<i>Background</i>. Computed X-ray tomography (CTX) is a high-end nondestructive approach for the visual assessment of root architecture in soil. Nevertheless, in order to evaluate high-resolution CTX data of root architectures, manual segmentation of the depicted root systems from large-scale volume data is currently necessary, which is both time consuming and error prone. The duration of such a segmentation is of importance, especially for time-resolved growth analysis, where several instances of a plant need to be segmented and evaluated. Specifically, in our application, the contrast between soil and root data varies due to different growth stages and watering situations at the time of scanning. Additionally, the root system itself is expanding in length and in the diameter of individual roots. <i>Objective</i>. For semiautomated and robust root system segmentation from CTX data, we propose the <i>RootForce</i> approach, which is an extension of Frangi’s “multi-scale vesselness” method and integrates a 3D local variance. It allows a precise delineation of roots with diameters down to several <i>μ</i>m in pots with varying diameters. Additionally, <i>RootForce</i> is not limited to the segmentation of small below-ground organs, but is also able to handle storage roots with a diameter larger than 40 voxels. <i>Results</i>. Using CTX volume data of full-grown bean plants as well as time-resolved (<svg xmlns="http://www.w3.org/2000/svg" id="M1" style="vertical-align:-0.6075296pt" height="9.3427pt" version="1.1" viewBox="-0.0498162 -8.73517 51.8539 9.3427" width="51.8539pt">


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</svg>) growth studies of cassava plants, <i>RootForce</i> produces similar (and much faster) results compared to manual segmentation of the regarded root architectures. Furthermore, <i>RootForce</i> enables the user to obtain traits not possible to be calculated before, such as total root volume (<svg xmlns="http://www.w3.org/2000/svg" id="M2" style="vertical-align:-3.25759pt" height="11.5729pt" version="1.1" viewBox="-0.0498162 -8.31531 22.8048 11.5729" width="22.8048pt">


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</svg>), total root length (<svg xmlns="http://www.w3.org/2000/svg" id="M3" style="vertical-align:-3.25759pt" height="11.5729pt" version="1.1" viewBox="-0.0498162 -8.31531 21.6142 11.5729" width="21.6142pt">


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</svg>), root volume over depth, root growth angles (<svg xmlns="http://www.w3.org/2000/svg" id="M4" style="vertical-align:-3.18309pt" height="11.7428pt" version="1.1" viewBox="-0.0498162 -8.55971 20.7407 11.7428" width="20.7407pt">


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</svg>, or form fraction <svg xmlns="http://www.w3.org/2000/svg" id="M8" style="vertical-align:-0.0498209pt" height="8.36513pt" version="1.1" viewBox="-0.0498162 -8.31531 9.11084 8.36513" width="9.11084pt">


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</svg>. <i>Discussion</i>. The proposed <i>RootForce</i> tool can provide a higher efficiency for the semiautomatic high-throughput assessment of the root architectures of different types of plants from large-scale CTX. Furthermore, for all datasets within a growth experiment, only a single set of parameters is needed. Thus, the proposed tool can be used for a wide range of growth experiments in the field of plant phenotyping.

Stefan Gerth

Joelle Clau&#x00DF;en

Anja Eggert

Norbert W&#x00F6;rlein

Michael Waininger

Thomas Wittenberg

Norman Uhlmann

Semiautomated 3D Root Segmentation and Evaluation Based on X-Ray CT Imagery

Consumers hesitate to purchase field-grown shoot-tops of amaranths in Sri Lanka, citing the low-cleanliness making growers focus on greenhouse farming. However, the photosynthetic and growth variations in relation to the organoleptic preference of the greenhouse-grown amaranths in comparison to field-grown counterparts have not been studied. Also, the species delimits of the amaranths in Sri Lanka have not been identified, limiting our ability to interpret species-specific production characteristics. Thus, we assessed the common types of amaranths under greenhouse and field conditions. The photosynthesis was measured using a MultispeQ device of the PhotosynQ phenomic platform, which records chlorophyll fluorescence-based parameters. The shoot-tops were harvested and prepared as dishes according to the typical recipe for amaranths in Sri Lanka. The dishes were subjected to an organoleptic assessment for the parameters color, aroma, bitterness, texture, and overall taste. The differences in plant and the shoot-top biomass were also assessed. The markers <i>atpB-rbcL</i>, <i>matk-trnT</i>, and <i>ITS</i> were used to define the species delimits. The field-grown and greenhouse-grown amaranths exhibited species/cultivar-specific photosynthetic variations. The texture and overall taste of the dishes were different among greenhouse and field-grown material. The tasters preferred the texture and the overall taste of the greenhouse-grown shoot-tops. The greenhouse-grown plants also yielded higher shoot-top harvests compared to field-grown counterparts. Out of the tested markers, <i>ITS</i> defines the delimits of amaranth species. The higher organoleptic preference, the appreciable yield levels, unique photosynthetic patterns of the greenhouse-grown amaranths, and species definitions provide the much-needed platform for clean shoot-top production guaranteeing the highest end-user trust.

S. D. S. S. Sooriyapathirana

L. T. Ranaweera

H. S. M. Jayarathne

T. H. I. Gayathree

P. G. R. G. Rathnayake

S. I. Karunarathne

S. M. N. K. Thilakarathne

R. Salih

C. K. Weebadde

C. P. Weebadde

Photosynthetic Phenomics of Field- and Greenhouse-Grown Amaranths vs. Sensory and Species Delimits

<i>Panax quinquefolium</i> is a perennial herbaceous plant that contains many beneficial ginsenosides with diverse pharmacological effects. 24(R)-pseudoginsenoside F<sub>11</sub> is specific to <i>P</i>. <i>quinquefolium</i>, a useful biomarker for distinguishing this species from other related plants. However, because of its nonconjugated property and the complexity of existing detection methods, this biomarker cannot be used as the identification standard. We herein present a stable 24(R)-pseudoginsenoside F<sub>11</sub> fingerprint spectrum in the terahertz band, thereby proving that F<sub>11</sub> can be detected and quantitatively analyzed via terahertz spectroscopy. We also analyzed the sample by high-performance liquid chromatography-triple quadrupole mass spectrometry. The difference between the normalized data for the two analytical methods was less than 5&#x0025;. Furthermore, <i>P</i>. <i>quinquefolium</i> from different areas and other substances can be clearly distinguished based on these terahertz spectra with a standard principal component analysis. Our method is a fast, simple, and cost-effective approach for identifying and quantitatively analyzing <i>P</i>. <i>quinquefolium</i>.

Tianyi Kou

Ji Ye

Jing Wang

Yan Peng

Zefang Wang

Chenjun Shi

Xu Wu

Xitian Hu

Haihong Chen

Ling Zhang

Xiaohong Chen

Yiming Zhu

Huiliang Li

Songlin Zhuang

Terahertz Spectroscopy for Accurate Identification of <i>Panax quinquefolium</i> Basing on Nonconjugated 24(R)-Pseudoginsenoside F<sub>11</sub>

Plants have developed multiple strategies to respond to salt stress. In order to identify new traits related to salt tolerance, with potential breeding application, the research focus has recently been shifted to include root system architecture (RSA) and root plasticity. Using a simple but effective root phenotyping system containing soil (rhizotrons), RSA of several tomato cultivars and their response to salinity was investigated. We observed a high level of root plasticity of tomato seedlings under salt stress. The general root architecture was substantially modified in response to salt, especially with respect to position of the lateral roots in the soil. At the soil surface, where salt accumulates, lateral root emergence was most strongly inhibited. Within the set of tomato cultivars, H1015 was the most tolerant to salinity in both developmental stages studied. A significant correlation between several root traits and aboveground growth parameters was observed, highlighting a possible role for regulation of both ion content and root architecture in salt stress resilience.

Jacinto Gandullo

Safarina Ahmad

Essam Darwish

Rumyana Karlova

Christa Testerink

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

About this journal

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


Journal profile

Meet the editorial board

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


Editorial board

More special issue details

<p>Published Special Issues:</p>

<p><br />
<strong><a href="https://spj.sciencemag.org/plant-phenomics-special-issues/image-analysis">Image Analysis and Machine Learning for Cyber-Agricultural Systems</a></strong><br />
&nbsp;</p>

<p><strong><a href="https://spj.sciencemag.org/plant-phenomics-special-issues/statistics-bioinformatics/">Statistics, Bioinformatics, and Machine Learning Methods in Phenomics</a></strong></p>
