Generalized Linear Model with Elastic Net Regularization and Convolutional Neural Network for Evaluating Aphanomyces Root Rot Severity in Lentil

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Journal profile

The open access journal Plant Phenomics, published in association with NAU, publishes novel research that advances plant phenotyping and connects phenomics with other research domains.

Editorial board

Plant Phenomics' editorial board is led by Seishi Ninomiya (University of Tokyo), Frédéric Baret (French National Institute of Agricultural Research), and Zong-Ming Cheng (Nanjing Agricultural University/University of Tennessee) and is comprised of leading experts in the field.

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Research Article

A Statistical Growth Property of Plant Root Architectures

Numerous types of biological branching networks, with varying shapes and sizes, are used to acquire and distribute resources. Here, we show that plant root and shoot architectures share a fundamental design property. We studied the spatial density function of plant architectures, which specifies the probability of finding a branch at each location in the 3-dimensional volume occupied by the plant. We analyzed 1645 root architectures from four species and discovered that the spatial density functions of all architectures are population-similar. This means that despite their apparent visual diversity, all of the roots studied share the same basic shape, aside from stretching and compression along orthogonal directions. Moreover, the spatial density of all architectures can be described as variations on a single underlying function: a Gaussian density truncated at a boundary of roughly three standard deviations. Thus, the root density of any architecture requires only four parameters to specify: the total mass of the architecture and the standard deviations of the Gaussian in the three growth directions. Plant shoot architectures also follow this design form, suggesting that two basic plant transport systems may use similar growth strategies.

Research Article

An Analysis of Soil Coring Strategies to Estimate Root Depth in Maize (Zea mays) and Common Bean (Phaseolus vulgaris)

A soil coring protocol was developed to cooptimize the estimation of root length distribution (RLD) by depth and detection of functionally important variation in root system architecture (RSA) of maize and bean. The functional-structural model OpenSimRoot was used to perform in silico soil coring at six locations on three different maize and bean RSA phenotypes. Results were compared to two seasons of field soil coring and one trench. Two one-sided -test (TOST) analysis of in silico data suggests a between-row location 5 cm from plant base (location 3), best estimates whole-plot RLD/D of deep, intermediate, and shallow RSA phenotypes, for both maize and bean. Quadratic discriminant analysis indicates location 3 has ~70% categorization accuracy for bean, while an in-row location next to the plant base (location 6) has ~85% categorization accuracy in maize. Analysis of field data suggests the more representative sampling locations vary by year and species. In silico and field studies suggest location 3 is most robust, although variation is significant among seasons, among replications within a field season, and among field soil coring, trench, and simulations. We propose that the characterization of the RLD profile as a dynamic rhizo canopy effectively describes how the RLD profile arises from interactions among an individual plant, its neighbors, and the pedosphere.

Research Article

“Macrobot”: An Automated Segmentation-Based System for Powdery Mildew Disease Quantification

Managing plant diseases is increasingly difficult due to reasons such as intensifying the field production, climatic change-driven expansion of pests, redraw and loss of effectiveness of pesticides, rapid breakdown of the disease resistance in the field, and other factors. The substantial progress in genomics of both plants and pathogens, achieved in the last decades, has the potential to counteract this negative trend, however, only when the genomic data is supported by relevant phenotypic data that allows linking the genomic information to specific traits. We have developed a set of methods and equipment and combined them into a “Macrophenomics facility.” The pipeline has been optimized for the quantification of powdery mildew infection symptoms on wheat and barley, but it can be adapted to other diseases and host plants. The Macrophenomics pipeline scores the visible powdery mildew disease symptoms, typically 5-7 days after inoculation (dai), in a highly automated manner. The system can precisely and reproducibly quantify the percentage of the infected leaf area with a theoretical throughput of up to 10000 individual samples per day, making it appropriate for phenotyping of large germplasm collections and crossing populations.

Research Article

A Deep Learning-Based Phenotypic Analysis of Rice Root Distribution from Field Images

Root distribution in the soil determines plants’ nutrient and water uptake capacity. Therefore, root distribution is one of the most important factors in crop production. The trench profile method is used to observe the root distribution underground by making a rectangular hole close to the crop, providing informative images of the root distribution compared to other root phenotyping methods. However, much effort is required to segment the root area for quantification. In this study, we present a promising approach employing a convolutional neural network for root segmentation in trench profile images. We defined two parameters, Depth50 and Width50, representing the vertical and horizontal centroid of root distribution, respectively. Quantified parameters for root distribution in rice (Oryza sativa L.) predicted by the trained model were highly correlated with parameters calculated by manual tracing. These results indicated that this approach is useful for rapid quantification of the root distribution from the trench profile images. Using the trained model, we quantified the root distribution parameters among 60 rice accessions, revealing the phenotypic diversity of root distributions. We conclude that employing the trench profile method and a convolutional neural network is reliable for root phenotyping and it will furthermore facilitate the study of crop roots in the field.

Research Article

Machine Learning-Based Presymptomatic Detection of Rice Sheath Blight Using Spectral Profiles

Early detection of plant diseases, prior to symptom development, can allow for targeted and more proactive disease management. The objective of this study was to evaluate the use of near-infrared (NIR) spectroscopy combined with machine learning for early detection of rice sheath blight (ShB), caused by the fungus Rhizoctonia solani. We collected NIR spectra from leaves of ShB-susceptible rice (Oryza sativa L.) cultivar, Lemont, growing in a growth chamber one day following inoculation with R. solani, and prior to the development of any disease symptoms. Support vector machine (SVM) and random forest, two machine learning algorithms, were used to build and evaluate the accuracy of supervised classification-based disease predictive models. Sparse partial least squares discriminant analysis was used to confirm the results. The most accurate model comparing mock-inoculated and inoculated plants was SVM-based and had an overall testing accuracy of 86.1% ( ), while when control, mock-inoculated, and inoculated plants were compared the most accurate SVM model had an overall testing accuracy of 73.3% ( ). These results suggest that machine learning models could be developed into tools to diagnose infected but asymptomatic plants based on spectral profiles at the early stages of disease development. While testing and validation in field trials are still needed, this technique holds promise for application in the field for disease diagnosis and management.

Research Article

Coffee Flower Identification Using Binarization Algorithm Based on Convolutional Neural Network for Digital Images

Crop-type identification is one of the most significant applications of agricultural remote sensing, and it is important for yield estimation prediction and field management. At present, crop identification using datasets from unmanned aerial vehicle (UAV) and satellite platforms have achieved state-of-the-art performances. However, accurate monitoring of small plants, such as the coffee flower, cannot be achieved using datasets from these platforms. With the development of time-lapse image acquisition technology based on ground-based remote sensing, a large number of small-scale plantation datasets with high spatial-temporal resolution are being generated, which can provide great opportunities for small target monitoring of a specific region. The main contribution of this paper is to combine the binarization algorithm based on OTSU and the convolutional neural network (CNN) model to improve coffee flower identification accuracy using the time-lapse images (i.e., digital images). A certain number of positive and negative samples are selected from the original digital images for the network model training. Then, the pretrained network model is initialized using the VGGNet and trained using the constructed training datasets. Based on the well-trained CNN model, the coffee flower is initially extracted, and its boundary information can be further optimized by using the extracted coffee flower result of the binarization algorithm. Based on the digital images with different depression angles and illumination conditions, the performance of the proposed method is investigated by comparison of the performances of support vector machine (SVM) and CNN model. Hence, the experimental results show that the proposed method has the ability to improve coffee flower classification accuracy. The results of the image with a 52.5° angle of depression under soft lighting conditions are the highest, and the corresponding Dice (F1) and intersection over union (IoU) have reached 0.80 and 0.67, respectively.