P. trifoliata, sendo 06 apoplásticos e 04 citosólicos. Os perfis de expressão dos 17 genes efetores de P. parasitica apresentaram dois picos máximos de expressão, indicativos da síntese de novo desses genes ao longo dos pontos temporais de interação, sendo o acúmulo dos transcritos mais precoce sobre P. trifoliata (as 6 h.a.i.) e mais tardio sobre C. sunki (as 96 h.a.i.). Os elevados níveis de expressão de genes efetores em P. parasitica induzidos por C. sunki as 96 h.a.i. devem corresponder a fase necrotrófica de vida do oomiceto, consequentemente devido ao sucesso na penetração das células vegetais suscetíveis e acúmulo de biomassa do patógeno. A presença de hifas intracelulares no córtex de raízes de C. sunki foi abundantemente visualizada em micrografias as 96 h.a.i., a qual deve ocorrer como consequência da suscetibilidade da planta ao patógeno. Seis grupos hierárquicos de genes co-regulados foram formados a partir dos perfis de expressão dos 17 genes efetores em P. parasitica, os quais são reagrupados de modo diferente de acordo com a interação com C. sunki ou com P. trifoliata, indicando que o patógeno foi capaz de reconhecer entre hospedeiros suscetível ou resistente e sintetizar seletivamente quais efetores e em que intensidade devem ser segregados. As raízes de C. sunki expressaram 10 componentes de cascatas de resistência mediada pelo SA em resposta não bem-sucedida a infecção por P. parasitica. A supressão por P. parasitica da expressão de 05 genes de cascatas de resistência mediada pelo SA foi observada em raízes de P. trifoliata e deve indicar tentativas do patógeno de burlar com a imunidade da planta. Entretanto, a resistência de P. trifoliata a P. parasitica não deve utilizar genes envolvidos na cascata de resistência mediada pelo SA, mas sim genes PR-5 e calose sintase, envolvendo barreiras bioquímicas e estruturais. Portanto, o presente trabalho fornece uma nova visão para o entendimento acerca do processo de modulação de efetores de P. parasitica em interações suscetíveis e resistentes e, a maneira como estes hospedeiros respondem mediante interação / The gummosis, mainly caused by the oomycete Phytophthora parasitica, is one of the most serious diseases affecting citrus crops worldwide. During the interaction, plants induce signaling cascades in order to induce defense responses. However, P. parasitica secrets effector proteins capable of modulating these host responses in order to promote the infection. In Citrus genus, commercially important species are susceptible to infection by this pathogen and the gummosis resistance is achieved in Poncirus trifoliata citrus species. Considering the lack of information on citrus-P. parasitica pathosystem, this study aimed to analyze, through RT-qPCR, the quantitative expression of P. parasitica effector and citrus defense genes during citrus-P. parasitica susceptible and resistant interactions, with Citrus sunki and P. trifoliata, respectively. As results, P. parasitica was able to recognize among susceptible or resistant host and selectively synthesize which effectors and in that intensity should be expressed. Of the 17 studied effector genes, 10 showed quantitative relative differential expression at significance level induced in P. parasitica after inoculation in trifoliate orange roots, being 06 apoplastics and 04 cytosolics. The expression profiles for the 17 effector genes in P. parasitica had two maximum peaks of expression, that are indicative of de novo synthesis of these genes along the time points of interaction, showing transcript accumulation earlier on P. trifoliata (at 6 h.a.i.) and later on C. sunki (at 96 h.a.i.). High levels of the effector gene expression in P. parasitica induced by C. sunki at 96 h.a.i. must match the necrotrophic phase of life of this oomycete, consequently due to their successful penetration into the susceptible plant cells and pathogen biomass accumulation. The presence of intracellular hyphae in cortex of C. sunki roots was abundantly visualized in the micrographs at 96 h.a.i., which may occur as a result of the plant susceptibility to the pathogen. Six hierarchical groups of co-regulated genes were formed from the expression profiles of the 17 effector genes in P. parasitica, which are grouped differently according to interact with C. sunki or P. trifoliata, indicating that the pathogen was able to recognize between susceptible or resistant host and selectively synthesize which effectors and in that intensity should be segregated. The roots of C. sunki expressed 10 components of the cascade resistance mediated by SA in response not successful to P. parasitica infection. The suppression by P. parasitica of the expression of 05 genes of the cascade resistance mediated by SA was found in P. trifoliata roots, and must indicate pathogen attempts to circumvent with the immunity of the plant. However, P. trifoliata resistance to P. parasitica should not use genes involved in the resistance cascade mediated by SA, but instead PR-5 and callose synthase genes, involving biochemical and estructural barriers. In conclusion, this study provides a new insight into the understanding of the effectors of modulation process of P. parasitica in susceptible and resistant interactions and how these hosts respond through interaction.

2 p. / Alfalfa varieties differ in fall dormancy, defined as growth during the fall. Nondormant alfalfa varieties are usually planted in mild winter areas for their ability to grow in the fall. However, fall growth of nondormant alfalfa may be undesirable in areas subject to repeated frosts or freezes. Nondormant, very nondormant, and extremely nondormant alfalfa varieties (fall dormancy class 8, 9, and 10) are adapted to elevations below 4000 feet in Arizona. Other dormancy classes not included in this publication are moderately nondormant varieties (fall dormancy class 7) which may be grown from 3000 to 5000 feet, and semi-dormant and dormant varieties (fall dormancy 6 and below) which are adapted to colder winter areas above 4000 feet.

Please read the Summary in the section 00front of this document / Thesis (PhD)--University of Pretoria, 2005. / Genetics / Unrestricted

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20752号 / 理博第4328号 / 新制||理||1622(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 石田 厚, 教授 工藤 洋, 教授 田村 実 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Thielaviopsis basicola (Berk. and Br.) is a widespread, soil-borne, pathogenic fungus which causes a root rot on tobacco (Nicotiana tabacum L.). Presently, control is achieved primarily through the use of resistant cultivars of tobacco or chemicals. In order to develop a disease prediction program, disease-inoculum density relationships must be determined. It was the purpose of this study to develop an improved procedure for estimating the populations of T. basicola in naturally infested soil. A second objective was to determine the horizontal inoculum pattern of T. basicola in tobacco field soil, and the third objective was to determine the relationship between black root rot of tobacco and inoculum density of T. basicola in naturally infested soil. Two fields in southwestern Virginia were randomly and systematically sampled to assay the population density of T. basicola in the soil. Populations of T. basicola were isolated using a modified carrot-disc baiting technique and calculated using a colonization correction factor. Frequencies of calculated population densities of T. basicola in soil samples were compared, using a Chi-square test, to the expected frequencies indicated by the Poisson, Neyman Type A, and negative binomial distributions. Temperature-tank studies were conducted to investigate inoculum density-disease relationships. Two cultivars of tobacco were grown in soil naturally infested with T. basicola. The soil was thoroughly mixed before use to preclude inoculum clumping. The results obtained with either systematic or random sampling indicated that propagules of T. basicola are clumped or aggregated in tobacco field soil, as there was a good fit of the data to the negative binomial distribution. Also, the variance to mean ratios were significantly (P = 0.05) greater than 1.0 which is indicative of a clumped pattern. Other indexes of aggregation indicated a low to moderate degree of inoculum clumping in soil. For soil temperature-tank tests, root rot incidence was 96-100% at all natural population densities for both slightly resistant cv. Burley 21 and susceptible cv. Judy's Pride plants, and T. basicola was consistently associated with rotted roots. Low R² values were obtained in regression analyses of T. basicola inoculum density versus mean percent root rot per Burley 21 plant and per Judy's Pride plant. / Master of Science

A new selective medium (TB-CEN) was developed for isolating Thielaviopsis basicola, cause of black root rot of tobacco, from soil. TB-CEN medium contains etridiazol and nystatin to inhibit the growth of undesired fungi, and unautoclaved extract from carrot to selectively enhance for the growth of T. basicola. Inoculum and/or population densities of T. basicola in five burley tobacco fields were 74-166 propagules per g of soil, and 0-12 propagules per g of soil in three other burley fields. Inoculum and/or population densities of T. basicola in 12 flue-cured and 2 sun-cured tobacco fields were 0-26 propagules per g of soil, and 101 and 402 propagules per g of soil in two other flue-cured fields. Environmental factors apparently had a strong effect on black root rot development, since root rot and plant stunting were severe in two burley fields that had 148 and 158 propagules per g of soil, but were not severe in the two flue-cured fields that had 101 and 402 propagules per g of soil. All of the cultivars planted in the four fields were susceptible. Black root rot was the major disease associated with the stunting of tobacco plants in the burley region of Virginia, but not in the flue- and sun-cured regions. No evidence was found to indicate that endomycorrhizae were involved in tobacco stunting in Virginia. T basicola inoculum density-disease severity studies were conducted both in soil-temperature tanks and in the field. Tobacco seedlings were grown in temperature tanks (20-23 C) for 30-31 days in naturally infested field soil (pH 6.5). For all cultivars tested (Burley 21, NC95, and Va Gold), the mean percent of roots that were rotted increased significantly (P=0.001) as inoculum density increased (R² range for regressions=0.93-0.97). Severe levels of root rot occurred at inoculum densities of 50-200 propagules per g of soil. Significant (P=0.01) reductions in plant growth occurred at inoculum densities as low as 5-10 propagules per g of soil. In a study conducted on a commercial burley tobacco (cv. B21-Ky10) field, inoculum densities of 150 and 683 propagules per g of soil were associated with moderate and severe levels of black root rot, respectively. Differences between soil-temperature tank and field studies appeared to be due to variations in environmental- and host-related factors. In another burley field study, the fungicide imazalil, which completely inhibited the growth of T. basicola when amended into agar media at a concentration of 1.0 μg a.i./ml, failed to control black root rot when it was added to transplanting water (50 ml/plant) at concentrations as high as 1,500 μg a.i./ml. / Ph. D. / incomplete_metadata

Fusarium oxysporum Schl. var. vanillae (Tucker) Gondon is known to cause root rot in Vanilla planifolia Andrews in most regions where it is grown, including the major plantations in Xishuangbanna, Yunnan Province of China. This is of serious economic concern to the Province since the vanilla flavouring extractable from the beans of the plant is a valuable food product and an important export commodity. There are no fungicides registered for the control of Fusarium root rot and the only available chemical control methods are ineffective and cause serious contamination of the soil. Breeding for resistance is difficult when no dominant gene is known or where little information is available on fungal pathogenicity. Biocontrol is the main alternative for disease control in this crop, an attractive approach because of increasing concerns for environmental protection. The investigation considers two biocontrol strategies: first the introduction of virulent, antagonistic, non-pathogenic strains, closely-related to the pathogen, to overcome pathogenic populations in infected soils; second the use of essential oils with antimicrobial properties when applied to infected soils. Pathogenicity tests have been done on 81 out of 87 F. oxysporum isolates collected in Yunnan Province. Among these, 32 isolates were non-pathogenic and 49 were pathogenic. The pathogenicity results showed the complexity of F. oxysporum in Yunnan. Seventeen isolates were recovered from the Daluo plantation, of which 14 were pathogenic isolates and 3 non-pathogenic isolates; 26 from the Menglun plantation, in which 12 were pathogenic and 14 were non-pathogenic; 18 isolates from the Manjingdai plantation, in which 12 isolates were pathogenic, whilst the other 6 were non-pathogenic and 20 were obtained from the plantation in Hekou i County, of which 11 were pathogenic isolates and 9 were non-pathogenic. Genetic diversity within this population of F. oxysporum has been investigated with respect to vegetative compatibility and to determine the relationship between VCGs and virulence. The VCG results showed that the 87 strains of Fusarium oxysporum f.sp vanillae isolated from Yunnan Province were complex. They could be distributed into 12 different VCGs and that a direct relationship between VCGs group and virulence could not be drawn. Two non-pathogenic strains, ML-5-2 and HK-5b-4-1, have been screened from 87 strains as candidate biocontrol agents by pathogenicity and VCG, which are self-incompatible and closely related to the pathogens. These two strains were effective in vanilla root rot control in controlled environments, but their effects in field experiments were less conclusive. Seven essential oils, which have long been regarded as having inhibitory effects on pathogens in nature, have also been investigated as biocontrol agents. Three oils, cinnamon oil, thyme oil and clove oil, were effective in inhibiting the growth of pathogen in vitro. These oils may develop into useful components of different management strategies with non-pathogenic strains. For the future, consideration will need to be given to the mechanism(s) of the interaction of the antagonistic components with the soil microbe population and host plant and also to appropriate formulation, to take account of soil type, crop status, cultural practices, environmental and economic factors. Biocontrol methods have considerable potential but must be acceptable to farmers as part of an overall crop management programme.

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.