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

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.

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

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.

scholarly journals Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Paulo Henrique Ramos Guimarães ◽  
Isabela Pereira de Lima ◽  
Adriano Pereira de Castro ◽  
Anna Cristina Lanna ◽  
Patrícia Guimarães Santos Melo ◽  
...  
Keyword(s):  
Root System ◽  
Water Deficit ◽  
High Throughput ◽  
Root Traits ◽  
Root Systems ◽  
Japonica Rice ◽  
Plastic Response ◽  
Reproductive Phase ◽  
High Throughput Phenotyping ◽  
Structural Traits

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.

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

2017 ◽  
Vol 44 (1) ◽  
pp. 76 ◽  
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.

scholarly journals High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napusL.)

2016 ◽  
Vol 118 (4) ◽  
pp. 655-665 ◽  
Author(s):  
C. L. Thomas ◽  
N. S. Graham ◽  
R. Hayden ◽  
M. C. Meacham ◽  
K. Neugebauer ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Seed Yield ◽  
High Throughput ◽  
Root Traits ◽  
Seedling Root ◽  
High Throughput Phenotyping

scholarly journals Mapping tree root systems with ground-penetrating radar

1999 ◽  
Vol 19 (2) ◽  
pp. 125-130 ◽  
Author(s):  
J. Hruska ◽  
J. Cermak ◽  
S. Sustek
Keyword(s):  
Ground Penetrating Radar ◽  
Root Systems ◽  
Ground Penetrating

scholarly journals ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture

2020 ◽  
Author(s):  
Nicolás Gaggion ◽  
Federico Ariel ◽  
Vladimir Daric ◽  
Éric Lambert ◽  
Simon Legendre ◽  
...  
Keyword(s):  
Deep Learning ◽  
Root System ◽  
High Throughput ◽  
System Architecture ◽  
Root Traits ◽  
Root System Architecture ◽  
Machine Intelligence ◽  
Reconstruction Process ◽  
High Throughput Phenotyping ◽  
3D Printed

ABSTRACTDeep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system which combines 3D printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. We developed a novel deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals. Altogether, our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies as well as the screening of clock-related mutants, revealing novel root traits.

scholarly journals Advanced GPR Signal Processing Techniques for Root Detection in Urban Environments

2020 ◽  
Author(s):  
Livia Lantini ◽  
Fabio Tosti ◽  
Iraklis Giannakis ◽  
Kevin Jagadissen Munisami ◽  
Dale Mortimer ◽  
...  
Keyword(s):  
Ground Penetrating Radar ◽  
Root Systems ◽  
Urban Environments ◽  
Street Trees ◽  
Destructive Testing ◽  
Root Detection ◽  
Charitable Trust ◽  
Ground Penetrating ◽  
Processing Techniques ◽  
Non Destructive

<p>Street trees are widely recognised to be an essential asset for the urban environment, as they bring several environmental, social and economic benefits [1]. However, the conflicting coexistence of tree root systems with the built environment, and especially with road infrastructures, is often cause of extensive damage, such as the uplifting and cracking of sidewalks and curbs, which could seriously compromise the safety of pedestrians, cyclists and drivers.</p><p>In this context, Ground Penetrating Radar (GPR) has long been proven to be an effective non-destructive testing (NDT) method for the evaluation and monitoring of road pavements. The effectiveness of this tool lies not only in its ease of use and cost-effectiveness, but also in the proven reliability of the results provided. Besides, recent studies have explored the capability of GPR in detecting and mapping tree roots [2]. Algorithms for the reconstruction of the tree root systems have been developed, and the spatial variations of root mass density have been also investigated [3].</p><p>The aim of this study is, therefore, to investigate the GPR potential in mapping the architecture of root systems in street trees. In particular, this research aims to improve upon the existing methods for detection of roots, focusing on the identification of the road pavement layers. In this way, different advanced signal processing techniques can be applied at specific sections, in order to remove reflections from the pavement layers without affecting root detection. This allows, therefore, to reduce false alarms when investigating trees with root systems developing underneath road pavements.</p><p>In this regard, data from trees of different species have been acquired and processed, using different antenna systems and survey methodologies, in an effort to investigate the impact of these parameters on the GPR overall performance.</p><p> </p><p><strong>Acknowledgements</strong></p><p>The authors would like to express their sincere thanks and gratitude to the following trusts, charities, organisations and individuals for their generosity in supporting this project: Lord Faringdon Charitable Trust, The Schroder Foundation, Cazenove Charitable Trust, Ernest Cook Trust, Sir Henry Keswick, Ian Bond, P. F. Charitable Trust, Prospect Investment Management Limited, The Adrian Swire Charitable Trust, The John Swire 1989 Charitable Trust, The Sackler Trust, The Tanlaw Foundation, and The Wyfold Charitable Trust. This paper is dedicated to the memory of our colleague and friend Jonathan West, one of the original supporters of this research project.</p><p> </p><p><strong>References</strong></p><p>[1] J. Mullaney, T. Lucke, S. J. Trueman, 2015. “A review of benefits and challenges in growing street trees in paved urban environments,” Landscape and Urban Planning, 134, 157-166.</p><p>[2] A. M. Alani, L. Lantini, 2019. “Recent advances in tree root mapping and assessment using non-destructive testing methods: a focus on ground penetrating radar,” Surveys in Geophysics, 1-42.</p><p>[3] L. Lantini, F. Tosti, Giannakis, I., Egyir, D., A. Benedetto, A. M. Alani, 2019. “A Novel Processing Framework for Tree Root Mapping and Density Estimation using Ground Penetrating Radar,” In 10th International Workshop on Advanced Ground Penetrating Radar, EAGE.</p>

scholarly journals On the Use of Short-Time Fourier Transform for the Analysis of Tree Root Systems using Ground Penetrating Radar

2021 ◽  
Author(s):  
Livia Lantini ◽  
Fabio Tosti ◽  
Luca Bianchini Ciampoli ◽  
Amir M. Alani
Keyword(s):  
Remote Sensing ◽  
Fourier Transform ◽  
Ground Penetrating Radar ◽  
Mass Density ◽  
Root Systems ◽  
Short Time Fourier Transform ◽  
Charitable Trust ◽  
Ground Penetrating ◽  
Short Time ◽  
Root Mapping

<p>Monitoring and protecting natural assets is increasingly important today, as aggressive pathogens are negatively impacting the trees' survival. In this regard, root systems are affected by fungal infections that cause roots’ rot and eventually lead to trees' death. Such disease can spread rapidly to the adjacent trees and affect larger areas. Since these decays generally do not display visible signs, early identification is the key to tree preservation.</p><p>Within this context, non-destructive testing (NDT) methods are becoming popular, being more versatile than destructive methods. Specifically, ground penetrating radar (GPR) is emerging as an accurate geophysical method for tree root mapping. Recent research has focused on implementing automated algorithms for 3D root mapping, improving root detection through advanced GPR signal processing and the estimation of tree roots' mass density [1]. Also, recent studies have proven that GPR is effective in mapping the root system's architecture of street trees [2].</p><p>The present research reports the preliminary results of an experimental study, conducted to investigate the feasibility of a novel tree root assessment methodology based on the analysis of GPR data both in time and frequency domain. To this end, data were processed using a short-time Fourier transform (STFT) approach [3], which allows the evaluation of how the frequency spectrum changes across the signal propagation time window. The suggested processing system may be implemented for expeditious analyses or on trees challenging to access, such as in urban environments, where more comprehensive survey methods are not applicable. The objectives of this study, therefore, are to investigate how different features (i.e., roots, layers) affect the time-frequency analysis of GPR data, and to identify recurring patterns in the results to set a coherent data processing methodology.</p><p>Results' interpretation has shown the viability of the presented approach in recognising the influence of different features on the analysis of GPR data as it changes over time. This also allowed the detection of recurring patterns in the analysed data, proving that this method is worthy of further investigations.</p><p>Acknowledgements<br>The authors would like to express their sincere thanks and gratitude to the following trusts, charities, organisations and individuals for their generosity in supporting this project: Lord Faringdon Charitable Trust, The Schroder Foundation, Cazenove Charitable Trust, Ernest Cook Trust, Sir Henry Keswick, Ian Bond, P. F. Charitable Trust, Prospect Investment Management Limited, The Adrian Swire Charitable Trust, The John Swire 1989 Charitable Trust, The Sackler Trust, The Tanlaw Foundation, and The Wyfold Charitable Trust.</p><p><br>References<br>[1]     Lantini, L., Tosti, F., Giannakis, I., Zou, L., Benedetto, A. and Alani, A. M., 2020. "An Enhanced Data Processing Framework for Mapping Tree Root Systems Using Ground Penetrating Radar," Remote Sensing 12(20), 3417.<br>[2]     Lantini, L., Alani, A., Giannakis, I., Benedetto, A. and Tosti, F., 2020. "Application of ground penetrating radar for mapping tree root system architecture and mass density of street trees," Advances in Transportation Studies (3), 51-62.<br>[3]     Bianchini Ciampoli, L., Calvi, A. and D'Amico, F., 2019. "Railway Ballast Monitoring by GPR: A Test Site Investigation," Remote Sensing 11(20), 238</p>

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