A Cost-effective Multispectral Sensor System for Leaf-Level Physiological Traits

With the concern of the global population to reach 9 billion by 2050, ensuring global food security is a prime challenge for the research community. One potential way to tackle this challenge is sustainable intensification; making plant phenotyping a high throughput may go a long way in this respect. Among several other plant phenotyping schemes, leaf-level plant phenotyping needs to be implemented on a large scale using existing technologies. Leaf-level chemical traits, especially macronutrients and water content are important indicators to determine crop’s health. Leaf nitrogen (N) level, is one of the critical macronutrients that carries a lot of worthwhile nutrient information for classifying the plant’s health. Hence, the non-invasive leaf’s N measurement is an innovative technique for monitoring the plant’s health. Several techniques have tried to establish a correlation between the leaf’s chlorophyll content and the N level. However, a recent study showed that the correlation between chlorophyll content and leaf’s N level is profoundly affected by environmental factors. Moreover, it is also mentioned that when the N fertilization is high, chlorophyll becomes saturated. As a result, determining the high levels of N in plants becomes difficult. Moreover, plants need an optimum level of phosphorus (P) for their healthy growth. However, the existing leaf-level P status monitoring methods are expensive, limiting their deployment for the farmers of low resourceful countries. The aim of this thesis is to develop a low-cost, portable, lightweight, multifunctional, and quick-read multispectral sensor system to sense N, P, and water in leaves non-invasively. The proposed system has been developed based on two reflectance-based multispectral sensors (visible and near-infrared (NIR)). In addition, the proposed device can capture the reflectance data at 12 different wavelengths (six for each sensor). By deploying state of the art machine learning algorithms, the spectroscopic information is modeled and validated to predict that nutrient status. A total of five experiments were conducted including four on the greenhouse-controlled environment and one in the field. Within these five, three experiments were dedicated for N sensing, one for water estimation, and one for P status determination. In the first experiment, spectral data were collected from 87 leaves of canola plants, subjected to varying levels of N fertilization. The second experiment was performed on 1008 leaves from 42 canola cultivars, which were subjected to low and high N levels, used in the field experiment. The K-Nearest Neighbors (KNN) algorithm was employed to model the reflectance data. The trained model shows an average accuracy of 88.4% on the test set for the first experiment and 79.2% for the second experiment. In the third and fourth experiments, spectral data were collected from 121 leaves for N and 186 for water experiments respectively; and Rational Quadratic Gaussian Process Regression (GPR) algorithm is applied to correlate the reflectance data with actual N and water content. By performing 5-fold cross-validation, the N estimation shows a coefficient of determination (R^2) of 63.91% for canola, 80.05% for corn, 82.29% for soybean, and 63.21% for wheat. For water content estimation, canola shows an R^2 of 18.02%, corn of 68.41%, soybean of 46.38%, and wheat of 64.58%. Finally, the fifth experiment was conducted on 267 leaf samples subjected to four levels of P treatments, and KNN exhibits the best accuracy, on the test set, of about 71.2%, 73.5%, and 67.7% for corn, soybean, and wheat, respectively. Overall, the result concludes that the proposed cost-effective sensing system can be viable in determining leaf N and P status/content. However, further investigation is needed to improve the water estimation results using the proposed device. Moreover, the utility of the device to estimate other nutrients as well as other crops has great potential for future research

Hyperspectral characterization of freezing injury and its biochemical impacts in oilseed rape leaves

Automatic detection and monitoring of freezing injury in crops is of vital importance for assessing plant physiological status and yield losses. This study investigates the potential of hyperspectral techniques for detecting leaves at the stages of freezing and post-thawing injury, and for quantifying the impacts of freezing injury on leaf water and pigment contents. Four experiments were carried out to acquire hyperspectral reflectance and biochemical parameters for oilseed rape plants subjected to freezing treatment. Principal component analysis and support vector machines were applied to raw reflectance, first and second derivatives (SDR), and inverse logarithmic reflectance to differentiate freezing and the different stages of post-thawing from the normal leaf state. The impacts on biochemical retrieval using particular spectral domains were also assessed using a multivariate analysis. Results showed that SDR generated the highest classification accuracy (> 95.6%) in the detection of post-thawed leaves. The optimal ratio vegetation index (RVI) generated the highest predictive accuracy for changes in leaf water content, with a cross validated coefficient of determination (R2cv) of 0.85 and a cross validated root mean square error (RMSEcv) of 2.4161 mg/cm2. Derivative spectral indices outperformed multivariate statistical methods for the estimation of changes in pigment contents. The highest accuracy was found between the optimal RVI and the change in carotenoids content (R2CV = 0.70 and RMSECV = 0.0015 mg/cm2). The spectral domain 400–900 nm outperformed the full spectrum in the estimation of individual pigment contents, and hence this domain can be used to reduce redundancy and increase computational efficiency in future operational scenarios. Our findings indicate that hyperspectral remote sensing has considerable potential for characterizing freezing injury in oilseed rape, and this could form a basis for developing satellite remote sensing products for crop monitoring

High-throughput phenotyping of plant leaf morphological, physiological, and biochemical traits on multiple scales using optical sensing

Acquisition of plant phenotypic information facilitates plant breeding, sheds light on gene action, and can be applied to optimize the quality of agricultural and forestry products. Because leaves often show the fastest responses to external environmental stimuli, leaf phenotypic traits are indicators of plant growth, health, and stress levels. Combination of new imaging sensors, image processing, and data analytics permits measurement over the full life span of plants at high temporal resolution and at several organizational levels from organs to individual plants to field populations of plants. We review the optical sensors and associated data analytics used for measuring morphological, physiological, and biochemical traits of plant leaves on multiple scales. We summarize the characteristics, advantages and limitations of optical sensing and data-processing methods applied in various plant phenotyping scenarios. Finally, we discuss the future prospects of plant leaf phenotyping research. This review aims to help researchers choose appropriate optical sensors and data processing methods to acquire plant leaf phenotypes rapidly, accurately, and cost-effectively

Remote Estimation of Rice Yield With Unmanned Aerial Vehicle (UAV) Data and Spectral Mixture Analysis

The accurate assessment of rice yield is crucially important for China’s food security and sustainable development. Remote sensing (RS), as an emerging technology, is expected to be useful for rice yield estimation especially at regional scales. With the development of unmanned aerial vehicles (UAVs), a novel approach for RS has been provided, and it is possible to acquire high spatio-temporal resolution imagery on a regional scale. Previous reports have shown that the predictive ability of vegetation index (VI) decreased under the influence of panicle emergence during the later stages of rice growth. In this study, a new approach which integrated UAV-based VI and abundance information obtained from spectral mixture analysis (SMA) was established to improve the estimation accuracy of rice yield at heading stage. The six-band image of all studied rice plots was collected by a camera system mounted on an UAV at booting stage and heading stage respectively. And the corresponding ground measured data was also acquired at the same time. The relationship of several widely-used VIs and Rice Yield was tested at these two stages and a relatively weaker correlation between VI and yield was found at heading stage. In order to improve the estimation accuracy of rice yield at heading stage, the plot-level abundance of panicle, leaf and soil, indicating the fraction of different components within the plot, was derived from SMA on the six-band image and in situ endmember spectra collected for different components. The results showed that VI incorporated with abundance information exhibited a better predictive ability for yield than VI alone. And the product of VI and the difference of leaf abundance and panicle abundance was the most accurate index to reliably estimate yield for rice under different nitrogen treatments at heading stage with the coefficient of determination reaching 0.6 and estimation error below 10%

Estimation of nitrogen in cotton leaves using different hyperspectral region data

As an important index of a plant’s N nutrition, leaf nitrogen content (LNC) can be quickly monitored in real time with hyperspectral information, which is helpful to guide the precise application of N in cotton leaves. In this study, taking cotton dripping in Xinjiang, China, as the object of study, five N application treatments (0, 120, 240, 360, 480 kg·ha-1) were set up, and the hyperspectral data and the N content of main stem functional leaves at the cotton flower and boll stage were collected. The results showed that (1) comparing the correlations of the three types of spectral data from the original spectra, first derivative spectra, and second derivative spectra with the LNC of cotton, the first derivative spectra increased the correlation between the reflectance in the peak and valley ranges of the spectral curves and the LNC of cotton; (2) in the three hyperspectral regions of VIS, NIR, and SWIR, all R2 values of the estimation model for the LNC of cotton established based on the characteristic wavelengths of the original and the first derivative spectra were greater than 0.8, and the model accuracy was better than that of the second derivative spectra; and (3) the normalized root mean square error (n-RMSE) values of the validated model using MLR, PCR, and PLSR regression methods were all in the range of 10–20%, indicating that the established model could well estimate the nitrogen content of cotton leaves. The results of this study demonstrate the potential of the three hyperspectral domains of VIR, NIR, and SWIR to estimate the LNC of cotton and provide a new basis for hyperspectral data application in crop nutrient monitoring

Air pollution and livestock production

The air in a livestock farming environment contains high concentrations of dust particles and gaseous pollutants. The total inhalable dust can enter the nose and mouth during normal breathing and the thoracic dust can reach into the lungs. However, it is the respirable dust particles that can penetrate further into the gas-exchange region, making it the most hazardous dust component. Prolonged exposure to high concentrations of dust particles can lead to respiratory health issues for both livestock and farming staff. Ammonia, an example of a gaseous pollutant, is derived from the decomposition of nitrous compounds. Increased exposure to ammonia may also have an effect on the health of humans and livestock. There are a number of technologies available to ensure exposure to these pollutants is minimised. Through proactive means, (the optimal design and management of livestock buildings) air quality can be improved to reduce the likelihood of risks associated with sub-optimal air quality. Once air problems have taken hold, other reduction methods need to be applied utilising a more reactive approach. A key requirement for the control of concentration and exposure of airborne pollutants to an acceptable level is to be able to conduct real-time measurements of these pollutants. This paper provides a review of airborne pollution including methods to both measure and control the concentration of pollutants in livestock buildings

Simulation of site-specific irrigation control strategies with sparse input data

Crop and irrigation water use efficiencies may be improved by managing irrigation application timing and volumes using physical and agronomic principles. However, the crop water requirement may be spatially variable due to different soil properties and genetic variations in the crop across the field. Adaptive control strategies can be used to locally control water applications in response to in-field temporal and spatial variability with the aim of maximising both crop development and water use efficiency. A simulation framework ‘VARIwise’ has been created to aid the development, evaluation and management of spatially and temporally varied adaptive irrigation control strategies (McCarthy et al., 2010). VARIwise enables alternative control strategies to be simulated with different crop and environmental conditions and at a range of spatial resolutions. An iterative learning controller and model predictive controller have been implemented in VARIwise to improve the irrigation of cotton. The iterative learning control strategy involves using the soil moisture response to the previous irrigation volume to adjust the applied irrigation volume applied at the next irrigation event. For field implementation this controller has low data requirements as only soil moisture data is required after each irrigation event. In contrast, a model predictive controller has high data requirements as measured soil and plant data are required at a high spatial resolution in a field implementation. Model predictive control involves using a calibrated model to determine the irrigation application and/or timing which results in the highest predicted yield or water use efficiency. The implementation of these strategies is described and a case study is presented to demonstrate the operation of the strategies with various levels of data availability. It is concluded that in situations of sparse data, the iterative learning controller performs significantly better than a model predictive controller

Breeding for Drought Tolerance by Monitoring Chlorophyll Content

Crop yields have increased substantially during the last 50 years, but the traits that drove these remarkable improvements, such as plant architecture, have a little remaining potential for improvement. New traits such as photosynthesis, as the ultimate determinant of yield, must be explored to support future demands. However, improving photosynthetic efficiency has played only a minor role in improving crop yield to date. Chlorophylls are the pigments allowing light to be transformed into carbohydrates, and therefore help to maintain crop yield under stress. Chlorophyll content correlates with higher yields in diverse conditions. In this review, we discuss using chlorophyll content as the basis of screens for drought tolerance. We review chlorophyll-related responses to drought in different plants and summarize the advantages and disadvantages of current methods to measure chlorophyll content, with the ultimate goal of improving the efficiency of crop breeding for drought tolerance.Instituto de Fisiología y Recursos Genéticos VegetalesFil: Monteoliva, Mariela Inés. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales.; ArgentinaFil: Monteoliva, Mariela Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Estudios Agropecuarios (UDEA); ArgentinaFil: Guzzo, María Carla. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales.; ArgentinaFil: Guzzo, María Carla. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Estudios Agropecuarios (UDEA); ArgentinaFil: Posada, Gisella Anabel. Instituto Superior Albert Sabin; Argentin

Remote Sensing for Precision Nitrogen Management

This book focuses on the fundamental and applied research of the non-destructive estimation and diagnosis of crop leaf and plant nitrogen status and in-season nitrogen management strategies based on leaf sensors, proximal canopy sensors, unmanned aerial vehicle remote sensing, manned aerial remote sensing and satellite remote sensing technologies. Statistical and machine learning methods are used to predict plant-nitrogen-related parameters with sensor data or sensor data together with soil, landscape, weather and/or management information. Different sensing technologies or different modelling approaches are compared and evaluated. Strategies are developed to use crop sensing data for in-season nitrogen recommendations to improve nitrogen use efficiency and protect the environment