High-Throughput, Noninvasive Imaging of Root Systems

Abstract Background The root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root phenotyping platform with a panel of 20 japonica rice accessions in order to: (i) assess their genetic diversity for a set of structural and morphological root traits and classify the different types; (ii) analyze the plastic response of their root system to a water deficit at reproductive phase and (iii) explore the ability of the platform for high-throughput phenotyping of root structure and morphology. Results High variability for the studied root traits was found in the reduced set of accessions. Using eight selected traits under irrigated conditions, five root clusters were found that differed in root thickness, branching index and the pattern of fine and thick root distribution along the profile. When water deficit occurred at reproductive phase, some accessions significantly reduced root growth compared to the irrigated treatment, while others stimulated it. It was found that root cluster, as defined under irrigated conditions, could not predict the plastic response of roots under drought. Conclusions This study revealed the possibility of reconstructing the structure of root systems from scanned images. It was thus possible to significantly class root systems according to simple structural traits, opening up the way for using such a platform for medium to high-throughput phenotyping. The study also highlighted the uncoupling between root structures under non-limiting water conditions and their response to drought.

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GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system based on germination paper to quantify crop phenotypic diversity and plasticity of root traits under varying nutrient supply

Functional Plant Biology ◽

10.1071/fp16128 ◽

2017 ◽

Vol 44 (1) ◽

pp. 76 ◽

Cited By ~ 22

Author(s):

Tania Gioia ◽

Anna Galinski ◽

Henning Lenz ◽

Carmen Müller ◽

Jonas Lentz ◽

...

Keyword(s):

High Throughput ◽

Phenotypic Diversity ◽

Crop Improvement ◽

Root Traits ◽

Root Systems ◽

Non Invasive ◽

Large Sets ◽

High Throughput Phenotyping ◽

Improvement Programs ◽

Root Phenotyping

New techniques and approaches have been developed for root phenotyping recently; however, rapid and repeatable non-invasive root phenotyping remains challenging. Here, we present GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system (4 plants min–1) based on flat germination paper. GrowScreen-PaGe allows the acquisition of time series of the developing root systems of 500 plants, thereby enabling to quantify short-term variations in root system. The choice of germination paper was found to be crucial and paper ☓ root interaction should be considered when comparing data from different studies on germination paper. The system is suitable for phenotyping dicot and monocot plant species. The potential of the system for high-throughput phenotyping was shown by investigating phenotypic diversity of root traits in a collection of 180 rapeseed accessions and of 52 barley genotypes grown under control and nutrient-starved conditions. Most traits showed a large variation linked to both genotype and treatment. In general, root length traits contributed more than shape and branching related traits in separating the genotypes. Overall, results showed that GrowScreen-PaGe will be a powerful resource to investigate root systems and root plasticity of large sets of plants and to explore the molecular and genetic root traits of various species including for crop improvement programs.

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High-throughput sensing and noninvasive imaging of protein nuclear transport by using reconstitution of split Renilla luciferase

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0401722101 ◽

2004 ◽

Vol 101 (32) ◽

pp. 11542-11547 ◽

Cited By ~ 81

Author(s):

S. B. Kim ◽

T. Ozawa ◽

S. Watanabe ◽

Y. Umezawa

Keyword(s):

High Throughput ◽

Nuclear Transport ◽

Noninvasive Imaging ◽

Renilla Luciferase

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Ground-penetrating Radar as Phenotyping Tool for Characterizing Intraspecific Variability in Root Traits of Pinus Halepensis

10.21203/rs.3.rs-161358/v1 ◽

2021 ◽

Author(s):

Erica Lombardi ◽

Juan Pedro Ferrio ◽

Ulises Rodríguez-Robles ◽

Víctor Resco de Dios ◽

Jordi Voltas

Keyword(s):

High Throughput ◽

Pinus Halepensis ◽

Genotypic Variation ◽

Intraspecific Variability ◽

Root Traits ◽

Root Systems ◽

Population Divergence ◽

Coarse Root ◽

The Mediterranean ◽

Root Frequency

Abstract Background and AimDrought is the main factor limiting Mediterranean forest ecosystem productivity. Root systems are responsible for water uptake but intraspecific variability in root morphology is poorly understood, mainly due to sampling complexity. The main aim of this study was to gain knowledge on the adaptive relevance of rooting traits for a widespread conifer using a non-invasive high-throughput technique.MethodsGround-Penetrating Radar (GPR) was used to characterize variability in coarse root features (frequency, depth, and diameter) among populations of the Mediterranean pine Pinus halepensis evaluated in a common garden. GPR records were analysed in relation to aboveground growth and also climate variables at origin of populations.ResultsGenotypic variability was detected for root traits among 56 range-wide populations categorized into 16 ecotypes. Root diameter of populations decreased eastward within the Mediterranean basin. Root frequency, but not depth and diameter, decreased following a northward gradient. Genotypic variation in root traits varied with climatic variables at origin such as summer to annual precipitation ratio, summer temperature and solar radiation. Particularly, root frequency increased with aridity, whereas root depth and diameter were maximum in ecotypes occupying the thermal midpoint of the species distribution range.Conclusion GPR is a high-throughput phenotyping tool that allows detection of intraspecific variation in root traits of Aleppo pine and its dependencies of eco-geographic characteristics at origin, thereby informing on the adaptive relevance of root systems for the species. It is also potentially suited for inferring population divergence in resource allocation above and belowground in forest genetic trials.

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Ground-Penetrating Radar as phenotyping tool for characterizing intraspecific variability in root traits of a widespread conifer

Plant and Soil ◽

10.1007/s11104-021-05135-0 ◽

2021 ◽

Author(s):

Erica Lombardi ◽

Juan Pedro Ferrio ◽

Ulises Rodríguez-Robles ◽

Víctor Resco de Dios ◽

Jordi Voltas

Keyword(s):

High Throughput ◽

Ground Penetrating Radar ◽

Intraspecific Variability ◽

Root Traits ◽

Root Systems ◽

Mediterranean Forests ◽

High Throughput Phenotyping ◽

The Mediterranean ◽

Ground Penetrating ◽

Root Frequency

Abstract Background and Aim Drought is the main abiotic stress affecting Mediterranean forests. Root systems are responsible for water uptake, but intraspecific variability in tree root morphology is poorly understood mainly owing to sampling difficulties. The aim of this study was to gain knowledge on the adaptive relevance of rooting traits for a widespread pine using a non-invasive, high-throughput phenotyping technique. Methods Ground-Penetrating Radar (GPR) was used to characterize variability in coarse root features (depth, diameter and frequency) among populations of the Mediterranean conifer Pinus halepensis evaluated in a common garden. GPR records were examined in relation to aboveground growth and climate variables at origin of populations. Results Variability was detected for root traits among 56 range-wide populations categorized into 16 ecotypes. Root diameter decreased eastward within the Mediterranean basin. In turn, root frequency, but not depth and diameter, decreased following a northward gradient. Root traits also varied with climatic variables at origin such as the ratio of summer to annual precipitation, summer temperature or solar radiation. Particularly, root frequency increased with aridity, whereas root depth and diameter were maximum for ecotypes occupying the thermal midpoint of the species distribution range. Conclusion GPR is a high-throughput phenotyping tool that allows detection of intraspecific variation in root traits of P. halepensis and its dependencies on eco-geographic characteristics at origin, thereby informing on the adaptive relevance of root systems for the species. It is also potentially suited for inferring population divergence in resource allocation above- and belowground in forest genetic trials.

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RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping

10.1101/569707 ◽

2019 ◽

Cited By ~ 1

Author(s):

Anand Seethepalli ◽

Haichao Guo ◽

Xiuwei Liu ◽

Marcus Griffiths ◽

Hussien Almtarfi ◽

...

Keyword(s):

Image Analysis ◽

High Throughput ◽

User Interfaces ◽

Copper Wire ◽

Principal Component ◽

Ground Truth ◽

Root Systems ◽

Plant Phenotyping ◽

Image Capture ◽

Crop Root

ABSTRACTRoot crown phenotyping measures the top portion of crop root systems and can be used for marker-assisted breeding, genetic mapping, and understanding how roots influence soil resource acquisition. Several imaging protocols and image analysis programs exist, but they are not optimized for high-throughput, repeatable, and robust root crown phenotyping. The RhizoVision Crown platform integrates an imaging unit, image capture software, and image analysis software that are optimized for reliable extraction of measurements from large numbers of root crowns. The hardware platform utilizes a back light and a monochrome machine vision camera to capture root crown silhouettes. RhizoVision Imager and RhizoVision Analyzer are free, open-source software that streamline image capture and image analysis with intuitive graphical user interfaces. RhizoVision Analyzer was physically validated using copper wire and features were extensively validated using 10,464 ground-truth simulated images of dicot and monocot root systems. This platform was then used to phenotype soybean and wheat root crowns. A total of 2,799 soybean (Glycine max) root crowns of 187 lines and 1,753 wheat (Triticum aestivum) root crowns of 186 lines were phenotyped. Principal component analysis indicated similar correlations among features in both species. The maximum heritability was 0.74 in soybean and 0.22 in wheat, indicating differences in species and populations need to be considered. The integrated RhizoVision Crown platform facilitates high-throughput phenotyping of crop root crowns, and sets a standard by which open plant phenotyping platforms can be benchmarked.

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RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping

Plant Phenomics ◽

10.34133/2020/3074916 ◽

2020 ◽

Vol 2020 ◽

pp. 1-15 ◽

Cited By ~ 1

Author(s):

Anand Seethepalli ◽

Haichao Guo ◽

Xiuwei Liu ◽

Marcus Griffiths ◽

Hussien Almtarfi ◽

...

Keyword(s):

Image Analysis ◽

High Throughput ◽

User Interfaces ◽

Copper Wire ◽

Principal Component ◽

Ground Truth ◽

Root Systems ◽

Plant Phenotyping ◽

Image Capture ◽

Crop Root

Root crown phenotyping measures the top portion of crop root systems and can be used for marker-assisted breeding, genetic mapping, and understanding how roots influence soil resource acquisition. Several imaging protocols and image analysis programs exist, but they are not optimized for high-throughput, repeatable, and robust root crown phenotyping. The RhizoVision Crown platform integrates an imaging unit, image capture software, and image analysis software that are optimized for reliable extraction of measurements from large numbers of root crowns. The hardware platform utilizes a backlight and a monochrome machine vision camera to capture root crown silhouettes. The RhizoVision Imager and RhizoVision Analyzer are free, open-source software that streamline image capture and image analysis with intuitive graphical user interfaces. The RhizoVision Analyzer was physically validated using copper wire, and features were extensively validated using 10,464 ground-truth simulated images of dicot and monocot root systems. This platform was then used to phenotype soybean and wheat root crowns. A total of 2,799 soybean (Glycine max) root crowns of 187 lines and 1,753 wheat (Triticum aestivum) root crowns of 186 lines were phenotyped. Principal component analysis indicated similar correlations among features in both species. The maximum heritability was 0.74 in soybean and 0.22 in wheat, indicating that differences in species and populations need to be considered. The integrated RhizoVision Crown platform facilitates high-throughput phenotyping of crop root crowns and sets a standard by which open plant phenotyping platforms can be benchmarked.

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