Detection, identification, and quantification of fungal diseases of sugar beet leaves using imaging and non-imaging hyperspectral techniques

Plant diseases influence the optical properties of plants in different ways. Depending on the host pathogen system and disease specific symptoms, different regions of the reflectance spectrum are affected, resulting in specific spectral signatures of diseased plants. The aim of this study was to examine the potential of hyperspectral imaging and non-imaging sensor systems for the detection, differentiation, and quantification of plant diseases. Reflectance spectra of sugar beet leaves infected with the fungal pathogens Cercospora beticola, Erysiphe betae, and Uromyces betae causing Cercospora leaf spot, powdery mildew, and sugar beet rust, respectively, were recorded repeatedly during pathogenesis. Hyperspectral data were analyzed using various methods of data and image analysis and were compared to ground truth data. Several approaches with different sensors on the measuring scales leaf, canopy, and field have been tested and compared. Much attention was paid on the effect of spectral, spatial, and temporal resolution of hyperspectral sensors on disease recording. Another focus of this study was the description of spectral characteristics of disease specific symptoms. Therefore, different data analysis methods have been applied to gain a maximum of information from spectral signatures. Spectral reflectance of sugar beet was affected by each disease in a characteristic way, resulting in disease specific signatures. Reflectance differences, sensitivity, and best correlating spectral bands differed depending on the disease and the developmental stage of the diseases. Compared to non-imaging sensors, the hyperspectral imaging sensor gave extra information related to spatial resolution. The preciseness in detecting pixel-wise spatial and temporal differences was on a high level. Besides characterization of diseased leaves also the assessment of pure disease endmembers as well as of different regions of typical symptoms was realized. Spectral vegetation indices (SVIs) related to physiological parameters were calculated and correlated to the severity of diseases. The SVIs differed in their sensitivity to the different diseases. Combining the information from multiple SVIs in an automatic classification method with Support Vector Machines, high sensitivity and specificity for the detection and differentiation of diseased leaves was reached in an early stage. In addition to the detection and identification, the quantification of diseases was possible with high accuracy by SVIs and Spectral Angle Mapper classification, calculated from hyperspectral images. Knowledge from measurements under controlled condition was carried over to the field scale. Early detection and monitoring of Cercospora leaf spot and powdery mildew was facilitated. The results of this study contribute to a better understanding of plant optical properties during disease development. Methods will further be applicable in precision crop protection, to realize the detection, differentiation, and quantification of plant diseases in early stages.Nachweis, Identifizierung und Quantifizierung pilzlicher Blattkrankheiten der Zuckerrübe mit abbildenden und nicht-abbildenden hyperspektralen Sensoren Pflanzenkrankheiten wirken sich auf die optischen Eigenschaften von Pflanzen in unterschiedlicher Weise aus. Verschiedene Bereiche des Reflektionsspektrums werden in Abhängigkeit von Wirt-Pathogen System und krankheitsspezifischen Symptomen beeinflusst. Hyperspektrale, nicht-invasive Sensoren bieten die Möglichkeit, optische Veränderungen zu einem frühen Zeitpunkt der Krankheitsentwicklung zu detektieren. Ziel dieser Arbeit war es, das Potential hyperspektraler abbildender und nicht abbildender Sensoren für die Erkennung, Identifizierung und Quantifizierung von Pflanzenkrankheiten zu beurteilen. Zuckerrübenblätter wurden mit den pilzlichen Erregern Cercospora beticola, Erysiphe betae bzw. Uromyces betae inokuliert und die Auswirkungen der Entwicklung von Cercospora Blattflecken, Echtem Mehltau bzw. Rübenrost auf die Reflektionseigenschaften erfasst und mit optischen Bonituren verglichen. Auf den Skalenebenen Blatt, Bestand und Feld wurden Messansätze mit unterschiedlichen Sensoren verglichen. Besonders berücksichtigt wurden hierbei Anforderungen an die spektrale, räumliche und zeitliche Auflösung der Sensoren. Ein weiterer Schwerpunkt lag auf der Beschreibung der spektralen Eigenschaften von charakteristischen Symptomen. Verschiedene Auswerteverfahren wurden mit dem Ziel angewendet, einen maximalen Informationsgehalt aus spektralen Signaturen zu gewinnen. Jede Krankheit beeinflusste die spektrale Reflektion von Zuckerrübenblättern auf charakteristische Weise. Differenz der Reflektion, Sensitivität sowie Korrelation der spektralen Bänder zur Befallsstärke variierten in Abhängigkeit von den Krankheiten. Eine höhere Präzision durch die pixelweise Erfassung räumlicher und zeitlicher Unterschiede von befallenem und gesundem Gewebe konnte durch abbildende Sensoren erreicht werden. Spektrale Vegetationsindizes (SVIs), mit Bezug zu pflanzenphysiologischen Parametern wurden aus den Hyperspektraldaten errechnet und mit der Befallsstärke korreliert. Die SVIs unterschieden sich in ihrer Sensitivität gegenüber den drei Krankheiten. Durch den Einsatz von maschinellem Lernen wurde die kombinierte Information der errechneten Vegetationsindizes für eine automatische Klassifizierung genutzt. Eine hohe Sensitivität sowie eine hohe Spezifität bezüglich der Erkennung und Differenzierung von Krankheiten wurden erreicht. Eine Quantifizierung der Krankheiten war neben der Detektion und Identifizierung mittels SVIs bzw. Klassifizierung mit Spektral Angle Mapper an hyperspektralen Bilddaten möglich. Die Ergebnisse dieser Arbeit tragen zu einem besseren Verständnis der optischen Eigenschaften von Pflanzen unter Pathogeneinfluss bei. Die untersuchten Methoden bieten die Möglichkeit in Anwendungen des Präzisionspflanzenschutzes implementiert zu werden, um eine frühzeitige Erkennung, Differenzierung und Quantifizierung von Pflanzenkrankheiten zu ermöglichen

Crop Disease Detection Using Remote Sensing Image Analysis

Pest and crop disease threats are often estimated by complex changes in crops and the applied agricultural practices that result mainly from the increasing food demand and climate change at global level. In an attempt to explore high-end and sustainable solutions for both pest and crop disease management, remote sensing technologies have been employed, taking advantages of possible changes deriving from relative alterations in the metabolic activity of infected crops which in turn are highly associated to crop spectral reflectance properties. Recent developments applied to high resolution data acquired with remote sensing tools, offer an additional tool which is the opportunity of mapping the infected field areas in the form of patchy land areas or those areas that are susceptible to diseases. This makes easier the discrimination between healthy and diseased crops, providing an additional tool to crop monitoring. The current book brings together recent research work comprising of innovative applications that involve novel remote sensing approaches and their applications oriented to crop disease detection. The book provides an in-depth view of the developments in remote sensing and explores its potential to assess health status in crops

Remote sensing and machine learning for prediction of wheat growth in precision agriculture applications

This thesis focuses on remote sensing and machine learning for prediction of wheat growth in precision agriculture applications. Agriculture is the primary productive force, which plays an important role in human activities. Wheat, as one of the essential sources of food, is also a widely planted crop. The impact of weather and climate and some other uncertain factors on wheat production is crucial. Therefore, it is necessary to use reliable and statistically reasonable models for crop growth and yield prediction based on vegetation index variables and other factors, so as to obtain reliable prediction for efficient production. Applying certain artificial intelligence algorithms to the precision agriculture can significantly improve the efficiency of traditional agriculture in crop planting and reduce the consumption of human and natural resources. Remote sensing can objectively, accurately and timely provide a large amount of information for ecological environment and crop growth in agriculture applications. By combining the image and spectral data obtained by remote sensing technology with machine learning, information about wheat growth, yield and insect pests can be learned in time. This thesis focuses on its applications in agriculture, particularly using effective prediction models such as the back propagation neural network and some optimisation algorithms for predicting wheat growth, yield and aphid. The work presented in this thesis address the issues of wheat growth prediction, yield assessment and aphid validation by model building and machine learning algorithm optimisation by means of remote sensing data. Specifically, the following objectives are defined: 1. Analyse multiple vegetation indexes based on the TM 1-4 band data of Landsat satellite and use regression algorithms to train the models and predict wheat growth; 2. Analyse and compare multiple vegetation indexes models by means of spectral data and use regression algorithms to predict wheat yield; 3. Combine spectral vegetation indexes and multiple regression algorithms to predict wheat aphid; 4. Use accurate evaluation criteria for validating the efficacy of the various algorithms. In this thesis, the remote sensing data from the satellite has been applied instead of the airborne-based remote sensing data. Based on the TM 1-4 band image data of Landsat satellite, multiple vegetation indexes were used as the input of regression algorithms. After that, four kinds of regression algorithms such as the multiple linear regression (MR) algorithm, back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm were used to train the model and predict the LAI and SPAD. The prediction results of each algorithm were compared with the ground truth information collected by hand held instruments on the ground. The relationship between wheat yield and spectral data has been studied. Based on the BPNN algorithm, four kinds of models such as visible hyperspectral index (VHI) model, hyperspectral vegetation index (HVI) model, difference hyperspectral index (DHI) model and normalized hyperspectral index (NHI) model have been utilized to predict wheat yield. For the optimal NHI model, three regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm, were compared to predict wheat yield, and RMSE and R-square of the three algorithms were compared and analysed. Finally, the relationship between wheat aphid and spectral data has been investigated. Nine vegetation indexes related to aphid have been estimated from spectral data as the input of regression algorithms. Five kinds of regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm, particle swarm optimisation (PSO) optimised BPNN algorithm, ant colony (ACO) optimisation algorithm optimised BPNN algorithm and cuckoo search (CS) optimised BPNN algorithm have been implemented to predict wheat aphid, which was validated with the ground truth information measured by hand-held instruments on the ground. The prediction results of each algorithm have been analysed. The major original contributions of this thesis are as follows: 1. A variety of optimisation algorithms are used to improve the regression analysis of the BPNN algorithm, so that the prediction results of each model for wheat growth, yield and aphid are more accurate. 2. The spectral characteristics of winter wheat canopy have been analysed. The correlation between the absorption band and the associated physical and chemical properties of crops, specially the red edge slope, with the crop yield and wheat aphid damage is established. 3. Adjusted MSE and un-centered R-square, as accurate evaluation criteria for practical applications, are used to compare the prediction results of the models under different dimensions of the observed data. 4. Improve algorithm training by using the cross-validation method to obtain reliable and stable models for the prediction of wheat growth, yield, and aphid. Through repeated cross-validation, a better model can be obtained in the last. Key word：Precision agriculture; BP network, wheat growth assessment; wheat yield prediction, wheat aphid validationThis thesis focuses on remote sensing and machine learning for prediction of wheat growth in precision agriculture applications. Agriculture is the primary productive force, which plays an important role in human activities. Wheat, as one of the essential sources of food, is also a widely planted crop. The impact of weather and climate and some other uncertain factors on wheat production is crucial. Therefore, it is necessary to use reliable and statistically reasonable models for crop growth and yield prediction based on vegetation index variables and other factors, so as to obtain reliable prediction for efficient production. Applying certain artificial intelligence algorithms to the precision agriculture can significantly improve the efficiency of traditional agriculture in crop planting and reduce the consumption of human and natural resources. Remote sensing can objectively, accurately and timely provide a large amount of information for ecological environment and crop growth in agriculture applications. By combining the image and spectral data obtained by remote sensing technology with machine learning, information about wheat growth, yield and insect pests can be learned in time. This thesis focuses on its applications in agriculture, particularly using effective prediction models such as the back propagation neural network and some optimisation algorithms for predicting wheat growth, yield and aphid. The work presented in this thesis address the issues of wheat growth prediction, yield assessment and aphid validation by model building and machine learning algorithm optimisation by means of remote sensing data. Specifically, the following objectives are defined: 1. Analyse multiple vegetation indexes based on the TM 1-4 band data of Landsat satellite and use regression algorithms to train the models and predict wheat growth; 2. Analyse and compare multiple vegetation indexes models by means of spectral data and use regression algorithms to predict wheat yield; 3. Combine spectral vegetation indexes and multiple regression algorithms to predict wheat aphid; 4. Use accurate evaluation criteria for validating the efficacy of the various algorithms. In this thesis, the remote sensing data from the satellite has been applied instead of the airborne-based remote sensing data. Based on the TM 1-4 band image data of Landsat satellite, multiple vegetation indexes were used as the input of regression algorithms. After that, four kinds of regression algorithms such as the multiple linear regression (MR) algorithm, back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm were used to train the model and predict the LAI and SPAD. The prediction results of each algorithm were compared with the ground truth information collected by hand held instruments on the ground. The relationship between wheat yield and spectral data has been studied. Based on the BPNN algorithm, four kinds of models such as visible hyperspectral index (VHI) model, hyperspectral vegetation index (HVI) model, difference hyperspectral index (DHI) model and normalized hyperspectral index (NHI) model have been utilized to predict wheat yield. For the optimal NHI model, three regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm, were compared to predict wheat yield, and RMSE and R-square of the three algorithms were compared and analysed. Finally, the relationship between wheat aphid and spectral data has been investigated. Nine vegetation indexes related to aphid have been estimated from spectral data as the input of regression algorithms. Five kinds of regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm, particle swarm optimisation (PSO) optimised BPNN algorithm, ant colony (ACO) optimisation algorithm optimised BPNN algorithm and cuckoo search (CS) optimised BPNN algorithm have been implemented to predict wheat aphid, which was validated with the ground truth information measured by hand-held instruments on the ground. The prediction results of each algorithm have been analysed. The major original contributions of this thesis are as follows: 1. A variety of optimisation algorithms are used to improve the regression analysis of the BPNN algorithm, so that the prediction results of each model for wheat growth, yield and aphid are more accurate. 2. The spectral characteristics of winter wheat canopy have been analysed. The correlation between the absorption band and the associated physical and chemical properties of crops, specially the red edge slope, with the crop yield and wheat aphid damage is established. 3. Adjusted MSE and un-centered R-square, as accurate evaluation criteria for practical applications, are used to compare the prediction results of the models under different dimensions of the observed data. 4. Improve algorithm training by using the cross-validation method to obtain reliable and stable models for the prediction of wheat growth, yield, and aphid. Through repeated cross-validation, a better model can be obtained in the last. Key word：Precision agriculture; BP network, wheat growth assessment; wheat yield prediction, wheat aphid validatio

In-field detection and quantification of Septoria tritici blotch in diverse wheat germplasm using spectral-temporal features

Hyperspectral remote sensing holds the potential to detect and quantify crop diseases in a rapid and non-invasive manner. Such tools could greatly benefit resistance breeding, but their adoption is hampered by i) a lack of specificity to disease-related effects and ii) insufficient robustness to variation in reflectance caused by genotypic diversity and varying environmental conditions, which are fundamental elements of resistance breeding. We hypothesized that relying exclusively on temporal changes in canopy reflectance during pathogenesis may allow to specifically detect and quantify crop diseases whilst minimizing the confounding effects of genotype and environment. To test this hypothesis, we collected time-resolved canopy hyperspectral reflectance data for 18 diverse genotypes on infected and disease-free plots and engineered spectral-temporal features representing this hypothesis. Our results confirm the lack of specificity and robustness of disease assessments based on reflectance spectra at individual time points. We show that changes in spectral reflectance over time are indicative of the presence and severity of septoria tritici blotch (STB) infections. Furthermore, the proposed time-integrated approach facilitated the delineation of disease from physiological senescence, which is pivotal for efficient selection of STB-resistant material under field conditions. A validation of models based on spectral-temporal features on a diverse panel of >300 wheat genotypes offered evidence for the robustness of the proposed method. This study demonstrates the potential of time-resolved canopy reflectance measurements for robust assessments of foliar diseases in the context of resistance breeding

A genome-wide association study of resistance to the yellow rust pathogen (Puccinia striiformis f. sp. tritici) in elite UK wheat germplasm

ABSTRACT Pauline G. M. Bansept-Basler, 2013 A genome wide association study of resistance to the yellow rust pathogen (Puccinia striiformis f. sp. tritici) in elite UK wheat germplasm Identification of marker-trait associations (MTA) in germplasm relevant to breeding program via association mapping (AM) can be an effective way to identify loci useful for selection. This approach does not require the generation of specific mapping populations and takes advantage of historical phenotypic data. In the present study, an association panel of 327 bread wheat varieties have been assembled and genotyped with 1806 DArT markers. Genetic structure analysis revealed a low stratification of the panel based on geographical origin (UK versus mixed European varieties) and a close relatedness between lines, which is confirmed by pedigree information. Historical evaluations against the yellow rust pathogen (Puccinia striiformis f.sp. tritici (Pst)) carried in the United Kingdom between 1990 and 2009, as well as de novo evaluations against recent Pst races have been collected and analysed for MTAs. Association scans considering historical data focused on specific Pst pathotypes and de novo seedling tests identified markers linked to known racespecific Yr genes Yr6, Yr7, Yr9, Yr17 and Yr32. When evaluated against current Pst races in the field, 35% of the lines from the panel presented repeatedly a high level of resistance (Area Under the Disease Progress Curve relative<0.2) which is due to the presence of seedling resistances as well as adult plant resistances within the lines. AM with de novo phenotypes revealed 23 MTA groups pointing to potential resistance loci, 14 of them were also identified with historical data and six seemed to point to adult plant resistance loci on chromosomes 2A, 2B, 3A, 6A, 6B and 7A. These results confirm the value of AM using historical data for QTL discovery and suggest the availability of diverse sources of yellow rust resistances within wheat elite UK germplasm

Finding spectral features for the early identification of biotic stress in plants

Early detection of biotic stress in plants is vital for precision crop protection, but hard to achieve. Prediction of plant diseases or weeds at an early stage has significant influence on the extent and effectiveness of crop protection measures. The precise measure depends on specific weeds and plant diseases and their economic thresholds. Weeds and plant diseases at an early stage, however, are difficult to identify. Non-invasive optical sensors with high resolution are promising for early detection of biotic stress. The data of these sensors, e.g. hyperspectral or fluorescence signatures, contain relevant information about the occurrence of pathogens. Shape parameters, derived from bispectral images, have enormous potential for an early identification of weeds in crops. The analysis of this high dimensional data for an identification of weeds and pathogens as early as possible is demanding as the sensor signal is affected by many influencing factors. Nevertheless, advanced methods of machine learning facilitate the interpretation of these signals. Whereas traditional statistics estimate the posterior probability of the class by probability distribution, machine learning methods provide algorithms for optimising prediction accuracy by the discriminant function. Machine learning methods with robust training algorithms play a key role in handling non-linear classification problems. This thesis presents an approach which integrates modern sensor techniques and advanced machine learning methods for an early detection and differentiation of plant diseases and weeds. Support vector machines (SVMs) equipped with non-linear kernels prove as effective and robust classifiers. Furthermore, it is shown that even a presymptomatic identification based on the combination of spectral vegetation indices is realised. Using well-established data analysis methods of this scientific field, this has not achieved so far. Identifying disease specific features from the underlying original high dimensional sensor data selection is conducted. The high dimensionality of data affords a careful selection of relevant and non-redundant features depending on classification problem and feature properties. In the case of fluorescence signatures an extraction of new features is necessary. In this context modelling of signal noise by an analytical description of the spectral signature improves the accuracy of classification substantially. In the case of weed discrimination accuracy is improved by exploiting the hierarchy of weed species. This thesis outlines the potential of SVMs, feature construction and feature selection for precision crop protection. A problem-specific extraction and selection of relevant features, in combination with task-oriented classification methods, is essential for robust identification of pathogens and weeds as early as possible.Früherkennung von biotischem Pflanzenstress ist für den Präzisionspflanzenschutz wesentlich, aber schwierig zu erreichen. Die Vorhersage von Pflanzenkrankheiten und Unkräutern in einem frühen Entwicklungsstadium hat signifikanten Einfluss auf das Ausmaß und die Effektivität einer Pflanzenschutzmaßnahme. Aufgrund der Abhängigkeit einer Maßnahme von der Art der Pflanzenkrankheit oder des Unkrauts und ihrer ökonomischer Schadschwelle ist eine präzise Identifizierung der Schadursache essentiell, aber gerade im Frühstadium durch die Ähnlichkeit der Schadbilder problematisch. Nicht-invasive optische Sensoren mit hoher Auflösung sind vielversprechend für eine Früherkennung von biotischem Pflanzenstress. Daten dieser Sensoren, beispielsweise Hyperspektral- oder Fluoreszenzspektren, enthalten relevante Informationen über das Auftreten von Pathogenen; Formparameter, abgeleitet aus bispektralen Bildern, zeigen großes Potential für die Früherkennung von Unkräutern in Kulturpflanzen. Die Analyse dieser hochdimensionalen Sensordaten unter Berücksichtigung vielfältiger Faktoren ist eine anspruchsvolle Herausforderung. Moderne Methoden des maschinellen Lernens bieten hier zielführende Möglichkeiten. Während die traditionelle Statistik die a-posteriori Wahrscheinlichkeit der Klasse basierend auf Wahrscheinlichkeitsverteilungen schätzt, verwenden maschinelle Lernverfahren Algorithmen für eine Optimierung der Vorhersagegenauigkeit auf Basis diskriminierender Funktionen. Grundlage zur Bearbeitung dieser nicht-linearen Klassi kationsprobleme sind robuste maschinelle Lernverfahren. Die vorliegende Dissertationsschrift zeigt, dass die Integration moderner Sensortechnik mit fortgeschrittenen Methoden des maschinellen Lernens eine Erkennung und Differenzierung von Pflanzenkrankheiten und Unkräutern ermöglicht. Einen wesentlichen Beitrag für eine effektive und robuste Klassifikation leisten Support Vektor Maschinen (SVMs) mit nicht-linearen Kernels. Weiterhin wird gezeigt, dass SVMs auf Basis spektraler Vegetationsindizes die Detektion von Pflanzenkrankheiten noch vor Auftreten visuell wahrnehmbarer Symptome ermöglichen. Dies wurde mit bekannten Verfahren noch nicht erreicht. Zur Identifikation krankheitsspezifischer Merkmale aus den zugrunde liegenden originären hochdimensionalen Sensordaten wurden Merkmale konstruiert und selektiert. Die Selektion ist sowohl vom Klassifikationsproblem als auch von den Eigenschaften der Merkmale abhängig. Im Fall von Fluoreszenzspektren war eine Extraktion von neuen Merkmalen notwendig. In diesem Zusammenhang trägt die Modellierung des Signalrauschens durch eine analytische Beschreibung der spektralen Signatur zur deutlichen Verbesserung der Klassifikationsgenauigkeit bei. Im Fall der Differenzierung von unterschiedlichen Unkräutern erhöht die Ausnutzung der Hierarchie der Unkrautarten die Genauigkeit signifikant. Diese Arbeit zeigt das Potential von Support Vektor Maschinen, Merkmalskonstruktion und Selektion für den Präzisionspflanzenschutz. Eine problemspezifische Extraktion und Selektion relevanter Merkmale in Verbindung mit sachbezogenen Klassifikationsmethoden ermöglichen eine robuste Identifikation von Pathogenen und Unkräutern zu einem sehr frühen Zeitpunkt

Investigation of Un8-Mediated Barley Loose Smut Resistance

Barley loose smut, caused by the basidiomycete pathogen Ustilago nuda (Jens.) Rostr. (U. nuda), is a common fungal disease throughout Canadian barley growing regions and can be effectively controlled by the Un8 resistance gene. The first study (Chapter 3) was designed to isolate the Un8 gene by map-based cloning. The Un8 gene was delimited to a 0.108 cM interval on chromosome arm 1HL and a minimal tiling path consisting of two overlapping bacterial artificial chromosomes was identified. Sequence analysis identified a Un8 candidate gene predicted to be a putative protein kinase with two kinase domains. Twenty-six cultivated and eight wild barley accessions with diverse genetic backgrounds were collected for the second study (Chapter 4) and sequence alignment revealed that all resistant accessions from Canada shared the same amino acid sequence with the landrace accession, CN91953, which was reported as the donor of Un8 to North American barley breeding programs. The remaining three studies focused on elucidating the mechanisms underlying Un8-mediated loose smut resistance. In Chapter 5, a simple and reliable diagnostic method was developed to examine the infection processes of U. nuda within barley seeds and it was found that the early seedling stage might be the most important time point for Un8-conditioned loose smut resistance. Seedling mortality was also observed in resistant and susceptible lines which led to questions as to whether this was a function of the high inoculum concentration used to evaluate disease response. To further investigate this resistance, the commonly used inoculation method was improved by reducing the inoculum concentration (Chapter 6). During this study a large fitness cost (i.e. seedling mortality) previously observed was associated only with resistant lines carrying the Un8 gene. In the final study (Chapter 7), expression analysis was undertaken to better understand Un8-mediated resistance and seedling mortality observed. Two barley genes involved in cytokinin regulation, CKX1 and CKX2.1, which encode cytokinin oxidase/dehydrogenase (CKX) enzymes to irreversibly degrade cytokinins, were significantly up-regulated at time points that coincided with early seed germination. This indicated that the cytokinin pathway may be involved in the loose smut resistance conditioned by the Un8 gene. Taken together, this study has provided deeper insight into the long-lived Un8 loose smut resistance gene, including a possible role for cytokinins in barley loose smut resistance

Thermography to assess grapevine status and traits opportunities and limitations in crop monitoring and phenotyping – a review

Mestrado em Engenharia de Viticultura e Enologia (Double degree) / Instituto Superior de Agronomia. Universidade de Lisboa / Faculdade de Ciências. Universidade do PortoClimate change and the increasing water shortage pose increasing challenges to agriculture and viticulture, especially in typically dry and hot areas such as the Mediterranean and demand for solutions to use water resources more effectively. For this reason, new tools are needed to precisely monitor water stress in crops such as grapevine in order to save irrigation water, while guaranteeing yield. Imaging technologies and remote sensing tools are becoming more common in agriculture and plant/crop science research namely to perform phenotyping/selection or for crop stress monitoring purposes. Thermography emerged as important tool for the industry and agriculture. It allows detection of the emitted infrared thermal radiation and conversion of infrared radiation into temperature distribution maps. Considering that leaf temperature is a feasible indicator of stress and/or stomatal behavior, thermography showed to be capable to support characterization of novel genotypes and/or monitor crop’s stress. However, there are still limitations in the use of the technique that need to be minimized such as the accuracy of thermal data due to variable weather conditions, limitations due to the high costs of the equipment/platforms and limitations related to image analysis and processing to extract meaningful thermal data. This work revises the role of remote sensing and imaging in modern viticulture as well as the advantages and disadvantages of thermography and future developments, focusing on viticultureN/