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Nguyen HA, Martre P, Collet C, Draye X, Salon C, Jeudy C, Rincent R, Muller B. Are high-throughput root phenotyping platforms suitable for informing root system architecture models with genotype-specific parameters? An evaluation based on the root model ArchiSimple and a small panel of wheat cultivars. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2510-2526. [PMID: 38520390 DOI: 10.1093/jxb/erae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
Given the difficulties in accessing plant roots in situ, high-throughput root phenotyping (HTRP) platforms under controlled conditions have been developed to meet the growing demand for characterizing root system architecture (RSA) for genetic analyses. However, a proper evaluation of their capacity to provide the same estimates for strictly identical root traits across platforms has never been achieved. In this study, we performed such an evaluation based on six major parameters of the RSA model ArchiSimple, using a diversity panel of 14 bread wheat cultivars in two HTRP platforms that had different growth media and non-destructive imaging systems together with a conventional set-up that had a solid growth medium and destructive sampling. Significant effects of the experimental set-up were found for all the parameters and no significant correlations across the diversity panel among the three set-ups could be detected. Differences in temperature, irradiance, and/or the medium in which the plants were growing might partly explain both the differences in the parameter values across the experiments as well as the genotype × set-up interactions. Furthermore, the values and the rankings across genotypes of only a subset of parameters were conserved between contrasting growth stages. As the parameters chosen for our analysis are root traits that have strong impacts on RSA and are close to parameters used in a majority of RSA models, our results highlight the need to carefully consider both developmental and environmental drivers in root phenomics studies.
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Affiliation(s)
- Hong Anh Nguyen
- LEPSE, Université de Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Pierre Martre
- LEPSE, Université de Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Clothilde Collet
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Xavier Draye
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Christian Jeudy
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Renaud Rincent
- GDEC, Université Clermont-Auvergne, INRAE, Clermont-Ferrand, France
| | - Bertrand Muller
- LEPSE, Université de Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska‐Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon‐Cochard C, Rose L, Ryser P, Scherer‐Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde‐Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021; 232:973-1122. [PMID: 34608637 PMCID: PMC8518129 DOI: 10.1111/nph.17572] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T. Freschet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
| | - Loïc Pagès
- UR 1115 PSHCentre PACA, site AgroparcINRAE84914Avignon cedex 9France
| | - Colleen M. Iversen
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Louise H. Comas
- USDA‐ARS Water Management Research Unit2150 Centre Avenue, Bldg D, Suite 320Fort CollinsCO80526USA
| | - Boris Rewald
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesVienna1190Austria
| | - Catherine Roumet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Jitka Klimešová
- Department of Functional EcologyInstitute of Botany CASDukelska 13537901TrebonCzech Republic
| | - Marcin Zadworny
- Institute of DendrologyPolish Academy of SciencesParkowa 562‐035KórnikPoland
| | - Hendrik Poorter
- Plant Sciences (IBG‐2)Forschungszentrum Jülich GmbHD‐52425JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | | | - Thomas S. Adams
- Department of Plant SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Agnieszka Bagniewska‐Zadworna
- Department of General BotanyInstitute of Experimental BiologyFaculty of BiologyAdam Mickiewicz UniversityUniwersytetu Poznańskiego 661-614PoznańPoland
| | - A. Glyn Bengough
- The James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundee,DD1 4HNUK
| | | | - Ivano Brunner
- Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
| | - Johannes H. C. Cornelissen
- Department of Ecological ScienceFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 1085Amsterdam1081 HVthe Netherlands
| | - Eric Garnier
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Arthur Gessler
- Forest DynamicsSwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH Zurich8092ZurichSwitzerland
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt PaulMN55108USA
| | - Ina C. Meier
- Functional Forest EcologyUniversity of HamburgHaidkrugsweg 122885BarsbütelGermany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupDepartment of Environmental SciencesWageningen University and ResearchPO Box 476700 AAWageningenthe Netherlands
| | | | - Laura Rose
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
- Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Peter Ryser
- Laurentian University935 Ramsey Lake RoadSudburyONP3E 2C6Canada
| | | | - Nadejda A. Soudzilovskaia
- Environmental Biology DepartmentInstitute of Environmental SciencesCMLLeiden UniversityLeiden2300 RAthe Netherlands
| | - Alexia Stokes
- INRAEAMAPCIRAD, IRDCNRSUniversity of MontpellierMontpellier34000France
| | - Tao Sun
- Institute of Applied EcologyChinese Academy of SciencesShenyang110016China
| | - Oscar J. Valverde‐Barrantes
- International Center for Tropical BotanyDepartment of Biological SciencesFlorida International UniversityMiamiFL33199USA
| | - Monique Weemstra
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Alexandra Weigelt
- Systematic Botany and Functional BiodiversityInstitute of BiologyLeipzig UniversityJohannisallee 21-23Leipzig04103Germany
| | - Nina Wurzburger
- Odum School of EcologyUniversity of Georgia140 E. Green StreetAthensGA30602USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sarah A. Batterman
- School of Geography and Priestley International Centre for ClimateUniversity of LeedsLeedsLS2 9JTUK
- Cary Institute of Ecosystem StudiesMillbrookNY12545USA
| | - Moemy Gomes de Moraes
- Department of BotanyInstitute of Biological SciencesFederal University of Goiás1974690-900Goiânia, GoiásBrazil
| | - Štěpán Janeček
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawley (Perth)WA 6009Australia
| | - Hans Lambers
- School of Biological SciencesThe University of Western AustraliaCrawley (Perth)WAAustralia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Nishanth Tharayil
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - M. Luke McCormack
- Center for Tree ScienceMorton Arboretum, 4100 Illinois Rt. 53LisleIL60532USA
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Beroueg A, Lecompte F, Mollier A, Pagès L. Genetic Variation in Root Architectural Traits in Lactuca and Their Roles in Increasing Phosphorus-Use-Efficiency in Response to Low Phosphorus Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:658321. [PMID: 34012460 PMCID: PMC8128164 DOI: 10.3389/fpls.2021.658321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/29/2021] [Indexed: 06/03/2023]
Abstract
Low phosphorus (P) bioavailability in the soil and concerns over global P reserves have emphasized the need to cultivate plants that acquire and use P efficiently. Root architecture adaptation to low P can be variable depending on species or even genotypes. To assess the genetic variability of root architectural traits and their responses to low P in the Lactuca genus, we examined fourteen genotypes including wild species, ancient and commercial lettuce cultivars at low (LP, 0.1 mmol. L-1) and high P (HP, 1 mmol. L-1). Plants were grown in cylindrical pots adapted for the excavation and observation of root systems, with an inert substrate. We identified substantial genetic variation in all the investigated root traits, as well as an effect of P availability on these traits, except on the diameter of thinner roots. At low P, the main responses were a decrease in taproot diameter, an increase in taproot dominance over its laterals and an increase in the inter-branch distance. Although the genotype x P treatment effect was limited to root depth, we identified a tradeoff between the capacity to maintain a thick taproot at low P and the dominance of the taproot over its laterals. Regardless of the P level, the phosphorus-use-efficiency (PUE) varied among lettuce genotypes and was significantly correlated with total root biomass regardless of the P level. As taproot depth and maximum apical diameter were the principal determinants of total root biomass, the relative increase in PUE at low P was observed in genotypes that showed the thickest apical diameters and/or those whose maximal apical diameter was not severely decreased at low P availability. This pre-eminence of the taproot in the adaptation of Lactuca genotypes to low P contrasts with other species which rely more on lateral roots to adapt to P stress.
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Affiliation(s)
| | | | - Alain Mollier
- ISPA Unit, Bordeaux Sciences Agro, INRAE, Villenave d’Ornon, France
| | - Loïc Pagès
- PSH Unit, INRAE, F-84914, Avignon, France
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4
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Individual-based 3D modelling of root systems in heterogeneous plant canopies at the multiannual scale. Case study with a weed dynamics model. Ecol Modell 2021. [DOI: 10.1016/j.ecolmodel.2020.109376] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Guimarães PHR, de Lima IP, de Castro AP, Lanna AC, Guimarães Santos Melo P, de Raïssac M. Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought? RICE (NEW YORK, N.Y.) 2020; 13:67. [PMID: 32930888 PMCID: PMC7492358 DOI: 10.1186/s12284-020-00404-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 06/23/2020] [Indexed: 05/13/2023]
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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Affiliation(s)
| | - Isabela Pereira de Lima
- Universidade Federal de Lavras, Departamento de Agricultura, Campus Universitário, Lavras, MG, 37200-000, Brazil
| | | | - Anna Cristina Lanna
- Embrapa Arroz e Feijão, Rodovia GO-462, km 12, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | | | - Marcel de Raïssac
- Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, AGAP, Montpellier, France.
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6
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Volaire F, Morvan-Bertrand A, Prud’homme MP, Benot ML, Augusti A, Zwicke M, Roy J, Landais D, Picon-Cochard C. The resilience of perennial grasses under two climate scenarios is correlated with carbohydrate metabolism in meristems. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:370-385. [PMID: 31557303 PMCID: PMC6913708 DOI: 10.1093/jxb/erz424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/10/2019] [Indexed: 05/30/2023]
Abstract
Extreme climatic events (ECEs) such as droughts and heat waves affect ecosystem functioning and species turnover. This study investigated the effect of elevated CO2 on species' resilience to ECEs. Monoliths of intact soil and their plant communities from an upland grassland were exposed to 2050 climate scenarios with or without an ECE under ambient (390 ppm) or elevated (520 ppm) CO2. Ecophysiological traits of two perennial grasses (Dactylis glomerata and Holcus lanatus) were measured before, during, and after ECE. At similar soil water content, leaf elongation was greater under elevated CO2 for both species. The resilience of D. glomerata increased under enhanced CO2 (+60%) whereas H. lanatus mostly died during ECE. D. glomerata accumulated 30% more fructans, which were more highly polymerized, and 4-fold less sucrose than H. lanatus. The fructan concentration in leaf meristems was significantly increased under elevated CO2. Their relative abundance changed during the ECE, resulting in a more polymerized assemblage in H. lanatus and a more depolymerized assemblage in D. glomerata. The ratio of low degree of polymerization fructans to sucrose in leaf meristems was the best predictor of resilience across species. This study underlines the role of carbohydrate metabolism and the species-dependent effect of elevated CO2 on the resilience of grasses to ECE.
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Affiliation(s)
| | | | | | - Marie-Lise Benot
- UCA, INRA, VetAgro Sup, UMR 874, Clermont-Ferrand, France
- INRA and Université de Bordeaux, UMR 1202 BIOGECO33610, Cestas, France
| | - Angela Augusti
- UCA, INRA, VetAgro Sup, UMR 874, Clermont-Ferrand, France
- CNR-Institute of Research on Terrestrial Ecosystems, Porano (TR), Italy
| | - Marine Zwicke
- UCA, INRA, VetAgro Sup, UMR 874, Clermont-Ferrand, France
| | - Jacques Roy
- CNRS, UPS 3248, Ecotron Européen de Montpellier, Montferrier-sur-Lez, France
| | - Damien Landais
- CNRS, UPS 3248, Ecotron Européen de Montpellier, Montferrier-sur-Lez, France
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7
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Pagès L. Analysis and Modeling of the Variations of Root Branching Density Within Individual Plants and Among Species. FRONTIERS IN PLANT SCIENCE 2019; 10:1020. [PMID: 31440270 PMCID: PMC6694179 DOI: 10.3389/fpls.2019.01020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Branching density (or the reciprocal: inter-branch distance) is an important trait which contributes to defining the number of roots in individual plants. The environmental and local variations in inter-branch distance have often been stressed, and simulations models have been put forward to take them into account within the dynamics of root system architecture (RSA). However, little is known about the interspecific and intra-plant variations of inter-branch distance. In this paper, we present an analysis which draws on 40 samples of plants belonging to 36 species collected in homogeneous soils, to address how the variations in inter-branch distance are structured within individual plants, and how this structure varies from one species to another. Using measurements of inter-branch distance on various roots of the same species and our knowledge of the branching process, we defined a simple and generic model dedicated to the simulation of the observed variations. This model distinguishes between two sub-processes: i) the longitudinal location of potential branching sites and ii) the effective emergence of lateral roots at these sites. Thus, it represents the variations in distance between the potential sites (with two parameters), and the probability of emergence of a lateral root at each site (one parameter). We show the ability of this model to account for the main variations in inter-branch distances with a limited number of parameters, and we estimated them for the different species. These parameters can be considered as promising traits to characterize-in a comprehensive and simple way-the genetic and environmental variations in the whole branching process at plant level. Based on the results, we make recommendations for carrying out comparable measurements of the branching density in developed plants. Moreover, we suggest the integration of this new model as a module in future RSA simulators, to improve their capacity to account for this important and highly variable characteristic of plant species.
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Affiliation(s)
- Loïc Pagès
- INRA, Centre PACA, UR 1115 PSH, Avignon, France
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8
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Pagès L, Kervella J. Seeking stable traits to characterize the root system architecture. Study on 60 species located at two sites in natura. ANNALS OF BOTANY 2018; 122:107-115. [PMID: 29697745 PMCID: PMC6025210 DOI: 10.1093/aob/mcy061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/06/2018] [Indexed: 05/17/2023]
Abstract
Background and Aims In several disciplines, identifying relevant root traits to characterize the root system architecture of species or genotypes is a crucial step. To address this question, we analysed the inter-specific variations of root architectural traits in two contrasting environments. Methods We sampled 60 species in natura, at two sites, each presenting homogeneous soil conditions. We estimated for each species and site a set of five traits used for the modelling of the root system architecture: extreme tip diameters (Dmin and Dmax), relative diameter range (Drange), mean inter-branch distance (IBD) and dominance slope between the diameters of parent and lateral roots (DlDm). Key Results The five traits presented a highly significant species effect, explaining between 77 and 98 % of the total variation. Dmin, Dmax and Drange were particularly determined by the species, while DlDm and IBD exhibited a higher percentage of environmental variations. These traits make it possible to confirm two main axes of variation: 'fineness-density' (defined by Dmin and IBD) and 'dominance-heterorhizy' (DlDm and Drange), that together accounted for 84 % of the variations observed. Conclusions We confirmed the interest of these traits in the characterization of the root system architecture in ecology and genetics, and suggest using them to enrich the 'root economic spectrum'.
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Affiliation(s)
- Loïc Pagès
- INRA, Centre PACA, UR 1115 PSH, Domaine Saint-Paul, Site Agroparc, Avignon cedex 9, France
| | - Jocelyne Kervella
- INRA, Centre PACA, UR 1052 GAFL, Domaine Saint-Maurice, Montfavet cedex, France
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9
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Keyes SD, Zygalakis KC, Roose T. An Explicit Structural Model of Root Hair and Soil Interactions Parameterised by Synchrotron X-ray Computed Tomography. Bull Math Biol 2017; 79:2785-2813. [PMID: 29030805 PMCID: PMC5709508 DOI: 10.1007/s11538-017-0350-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/19/2017] [Indexed: 11/29/2022]
Abstract
The rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger-scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale. By combining synchrotron X-ray computed tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root hair detection via structural root hair growth modelling. The growth model is explicitly parameterised with SRXCT data and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models. The study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealised and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results in field-derived soil suggest that hair access to poorly mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.
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Affiliation(s)
- Samuel David Keyes
- Bioengineering Sciences Research Group, Faculty of Engineering and Environment, University of Southampton, Southampton, SO17 1BJ, UK.
| | | | - Tiina Roose
- Bioengineering Sciences Research Group, Faculty of Engineering and Environment, University of Southampton, Southampton, SO17 1BJ, UK
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10
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Norby RJ, Iversen CM. Introduction to a Virtual Issue on root traits. THE NEW PHYTOLOGIST 2017; 215:5-8. [PMID: 28560788 DOI: 10.1111/nph.14522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Richard J Norby
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
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11
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Delory BM, Weidlich EWA, Meder L, Lütje A, Duijnen R, Weidlich R, Temperton VM. Accuracy and bias of methods used for root length measurements in functional root research. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12771] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Benjamin M. Delory
- Ecosystem Functioning and Services Institute of Ecology Leuphana University Scharnhorststrasse 1 21335 Lüneburg Germany
| | - Emanuela W. A. Weidlich
- Ecosystem Functioning and Services Institute of Ecology Leuphana University Scharnhorststrasse 1 21335 Lüneburg Germany
| | - Leonie Meder
- Ecosystem Functioning and Services Institute of Ecology Leuphana University Scharnhorststrasse 1 21335 Lüneburg Germany
| | - Anna Lütje
- Ecosystem Functioning and Services Institute of Ecology Leuphana University Scharnhorststrasse 1 21335 Lüneburg Germany
| | - Richard Duijnen
- Ecosystem Functioning and Services Institute of Ecology Leuphana University Scharnhorststrasse 1 21335 Lüneburg Germany
| | - Rafael Weidlich
- Ecosystem Functioning and Services Institute of Ecology Leuphana University Scharnhorststrasse 1 21335 Lüneburg Germany
| | - Vicky M. Temperton
- Ecosystem Functioning and Services Institute of Ecology Leuphana University Scharnhorststrasse 1 21335 Lüneburg Germany
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12
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Pagès L. Branching patterns of root systems: comparison of monocotyledonous and dicotyledonous species. ANNALS OF BOTANY 2016; 118:1337-1346. [PMID: 27634575 PMCID: PMC5155602 DOI: 10.1093/aob/mcw185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/22/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Acropetal root branching is a major process which increases the number of growing tips and distributes their growth potential within the whole root system. METHODS Using a method presented in a recent paper, the defined branching traits were estimated in 140 different species, and the branching patterns of monocots (45 species) and dicots (95 species) were compared. KEY RESULTS It was checked that the method also applied to monocots (not considered in the previous paper), and that all traits could be estimated in each species. Variations of most traits were even larger for monocots than for dicots. Systematic differences appeared between these two groups: monocots tended to have a larger range in apical diameters (stronger heterorhizy), with both finer and thicker roots; the diameters of their lateral roots were also more variable; their roots exerted a stronger dominance over lateral branches. Altogether, species exhibited two main dependencies among their traits that were illustrated using two axes: (1) the 'fineness-density' axis separated the species which develop very fine roots and branch densely, from species without fine roots which space out their branches; and (2) the 'dominance-heterorhizy' axis separated the species according to the range in their apical diameter which was positively correlated to the level of dominance of mother roots over their branches. Both axes and correlations were remarkably similar for monocots and dicots. CONCLUSIONS Beyond the overall typology, this study went on to validate the phenotyping method in Natura, and showed its potential to characterize the differences in groups of species.
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Affiliation(s)
- Loïc Pagès
- INRA, Centre PACA, UR 1115 PSH, Domaine Saint-Paul, Site Agroparc, 84914 Avignon cedex 9, France
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13
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Koevoets IT, Venema JH, Elzenga JTM, Testerink C. Roots Withstanding their Environment: Exploiting Root System Architecture Responses to Abiotic Stress to Improve Crop Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:1335. [PMID: 27630659 PMCID: PMC5005332 DOI: 10.3389/fpls.2016.01335] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/18/2016] [Indexed: 05/18/2023]
Abstract
To face future challenges in crop production dictated by global climate changes, breeders and plant researchers collaborate to develop productive crops that are able to withstand a wide range of biotic and abiotic stresses. However, crop selection is often focused on shoot performance alone, as observation of root properties is more complex and asks for artificial and extensive phenotyping platforms. In addition, most root research focuses on development, while a direct link to the functionality of plasticity in root development for tolerance is often lacking. In this paper we review the currently known root system architecture (RSA) responses in Arabidopsis and a number of crop species to a range of abiotic stresses, including nutrient limitation, drought, salinity, flooding, and extreme temperatures. For each of these stresses, the key molecular and cellular mechanisms underlying the RSA response are highlighted. To explore the relevance for crop selection, we especially review and discuss studies linking root architectural responses to stress tolerance. This will provide a first step toward understanding the relevance of adaptive root development for a plant's response to its environment. We suggest that functional evidence on the role of root plasticity will support breeders in their efforts to include root properties in their current selection pipeline for abiotic stress tolerance, aimed to improve the robustness of crops.
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Affiliation(s)
- Iko T. Koevoets
- Swammerdam Institute for Life Sciences, Plant Cell Biology, University of AmsterdamAmsterdam, Netherlands
| | - Jan Henk Venema
- Genomics Research in Ecology and Evolution in Nature – Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
| | - J. Theo. M. Elzenga
- Genomics Research in Ecology and Evolution in Nature – Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
| | - Christa Testerink
- Swammerdam Institute for Life Sciences, Plant Cell Biology, University of AmsterdamAmsterdam, Netherlands
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14
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Evers JB, Bastiaans L. Quantifying the effect of crop spatial arrangement on weed suppression using functional-structural plant modelling. JOURNAL OF PLANT RESEARCH 2016; 129:339-51. [PMID: 27000875 PMCID: PMC4850179 DOI: 10.1007/s10265-016-0807-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/18/2016] [Indexed: 05/06/2023]
Abstract
Suppression of weed growth in a crop canopy can be enhanced by improving crop competitiveness. One way to achieve this is by modifying the crop planting pattern. In this study, we addressed the question to what extent a uniform planting pattern increases the ability of a crop to compete with weed plants for light compared to a random and a row planting pattern, and how this ability relates to crop and weed plant density as well as the relative time of emergence of the weed. To this end, we adopted the functional-structural plant modelling approach which allowed us to explicitly include the 3D spatial configuration of the crop-weed canopy and to simulate intra- and interspecific competition between individual plants for light. Based on results of simulated leaf area development, canopy photosynthesis and biomass growth of the crop, we conclude that differences between planting pattern were small, particularly if compared to the effects of relative time of emergence of the weed, weed density and crop density. Nevertheless, analysis of simulated weed biomass demonstrated that a uniform planting of the crop improved the weed-suppression ability of the crop canopy. Differences in weed suppressiveness between planting patterns were largest with weed emergence before crop emergence, when the suppressive effect of the crop was only marginal. With simultaneous emergence a uniform planting pattern was 8 and 15 % more competitive than a row and a random planting pattern, respectively. When weed emergence occurred after crop emergence, differences between crop planting patterns further decreased as crop canopy closure was reached early on regardless of planting pattern. We furthermore conclude that our modelling approach provides promising avenues to further explore crop-weed interactions and aid in the design of crop management strategies that aim at improving crop competitiveness with weeds.
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Affiliation(s)
- Jochem B Evers
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
| | - Lammert Bastiaans
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
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15
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Roumet C, Birouste M, Picon-Cochard C, Ghestem M, Osman N, Vrignon-Brenas S, Cao KF, Stokes A. Root structure-function relationships in 74 species: evidence of a root economics spectrum related to carbon economy. THE NEW PHYTOLOGIST 2016; 210:815-26. [PMID: 26765311 DOI: 10.1111/nph.13828] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/25/2015] [Indexed: 05/03/2023]
Abstract
Although fine roots are important components of the global carbon cycle, there is limited understanding of root structure-function relationships among species. We determined whether root respiration rate and decomposability, two key processes driving carbon cycling but always studied separately, varied with root morphological and chemical traits, in a coordinated way that would demonstrate the existence of a root economics spectrum (RES). Twelve traits were measured on fine roots (diameter ≤ 2 mm) of 74 species (31 graminoids and 43 herbaceous and dwarf shrub eudicots) collected in three biomes. The findings of this study support the existence of a RES representing an axis of trait variation in which root respiration was positively correlated to nitrogen concentration and specific root length and negatively correlated to the root dry matter content, lignin : nitrogen ratio and the remaining mass after decomposition. This pattern of traits was highly consistent within graminoids but less consistent within eudicots, as a result of an uncoupling between decomposability and morphology, and of heterogeneity of individual roots of eudicots within the fine-root pool. The positive relationship found between root respiration and decomposability is essential for a better understanding of vegetation-soil feedbacks and for improving terrestrial biosphere models predicting the consequences of plant community changes for carbon cycling.
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Affiliation(s)
- Catherine Roumet
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Marine Birouste
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Catherine Picon-Cochard
- INRA, UR 874, UREP, Grassland Ecosystem Research, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Murielle Ghestem
- INRA, UMR AMAP, Boulevard de la Lironde, 34398, Montpellier Cedex 5, France
| | - Normaniza Osman
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sylvain Vrignon-Brenas
- INRA, UR 874, UREP, Grassland Ecosystem Research, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Kun-Fang Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, and College of Forestry, Guangxi University, Nanning, Guangxi, 530004, China
| | - Alexia Stokes
- INRA, UMR AMAP, Boulevard de la Lironde, 34398, Montpellier Cedex 5, France
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16
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Nippert JB, Holdo RM. Challenging the maximum rooting depth paradigm in grasslands and savannas. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12390] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jesse B. Nippert
- Division of Biology Kansas State University 106 Ackert Hall Manhattan KS 66506 USA
| | - Ricardo M. Holdo
- Division of Biological Sciences University of Missouri 217 Tucker HallColumbia MO 65211 USA
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