The utility of very-high resolution unmanned aerial vehicles (UAV) imagery in monitoring the spatial and temporal variations in leaf moisture content of smallholder maize farming systems.

Masters Degree. University of KwaZulu-Natal, Pietermaritzburg.Maize moisture stress, resulting from rainfall variability, is a primary challenge in the production of rain-fed maize farming, especially in water-scarce regions such as southern Africa. Quantifying maize moisture variations throughout the growing season can support agricultural decision-making and prompt the rapid and robust detection of smallholder maize moisture stress. Unmanned Aerial Vehicles (UAVs), equipped with light-weight multispectral sensors, provide spatially explicit near real-time information for determining maize moisture content at farm scale. Therefore, this study evaluated the utility of UAV derived multispectral imagery in estimating maize leaf moisture content indicators on smallholder farming systems throughout the maize growing season. The first objective of the study was to conduct a comparative analysis in order to evaluate the performance of five regression techniques (support vector regression, random forest regression, decision trees regression, artificial neural network regression and the partial least squares regression) in predicting maize water content indicators (i.e. equivalent water thickness (EWT), fuel moisture content (FMC) and specific leaf area (SLA)), and determine the most suitable indicator of smallholder maize water content variability based on multispectral UAV data. The results illustrated that both NIR and red-edge derived spectral variables were critical in characterising maize moisture indicators on smallholder farms. Furthermore, the best models for estimating EWT, FMC and SLA were derived from the random forest regression algorithm with a relative root mean square error (rRMSE) of 3.13%, 1% and 3.48 %, respectively. Additionally, EWT and FMC yielded the highest predictive performance of maize leaf moisture and demonstrated the best correlation with remotely sensed data. The study’s second objective was to evaluate the utility of UAVderived multispectral imagery in estimating the temporal variability of smallholder maize moisture content across the maize growing season using the optimal maize moisture indicators. The findings illustrated that the NIR and red-edge wavelengths were influential in characterising maize moisture variability with the best models for estimating maize EWT and FMC resulting in a rRMSE of 2.27 % and 1%, respectively. Furthermore, the early reproductive stage was the most optimal for accurately estimating maize EWT and FMC using UAVproximal remote sensing. The findings of this study demonstrate the prospects of UAV- derived multispectral data for deriving insightful information on maize moisture availability and overall health conditions. This study serves as fundamental step towards the creation of an early maize moisture stress detection and warning systems, and contributes towards climate change adaptation and resilience of smallholder maize farming

Sources of Atmospheric Fine Particles and Adsorbed Polycyclic Aromatic Hydrocarbons in Syracuse, New York

Land surface temperature (LST) images from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor have been widely utilized across scientific disciplines for a variety of purposes. The goal of this dissertation was to utilize MODIS LST for three spatial modeling applications within the conterminous United States (CONUS). These topics broadly encompassed agriculture and human health. The first manuscript compared the performance of all methods previously used to interpolate missing values in 8-day MODIS LST images. At low cloud cover (\u3c30%), the Spline spatial method outperformed all of the temporal and spatiotemporal methods by a wide margin, with median absolute errors (MAEs) ranging from 0.2°C-0.6°C. However, the Weiss spatiotemporal method generally performed best at greater cloud cover, with MAEs ranging from 0.3°C-1.2°C. Considering the distribution of cloud contamination and difficulty of implementing Weiss, using Spline under all conditions for simplicity would be sufficient. The second manuscript compared the corn yield predictive capability across the US Corn Belt of a novel killing degree day metric (LST KDD), computed with daily MODIS LST, and a traditional air temperature-based metric (Tair KDD). LST KDD was capable of predicting annual corn yield with considerably less error than Tair KDD (R2 /RMSE of 0.65/15.3 Bu/Acre vs. 0.56/17.2 Bu/Acre). The superior performance can be attributed to LST’s ability to better reflect evaporative cooling and water stress. Moreover, these findings suggest that long-term yield projections based on Tair and precipitation alone will contain error, especially for years of extreme drought. Finally, the third manuscript assessed the extent to which daily maximum heat index (HI) across the CONUS can be estimated by MODIS multispectral imagery in conjunction with land cover, topographic, and locational factors. The derived model was capable of estimating HI in 2012 with an acceptable level of error (R 2 = 0.83, RMSE = 4.4°F). LST and water vapor (WV) were, by far, the most important variables for estimation. Expanding this analytical framework to a more extensive study area (both temporally and spatially) would further validate these findings. Moreover, identifying an appropriate interpolation and downscaling approach for daily MODIS imagery would substantially increase the utility of the corn yield and HI models

Thermal imaging to monitor soil and canopy temperature under mulching and natural soil cover conditions

Mestrado em Engenharia de Viticultura e Enologia. Universidade de Lisboa, Instituto Superior de Agronomia. Universidade do Porto, Faculdade de CiênciasThe Mediterranean viticulture is increasingly exposed to more severe and frequent heat waves and droughts. Therefore, short to medium-term adaptation strategies are needed to minimize risks and losses. The use of organic mulching can be a potential a short-term adaptation strategy as well as a tool to control soil water loss and decrease soil and canopy temperature. Meanwhile, imaging technologies are becoming more affordable and can be used to support crop and soil monitoring. However, low-cost thermal imaging and low-cost image analysis need still optimization to be applied in modern viticulture. In this study, we evaluated the impact of organic mulching, by analysing its effects on the temperature of the ground surface and of vine’s canopy using low-cost thermography. A preliminary study was carried out at the Instituto Superior de Agronomia to optimise the use of two low to medium-cost thermal cameras (Flir One Pro LT and Flir A35) and further image analysis and processing, to assess their potential use for field monitoring and in order to implement simple protocols to support ground-based thermal imaging analysis. Three treatments were monitored: 1) Control – natural soil vegetation 2) Eucalyptus leaves and branches mulching 3) Rice straw mulching. Visible RGB and thermal images were done from the soil (sunlit and shadow) and from the sunlit side of the canopies along the season, on 9 June, (Flowering) 1 July (Veraison) and 12 August (pre-harvest) at 9-10.30h and 15-16.30h. Thermal data was complemented by leaf gas exchange and chlorophyll fluorescence at veraison and at pre-harvest. The Flir tools software (FLIR Systems) was used for image acquisition, while the Fiji (ImageJ distribution) adapted with a ThermimageJ plug was used for further image analysis. The output of the Flir A35 revealed to be much superior to the one of Flir One. The A35 was able to detect canopy temperature differences such that thermal indices were constructed. The output of A35 output showed that mulching resulted in lower surface temperature than the control and smaller diurnal variation of the ground surface. The upper part of the canopy remained cooler than the lower part, independently of the mulch treatment. Using the Fiji software, it was possible to standardise the analysis process, but the protocols still require additional work to increase accuracy and precision.A viticultura mediterrânica enfrenta situações cada vez mais frequentes de ondas de calor e de seca extrema pelo que são necessárias estratégias de adaptação de curto a médio prazo para minimizar os riscos e as perdas. O uso de coberturas mortas orgânicas para limitar a perda de água e diminuir a temperatura do solo e da sebe são possíveis estratégias de adaptação. Entretanto, as tecnologias de imagem estão a tornar-se mais acessíveis e podem ser utilizadas para apoiar a monitorização das culturas e do solo. Nesse sentido avaliamos o impacto do mulching orgânico, uma estratégia de adaptação a curto prazo, analisando os seus efeitos na superfície do solo e na temperatura da sebe. O uso de sistemas de imagem térmica de baixo custo e de softwares de análise de imagem de baixo custo necessitam ainda de otimização para serem aplicadas na viticultura moderna. Assim foi realizado um ensaio preliminar no Instituto Superior de Agronomia para testar três tratamentos do solo: 1) Testemunha - solo com vegetação natural 2) Mulch com folhas de Eucalipto folhas e ramos e 3) Mulch com palha de arroz. Testou-se também o uso de duas câmaras térmicas de baixo a médio custo (Flir One Pro LT e Flir A35). Foram feitas imagens térmicas e no visível RGB do solo (lado exposto ao sol e sombra) e da sebe (lado exposto) ao longo do ensaio: - 9 Junho, (Floração) 1 Julho (Veraison) e 12 Agosto (pré-colheita). As medições foram feitas de manhã (9-10,30h) e á tarde (15-16,30h). Os dados térmicos foram complementados com a medição das trocas gasosas e fluorescência de clorofila ao pintor e na pré-colheita. Os resultados obtidos pela Flir A35 foram superiores aos da Flir One Pro LT. A FlirA435 mostrou diferenças de temperatura no solo e na sebe e permitiu calcular índices térmicos (CWSI). Os resultados obtidos com a Flir A35 mostraram que mulching resultou numa temperatura superficial mais baixa que a da testemunha e que a parte superior da sebe estava mais fresca que a inferior (zona dos cachos), independentemente dos tratamentos. Utilizando o software de Fiji, foi possível padronizar o processo de análise de imagem, mas é ainda necessário otimizar o protocolo de campo para se obter dados térmicos mais precisos e de uma forma mais eficienteN/

New strategies to study and control plant diseases and their application to Kiwifruit Decline

openIn 2012, leaf scorches, wilting, sudden defoliation and dieback symptoms were observed for the first time on several kiwifruit plants in orchards located in Veneto (Northeast of Italy). Diseased plants were also characterised by a heavily compromised root system with none or very few feeding roots, rotting tissues on smaller roots and lack of cohesion between the external cylinder and the core. In relation to these symptoms the new disease was named Kiwifruit Decline (KD). KD rapidly spread in all the most important Italian growing areas and probably up to date is the most concerning phyto-pathological issue for kiwifruit growers. With the main aim to determine KD aetiology and to identify the epidemiological pattern of this disease outbreaks, canonical strategies and new technologies were integrated in an interdisciplinary approach. The work started with the definition of a conceptual framework on the symptoms observed in the field and with the reconstruction of the history of the disease based on the farmers’ experiences. These evidences were used as first-hand source of information and integrated with the experiences gathered by other Italian research groups to hypothesize the etiological causes most probably involved in the disease. From this analysis waterlogging and soil-borne pathogens emerged as the two most probable factors involved in the disease, although their role in the disease was still unknown. Therefore, the following step was the setup of a canonical experimental trial, where the effect of the two most probable etiological causes were compared under controlled conditions. The trial gave unequivocal results clearly stating the necessary interaction between waterlogging and soil borne pathogens to incite the disease. Furthermore, axenic isolation starting from plants that became diseased during this trial, allowed to have a first insight on soil-borne microorganisms potentially involved in the disease, suggesting that one or more pathogens (most probably Oomycetes) might be involved in the disease. Given these results a pathogenicity test was set up and confirmed that Phytopythium vexans was able to induce KD symptoms in both canopy and roots of kiwifruit plants. Once the role of a biotic factor was demonstrated, the studies moved back to the field focusing mostly on remote sensing technologies able to infer the physiological traits of the plants. Thermal and multispectral imagery acquired over a diseased field and classified with unsupervised clustering algorithms allowed to efficiently distinguish asymptomatic from symptomatic plants and to predict, one year in advance, the disease outbreak. Since the involvement of one or more potential soil-borne pathogens was proposed, a metabarcoding study was performed to have a first insight on fungal and oomycete communities associated with KD. Interestingly, Phytopythium vexans not only was found with a low relative abundance within diseased samples, but it was also recorded in healthy samples suggesting that the asymptomatic state of the plants is most probably linked to the environmental conditions averse to the development of the pathogens. Metabarcoding analysis also suggested Phytophthora sojae and Ilyonectria macrodidyma as new potential pathogen candidates. Results from this thesis provided several breakthroughs regarding the KD syndrome and defined the starting point for future studies. Indeed, not only the disease is now clearly associated to a combination of waterlogging conditions and soil-borne pathogens, but also a standardized protocol was setup to reproduce the disease. Moreover, new tools for in-field early disease detection are proposed and the first overview of fungal and oomycete community associated to KD is given for both root endosphere and rhizosphere compartments.Dottorato di ricerca in Scienze e biotecnologie agrarieopenSavian, Francesc

Assessment of maize crop health and water stress based on multispectral and thermal infrared unmanned aerial vehicle phenotyping in smallholder farms.

Masters Degree. University of KwaZulu-Natal, Pietermaritzburg.Abstract available in PDF.No submissions form available

Precision irrigation management through thermal and multispectral remote sensing: An integration of sensing systems and analytical techniques

Doctor of PhilosophyDepartment of Biological & Agricultural EngineeringAjay ShardaIrrigation water management starts with quantifying irrigation prescriptions based on crop water requirements at a spatial scale. For determining the water requirement of the plants, canopy temperature-dependent crop water stress could provide a potential solution. The use of a small unmanned aerial system (sUAS) with a thermal infrared (TIR) camera has long been established as an effective method of measuring plant canopy temperatures at a spatial scale. However, concerns still exist about the accuracy of these systems in collecting canopy temperatures and estimating crop water stress. The overall goal of this research is to assess high spatial resolution crop water stress in a corn field and evaluate UAS-based thermal imagery’s capacity to provide precise canopy temperature. As a part of this study, the capacity and feasibility of UAV-based imagery to detect infield crop health variability were also evaluated against aircraft and satellite imagery. To analyze the effects of flying altitude and camera view angle on thermal infrared imagery, thermal cameras with different focal lengths (9 mm, 13 mm, and 19 mm) were flown at different altitudes (30 m, 50 m, and 70 m). The orthomosaics generated from images were examined for the accuracy of the corn-canopy temperature sensing, ability to differentiate between hot and cold surfaces, ease of image stitching, geometric accuracy, image quality, and spatial resolution. The results indicated that a canopy temperature map of crops with a temperature error of less than 2° C from the actual canopy temperature can be produced with the combination of appropriate camera focal length, altitude, and image calibration techniques. A narrow-angle thermal camera flying at low altitudes (<50 m) was found to be the least suitable combination for corn canopy temperature sensing. The most appropriate combination for temperature estimation of corn canopies was with a 13 mm focal length camera flying at an altitude of 50 m above ground level. To quantify corn’s crop water stress index (CWSI), images were collected using a thermal camera and a multispectral camera mounted on a Matrice 100 sUAS, over a four acres corn field divided into three irrigation levels (50%, 75%, and 100% irrigation level). Field-specific water stress baselines were developed and used in CWSI quantification to consider the effect of the instant local environment. High-resolution precise crop water stress maps developed from thermal images were capable of inter-row and intra-row detection of corn water stress. The vegetative indices significantly explained variation in crop water stress, with NDRE (Normalized Difference Red Edge index) having the highest R2 value of 0.8 and NDVI (Normalized Difference Vegetation Index) having an R2 value of 0.7. Field-measured leaf water potential also significantly affected water stress but showed a weaker correlation with R2 values of 0.6. Overall results from this study showed that the combination of thermal imaging and NIR imaging could be utilized to determine accurate crop water stress on the spatial scale for irrigation water management and scheduling. A comparative assessment of UAS (Matrice-100), aircraft (Ceres Imaging), and satellite (Landsat-8) imagery to detect infield crop health variability for the implementation of a precision irrigation system was also accomplished. Spatial maps of canopy temperature and NDVI were developed using the images from different imaging platforms and analyzed for capacity to capture water requirements and crop health accurately. UAV imagery outperformed the other two platforms by providing the highest number of pixels and variations in temperatures and NDVI values to represent a given target area. Moderate and low spatial resolution imagery from aircraft (1-1.5 m/pixel) and satellite (30 m/pixel) was limited in detecting inter-row variability and outputting the average pixels of the crop canopy and inter-row space. Whereas high-resolution UAV imagery (1.5 cm/pixel – 6 cm/pixel) precisely distinguished inter-row gap from plants and provided crop-only pixels without mixing with background soil. UAV imagery and aircraft imagery remains competitive in detecting crop variability between two nozzles of an irrigation pivot. UAV imagery was much more sensitive and precise in detecting minute changes as compared to other platforms. Satellite imagery was limited in capturing the variations at this small scale. In summary, this study provided an appropriate combination of camera focal length and flying altitude to accurately and efficiently estimate canopy temperature and crop water stress in corn. Methods were developed to precisely detect inter and intra-row crop water stress and health variability using low-altitude high-resolution UAV imagery. Detailed insight into the capacity of different remote sensing platforms was provided to detect crop health variability in small-scale farms and implement crop irrigation management based on crop canopy temperatures

Detección presintomática y no destructiva de enfermedades causadas por patógenos de suelo en maíz (Marchitez tardía) y en girasol (Jopo) mediante medidas térmicas y de fluorescencia multicolor

Algunas enfermedades de cultivos originadas por patógenos de suelo se caracterizan por la tardía aparición de síntomas. Este es el caso de la Marchitez tardía del maíz (causada por el hongo Harpophora maydis) y del Jopo del girasol (causado por la planta parásita de raíz Orobanche cumana). Harpophora maydis se refirió por vez primera en la Península Ibérica en 2010 y durante los últimos años se ha convertido en una preocupación importante para los productores de maíz. Por el contrario, los ataques de O. cumana son frecuentes en los cultivos españoles de girasol desde los años 80. Esta parásita es actualmente el principal limitante biótico de la producción de aceite de girasol en el mundo. Tanto H. maydis como O. cumana infectan la planta hospedante durante las primeras semanas después de la siembra, aunque los síntomas no se hacen visibles hasta la floración del cultivo o poco después de que ésta tenga lugar. También ambas enfermedades se controlan mediante la incorporación de genes de resistencia en las variedades cultivadas. El progreso y el éxito de los programas de mejora para resistencia a enfermedades dependen enormemente de un acertado y eficaz diagnóstico de la reacción de la planta hospedante al patógeno. Por otro lado, en la actualidad son frecuentes las técnicas basadas en el uso de sensores lejanos y/o de proximidad utilizadas en agronomía. Como alternativa a la inspección visual y al análisis de ADN destructivo, y debido a su sensibilidad a desórdenes fisiológicos en las plantas asociados al ataque de patógenos, estas técnicas pueden ser eficaces herramientas de detección en fitopatología. En el caso de proximidad, la monitorización indirecta de las plantas se efectúa principalmente mediante termometría, termografía,medidas de fluorescencia y técnicas espectrales. En el Capítulo 1 de esta Tesis Doctoral se desarrolla el estado del arte de la Marchitez tardía del maíz y del Jopo del girasol. También se presenta información científica actualizada sobre las técnicas de sensores lejanos y/o de proximidad utilizadas más comúnmente en fitopatología. Los objetivos se presentan en el Capítulo 2. En primer lugar se estudió la distribución de H. maydis en la Península Ibérica, se caracterizó su patogenicidad y también se determinaron otras especies de hongos presentes en maíz afectado por marchitez. Además, se evaluó el potencial de la termometría infrarroja para detectar las infecciones por H. maydis. En segundo lugar se detectó la presencia de O. cumana en girasol durante las fases de crecimiento subterráneo de la planta parásita utilizando para ello imágenes de fluorescencia multicolor (FMC). También se consideraron las posibles alteraciones fisiológicas en el girasol como consecuencia de la infección por O. cumana. En el Capítulo 3 se estudió la distribución geográfica de H. maydis en las principales zonas de cultivo de maíz en España y el sur de Portugal, prospectando 59 campos entre 2009 y 2013. La identidad de 14 de entre todos los aislados de H. maydis obtenidos se confirmó mediante amplificación ITS y estos mismos aislados se caracterizaron por su agresividad mediante inoculación y crecimiento de maíz susceptible crecido en condiciones de umbráculo durante todo el ciclo del cultivo. Uno de los aislados del hongo fue muy agresivo, causando síntomas severos en las plantas y reducciones significativas de peso de sus raíces y partes aéreas. Los aislados moderadamente agresivos causaron valores de enfermedad significativos, pero no todos ellos se asociaron a reducciones de peso de las plantas. En 2012 y 2013 se monitorizó la infección por H. maydis en maceta al aire libre y mediante medidas de temperatura de cubierta y del índice de estrés hídrico del cultivo en plantas control y en plantas inoculadas con el aislado más agresivo. Ambos índices respondieron a la infección por el hongo en los dos años, pudiendo detectarse dicha infección hasta 17 días antes de que los síntomas fueran visibles. Este estudio ha revelado la amplia distribución de H. maydis, que se localiza en los valles de todos los ríos de la Península Ibérica excepto el del Ebro y pone de relieve la importancia de la resistencia genética para controlar este patógeno en el sur de Europa. Además, la detección térmica de la infección previa al desarrollo de síntomas podría resultar en aplicaciones útiles para el diagnóstico presintomático y no destructivo de la enfermedad. En el Capítulo 4 se determinaron las especies de hongos asociadas a H. maydis como agente causal de marchitez de maíz. Para ello, se muestrearon 19 campos con síntomas de marchitez en las principales zonas de cultivo de la Península Ibérica entre 2011 y 2012. En el 47% de ellos no se identificó H. maydis sino otras especies: Fusarium graminearum, F. verticillioides, F. equiseti, F. proliferatum, Macrophomina phaseolina, Rhizoctonia solani y Trichoderma harzianum. En los campos restantes, junto a H. maydis se identificaron otros hongos de suelo en porcentajes apreciables: F. verticillioides (19%), F. proliferatum (19%), F. equiseti (9%), F. oxysporum (9%) y Pythium oligandrum (9%). El crecimiento vascular de H. maydis y de otras especies de hongos en maíz se confirmó analizando plantas con marchitez procedentes de tres campos diferentes. Tanto H. maydis como F. graminearum, F. equiseti, F. proliferatum y T. harzianum se recuperaron de la inserción entre la raíz y tallo y a 10 cm de altura en el tallo de las plantas. El efecto de la infección por H. maydis sobre la producción de las plantas de maíz se cuantificó en macetas y condiciones seminaturales en 2011. El peso de las mazorcas de plantas inoculadas se redujo en un 54%. Estas plantas también tuvieron pesos de raíz y de parte aérea (tallo y hojas) significativamente menores que los de las plantas control. Estos resultados apuntan al gran impacto que puede tener la Marchitez tardía sobre la producción de maíz en campo. Además, y aunque la patogenicidad de los hongos de suelo identificados en maíz debería ser confirmada, los resultados de este trabajo sugieren que la Marchitez tardía del maíz puede tener una etiología compleja. En cuanto al Capítulo 5, en él se analizó por primera vez la fluorescencia emitida por la clorofila de girasol en las bandas espectrales con máximos en el rojo (F680) y en el rojo lejano (F740). Se incubaron plantas sanas de girasol en macetas y condiciones de invernadero y, entre la segunda y la quinta semana de crecimiento se compararon los patrones de emisión de fluorescencia de los cuatro primeros pares de hojas (PHs) tanto en la superficie de la hoja como entre PHs. Los PHs de plantas sanas de girasol presentaron similares patrones de fluorescencia, tanto en el rojo como en el rojo lejano, que variaron dependiendo del grado de desarrollo de la hoja. La utilidad de F680 y F740 como indicadores de la infección de girasol por O. cumana durante las fases de desarrollo subterráneo de la plana parásita se evaluó en condiciones experimentales similares. En plantas infectadas por O. cumana se detectaron aumentos tempranos de F680 y F740, así como reducciones del ratio F680/F7403. Por otro lado, la significación de las diferencias de fluorescencia emitida por plantas control y plantas inoculadas dependió del PH que se considerara en cada momento. Las medidas de contenido clorofílico y de contenido de clorofila total apoyaron los resultados de la FMC, aunque fueron menos sensibles en la discriminación de plantas control y plantas inoculadas. Al final del experimento se confirmó la infección del girasol por la presencia de nódulos en las raíces de las plantas. Este trabajo revela el potencial de la fluorescencia en las regiones del rojo y el rojo-lejano para detectar de forma temprana la infección de girasol por O. cumana, lo que podría ser especialmente interesante para llevar a cabo un fenotipado temprano de material de programas de mejora. Más aún, y hasta donde hemos podido conocer, este es el primer trabajo donde se analiza el efecto de una planta parásita sobre su hospedante utilizando imágenes de fluorescencia en el rojo y en el rojo lejano. En el Capítulo 6 se analizó la emisión de fluorescencia azul y verde (FAV) en hojas de plántulas sanas de girasol. Además, se aplicaron tanto la FAV como la técnica de termografía para detectar la infección del girasol por O. cumana durante el desarrollo subterráneo de la planta parásita. En ambos experimentos se incubaron las plantas de girasol en macetas en invernadero y las medidas se tomaron tras el traslado temporal a cámara de condiciones controladas. En el primer experimento se observó que la FAV emitida por hojas de girasol sano aumentaba a lo largo de su desarrollo. En el caso de girasol parasitado, las hojas presentaban emisiones de FAV menores, y esta diferencia respecto a las hojas de las plantas control fue consistente a lo largo de todo su desarrollo. Al final del experimento se obtuvieron menores concentraciones de pigmentos, lo que sugiere que en las hojas de girasol ocurre un descenso de metabolitos secundarios tras la infección por O. cumana. Por otro lado, a lo largo de todo el experimento se detectaron mayores temperaturas de hoja en girasol inoculado con O. cumana en comparación con la temperatura de hojas de plantas control. Esto podría indicar que el ataque de la planta parásita induce un cierre estomático y una reducción de la transpiración del girasol. En el trabajo de nuevo se ha demostrado que es posible efectuar una monitorización no destructiva de la infección de girasol por O. cumana, en este caso utilizando FAV y termografía, y que dicha monitorización podría aplicarse al fenotipado rápido de girasol. Además, ambas técnicas se han revelado como útiles aproximaciones para estudiar los procesos mediante los cuales O. cumana altera la fisiología de su hospedante (metabolismo secundario y fotosíntesis). Por último, la discusión general de todos los resultados obtenidos en esta Tesis Doctoral y las conclusiones derivadas se presentan en los Capítulos 7 y 8 respectivamente.Some crop diseases caused by soilborne pathogens are characterised by very late symptoms appearance. This is the case of Late wilt of maize (caused by the fungus Harpophora maydis) and that of Broomrape of sunflower (caused by the root parasitic plant Orobanche cumana). Harpophora maydis was first reported in the Iberian Peninsula in 2010, and during the last years it has become a major concern to maize growers. On the contrary, attacks of O. cumana are frequent in sunflower growing areas of Spain since the 1980’s. Currently, the parasite is the first biotic constraint to sunflower oil production worldwide. Both H. maydis and O. cumana infect the host plant during the first weeks after sowing but symptoms are not observed until flowering or shortly after it. Also, they are controlled through the incorporation of genes of resistance into the crop varieties. The advancement and success of breeding programmes is highly dependent on an accurate and fast screening of the reaction of the host plant to the pathogen. On the other hand, techniques based on the use of remote and/or proximal sensors are frequently used with agronomical purposes. As an alternative to visual inspection and to destructive analyses of DNA, and because its sensitivity to physiological disorders in plants associated with pathogen attack, these techniques can constitute efficient detection tools in phytopathology. In the case of near distance, indirect monitoring of plants is majorly conducted by means of thermometry, thermography, fluorescence measurements and spectral techniques. In Chapter 1 of this Ph.D. Thesis, the state of the art of maize late wilt and sunflower broomrape is presented, as well as updated scientific information about the remote and proximal sensing techniques that are most commonly used in plant pathology. The objectives are presented in Chapter 2. First, the distribution of H. maydis in the Iberian Peninsula and its pathogenic characterization were addressed as well as the identification of other fungal species found in symptomatic maize. Also, the utility of infrared thermometry on the detection of maize infections by H. maydis was assessed. Second, the presence of O. cumana in sunflower was analysed during underground development stages by means of multicolour fluorescence (MCF). Possible physiological disorders in sunflower as a consequence of O. cumana infection were also considered. In Chapter 3 the geographical distribution of H. maydis in the main maize growing areas in the South of Portugal and Spain was determined by prospecting 59 fields from 2009 to 2013. Fourteen out of all the isolates of H. maydis were molecularly confirmed by ITS amplification, and their aggressiveness was analysed by inoculation and growth of susceptible maize under shadehouse conditions for the whole growing season. One of the isolates was highly aggressive, causing severe symptoms as well as significant weight reductions of both aboveground parts and roots of the inoculated plants. Moderately aggressive isolates caused significantly high symptoms severity, but not all of them were related to reductions in plant weight. In 2012 and 2013, the infection by H. maydis was monitored outdoors by means of measurements of canopy temperature and crop water stress index of potted control plants and plants inoculated with the most aggressive isolate. Both indices responded to the presence of fungal infection in both years, this infection being detected up to 17 days before symptoms in the plants were visible. This study shows the distribution of H. maydis in all the river valleys of the Iberian Peninsula, except that of the Ebro River, and highlights the importance of genetic resistance for controlling the pathogen in southern Europe. In addition, the thermal detection of the infection prior to symptoms development was possible, what might be further applied to the non-destructive pre-symptomatic diagnosis of Late wilt of maize. The species of fungi that are associated to H. maydis as the causal agent of maize wilt were identified in Chapter 4. Surveys were conducted in 2011 and 2012 in 19 fields where symptomatic plants were collected. The fields were located in the main maize growing areas of the Iberian Peninsula. In 47% of them the fungus infecting diseased plants was not H. maydis but Fusarium graminearum, F. verticillioides, F. equiseti, F. proliferatum, Macrophomina phaseolina, Rhizoctonia solani and/or Trichoderma harzianum. In the remaining fields H. maydis was identified together with other soilborne fungi that were also frequently isolated from diseased plants: F. verticillioides (19%), F. proliferatum (19%), F. equiseti (9%), F. oxysporum (9%) and Pythium oligandrum (9%). The vascular growth of H. maydis and other fungi into the host was confirmed by means of tissue analyses of diseased plants collected at three different locations. Harpophora maydis, as well as F. graminearum, F. equiseti, F. proliferatum and T. harzianum were recovered from the root-stem insertion, and from stem tissues up to 10 cm high. The effect of the infection by H. maydis on maize yield was assessed in inoculated potted plants that were grown in shadehouse in 2011. Cob production was reduced in 54% upon fungal infection. In addition, significantly low weights of roots and aboveground parts (stems and leaves) were obtained. These results point to the great economic impact that Late wilt can have on the yield of maize under field conditions. Likewise, this work suggests that it can be a disease of a complex etiology. Further work should address the pathogenicity of fungal species other than H. maydis on maize, so that the role they may play on disease incidence and on symptoms severity can be determined. Concerning Chapter 5, the fluorescence emitted by chlorophyll (Chl) of sunflower leaves in the spectral bands with peaks near red (F680) and far-red (F740) was analysed for the first time. Healthy sunflowers were grown in pots under greenhouse conditions. Fluorescence emission patterns across the leaf surface and throughout the plant were compared for the first four leaf pairs (LPs) and between the second and fifth weeks of growth. Similar fluorescence patterns, with a delay of three or four days between them, were obtained for LPs of healthy sunflower, showing that red and far-red fluorescence varied with the developmental stage of the leaves. The use of F680 and F740 as indicators of the infection of sunflower by O. cumana during underground development stages of the parasite was also evaluated under similar experimental conditions. Early increases in F680 and F740 as well as decreases in F680/F740 were detected upon infection, significant differences between inoculated and control plants being dependent on the LP that was considered at any time. Measurements of Chl contents and final total Chl content supported the results of MCFI, although they were less sensitive in differentiating healthy from inoculated plants. The infection of sunflowers was confirmed by the presence of broomrape nodules in the roots at the end of the experiment. This work revealed the potential of MCFI in the red and far-red regions for early detecting O. cumana in sunflower, what might be particularly interesting for early phenotyping in sunflower breeding programmes. Furthermore, and to the best of our knowledge, this is the first time that the effect of a parasitic plant in its host is analysed by means of MCFI. In Chapter 6 we analysed the blue-green fluorescence (BGF) emission of leaves of healthy sunflower plantlets, and we implemented BGF and thermal imaging in the detection of the infection by O. cumana during underground parasite development. In both experiments sunflowers were grown in pots and under greenhouse conditions and measurements were made after temporary movement to chamber of controlled conditions. Increases in BGF emission were observed in leaf pairs of healthy sunflowers during their development. Besides, lower BGF emission was consistently detected in parasitised plants throughout leaf expansion, and low pigment concentration was obtained at final time, supporting the interpretation of a decrease in secondary metabolites upon parasite infection. Also, parasite-induced stomatal closure and transpiration reduction were suggested by warmer leaves of inoculated sunflowers throughout the experiment. Techniques of BGF and thermal imaging allowed the non-destructive monitoring of sunflower broomrape, and they could be implemented for fast screening of sunflower genotypes. Additionally, these techniques were shown as valuable approaches to assess the processes by which O. cumana alters physiology (secondary metabolism and photosynthesis) of sunflower. Finally, the general discussion of all the results from the work included in this Ph.D. Thesis and the conclusions drawn from them are presented in Chapters 7 and 8 respectively