Phenotyping Tomato Root Developmental Plasticity in Response to Salinity in Soil Rhizotrons

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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

Canopy Roughness: A New Phenotypic Trait to Estimate Aboveground Biomass from Unmanned Aerial System

Cost-effective phenotyping methods are urgently needed to advance crop genetics in order to meet the food, fuel, and fiber demands of the coming decades. Concretely, characterizing plot level traits in fields is of particular interest. Recent developments in high-resolution imaging sensors for UAS (unmanned aerial systems) focused on collecting detailed phenotypic measurements are a potential solution. We introduce canopy roughness as a new plant plot-level trait. We tested its usability with soybean by optical data collected from UAS to estimate biomass. We validate canopy roughness on a panel of 108 soybean [Glycine max (L.) Merr.] recombinant inbred lines in a multienvironment trial during the R2 growth stage. A senseFly eBee UAS platform obtained aerial images with a senseFly S.O.D.A. compact digital camera. Using a structure from motion (SfM) technique, we reconstructed 3D point clouds of the soybean experiment. A novel pipeline for feature extraction was developed to compute canopy roughness from point clouds. We used regression analysis to correlate canopy roughness with field-measured aboveground biomass (AGB) with a leave-one-out cross-validation. Overall, our models achieved a coefficient of determination ( ) greater than 0.5 in all trials. Moreover, we found that canopy roughness has the ability to discern AGB variations among different genotypes. Our test trials demonstrate the potential of canopy roughness as a reliable trait for high-throughput phenotyping to estimate AGB. As such, canopy roughness provides practical information to breeders in order to select phenotypes on the basis of UAS data.

Research Article

Global Trends of Usage of Chlorophyll Fluorescence and Projections for the Next Decade

Chlorophyll fluorescence is the most widely used set of techniques to probe photosynthesis and plant stress. Its great versatility has given rise to different routine methods to study plants and algae. The three main technical platforms are pulse amplitude modulation (PAM), fast rise of chlorophyll fluorescence, and fast repetition rate. Solar-induced fluorescence (SIF) has also gained interest in the last few years. Works have compared their advantages and their underlying theory, with many arguments advanced as to which method is the most accurate and useful. To date, no data has assessed the exact magnitude of popularity and influence for each methodology. In this work, we have taken the bibliometrics of the past decade for each of the four platforms, have evaluated the public scientific opinion toward each method, and possibly identified a geographical bias. We used various metrics to assess influence and popularity for the four routine platforms compared in this study and found that, overall, PAM currently has the highest values, although the more recent SIF has increased in popularity rapidly during the last decade. This indicates that PAM is currently one of the fundamental tools in chlorophyll fluorescence.

Perspective

A 3D Print Repository for Plant Phenomics

Research Article

Water Dynamics on Germinating Diaspores: Physiological Perspectives from Biophysical Measurements

We demonstrated that classical biophysical measurements of water dynamics on germinating diaspores (seeds and other dispersal units) can improve the understanding of the germination process in a simpler, safer, and newer way. This was done using diaspores of cultivated species as a biological model. To calculate the water dynamics measurements (weighted mass, initial diffusion coefficient, velocity, and acceleration), we used the mass of diaspores recorded over germination time. Weighted mass of germinating diaspores has a similar pattern, independent of the physiological quality, species, or genetic improvement degree. However, the initial diffusion coefficient (related to imbibition per se), velocity, and acceleration (related to the whole germination metabolism) are influenced by species characters, highlighting the degree of genetic improvement and physiological quality. Changes in the inflection of velocity curves demonstrated each phase of germination sensu stricto. There is no pattern related to the number of these phases, which could range between three and six. Regression models can demonstrate initial velocity and velocity increments for each phase, giving an idea of the management of germinative metabolism. Our finds demonstrated that germination is a polyphasic process with a species-specific pattern but still set by the degree of genetic improvement and (or) physiological quality of diaspores. Among the biophysical measurements, velocity has the greatest potential to define the germination metabolism.

Research Article

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

Phenomics technologies allow quantitative assessment of phenotypes across a larger number of plant genotypes compared to traditional phenotyping approaches. The utilization of such technologies has enabled the generation of multidimensional plant traits creating big datasets. However, to harness the power of phenomics technologies, more sophisticated data analysis methods are required. In this study, Aphanomyces root rot (ARR) resistance in 547 lentil accessions and lines was evaluated using Red-Green-Blue (RGB) images of roots. We created a dataset of 6,460 root images that were annotated by a plant breeder based on the disease severity. Two approaches, generalized linear model with elastic net regularization (EN) and convolutional neural network (CNN), were developed to classify disease resistance categories into three classes: resistant, partially resistant, and susceptible. The results indicated that the selected image features using EN models were able to classify three disease categories with an accuracy of up to ( resistant, partially resistant, and susceptible) compared to CNN with an accuracy of about ( resistant, partially resistant, and susceptible). The resistant class was accurately detected using both classification methods. However, partially resistant class was challenging to detect as the features (data) of the partially resistant class often overlapped with those of resistant and susceptible classes. Collectively, the findings provided insights on the use of phenomics techniques and machine learning approaches to provide quantitative measures of ARR resistance in lentil.

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.