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Root system of a rapeseed at high soil‑nitrogen, b rapeseed at low soil‑nitrogen, c Vulpia at high soil‑nitrogen and d Vulpia at high low‑ nitrogen. Images were taken at 29 (a, b) and 51 days (c, d) after sowing for rapeseed and Vulpia respectively
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Background
In order to maintain high yields while saving water and preserving non-renewable resources and thus limiting the use of chemical fertilizer, it is crucial to select plants with more efficient root systems. This could be achieved through an optimization of both root architecture and root uptake ability and/or through the improvement of po...
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Citations
... Alternative to the field-based methods are the lab and greenhouse-based methods. These include cheaper setups like the filter paper method (Rattanapichai & Klem, 2016), cloth pouch method , clear pot method (Richard et al., 2015), agar plates and hydroponics to expensive methods involving X-ray computed tomography (Mairhofer et al., 2015), magnetic resonance imaging (van Dusschoten et al., 2016), positron emission tomography (Garbout et al., 2012), electrical resistance tomography (Srayeddin & Doussan, 2009) and rhizotrons (Jeudy et al., 2016). These methods eliminate the variability arising due to the effect of climate and soil heterogeneity. ...
A well-developed root system is essential for efficient nutrient and water uptake. We phenotyped a set of 172 Triticum durum–Aegilops speltoides backcross introgression lines (BILs) for various root architecture traits during 2019–2020 and 2020–2021 cropping seasons. The roots were sampled at the maximum tillering stage, and data on various root architecture traits were recorded. The quantitative trait loci (QTL) mapping was carried out using 5672 polymorphic SNPs obtained from genotyping-by-sequencing. A total of 21 QTLs were detected for various root architecture traits on chromosomes 1A, 2A, 2B, 3B, 5A and 6B. Stable QTLs were detected for total root length, number of root tips and root dry weight over the two seasons. Candidate genes were identified by scanning the physical interval corresponding to the linkage disequilibrium (LD) decay flanking the SNPs linked to the stable QTLs. In silico expression studies of postulated candidate genes revealed root-specific upregulation of some of the genes. These QTLs can be used in breeding programmes after the development and validation of suitable marker assays.
... We took advantage of the Rhizotube® technology and imaging facility (Jeudy et al. 2016) to analyse dynamic shoot and root allocation over 50 days and to derive some key parameters explaining root growth and root branching ability during plant establishment. ...
... The major advantage of RT is total visibility of the root system and the facilitated detection of roots via image analysis algorithms (blue coloured background). As they offer a root prospecting area of approximately 50 × 50 cm for a reduced footprint (20 × 20 cm base), they enable a fairly long monitoring of root growth (more than 30 days in most crop species) without observing the appearance of environmental constraints, and are they easily included in high-throughput phenotyping platforms (Jeudy et al. 2016). ...
... Non-destructive images of each plant (both shoot and root parts) were acquired three times a week using the RhizoCab® high-throughput phenotyping cabin (Jeudy et al. 2016;Fig. 1B-C) at the 4PMI platform. ...
Background and aims
Root phenotyping and breeding for desirable root traits have been limited in small seed forage species. The objectives of this study were to analyse the degree of within-species variation regarding initial root allocation in two forage legumes and to assess the covariation between root allocation patterns and root and shoot morphogenetic traits involved in carbon source-sink relationships.
Methods
Experiments were carried out at a phenotyping platform to grow alfalfa and red clover plants of five contrasting cultivars under nutrient conditions non-limiting for growth. An automatic image analysis pipeline was used to characterise dynamic root-shoot allocation over 50 days during plant establishment. Measurements were also performed to characterise plant traits related to potential shoot and root development.
Results
In both species, genetic variability was found regarding the allocation of biomass to roots and root morphological traits controlling root elongation and branching. The degree of variability was high for most root traits, within a range similar to that found for the shoot traits usually targeted by breeders. A clear dependency of initial biomass allocation to roots on the shoot traits controlling plant leaf area, and favouring carbon acquisition, was identified. Analysis of covariation between root traits revealed they were largely independent, suggesting considerable potential for their recombination to achieve improved root phenotypes capturing more soil resources at a given biomass.
Conclusion
This study demonstrates the feasibility of direct breeding for root traits in legumes and could help to identify trait combinations that promote their rapid establishment and competitive ability.
... This challenge has underscored the emergence of HTP technologies. In 2016, Jeudy et al. [70] proposed the use of RhizoTube, a root tube for plant cultivation. Seeds are placed between an external transparent tube and a physiological membrane, allowing for root imaging while cultivating plants. ...
In order to rapidly breed high-quality varieties, an increasing number of plant researchers have identified the functions of a large number of genes, but there is a serious lack of research on plants’ phenotypic traits. This severely hampers the breeding process and exacerbates the dual challenges of scarce resources and resource development and utilization. Currently, research on crop phenotyping has gradually transitioned from traditional methods to HTP technologies, highlighting the high regard scientists have for these technologies. It is well known that different crops’ phenotypic traits exhibit certain differences. Therefore, in rapidly acquiring phenotypic data and efficiently extracting key information from massive datasets is precisely where HTP technologies play a crucial role in agricultural development. The core content of this article, starting from the perspective of crop phenomics, summarizes the current research status of HTP technology, both domestically and internationally; the application of HTP technology in above-ground and underground parts of crops; and its integration with precision agriculture implementation and multi-omics research. Finally, the bottleneck and countermeasures of HTP technology in the current agricultural context are proposed in order to provide a new method for phenotype research. HTP technologies dynamically monitor plant growth conditions with multi-scale, comprehensive, and automated assessments. This enables a more effective exploration of the intrinsic “genotype-phenotype-environment” relationships, unveiling the mechanisms behind specific biological traits. In doing so, these technologies support the improvement and evolution of superior varieties.
... In parallel, a series of artificial, high-throughput root phenotyping (HTRP) platforms have been developed where the root system is accessible non-destructively. These platforms are based on hydroponics (Kuijken et al., 2015b;Guo et al., 2021), transparent cylinders (Jeudy et al., 2016), filter paper (Le Marié et al., 2014;Falk et al., 2020), or aeroponics (Zhu et al., 2011). Such set-ups are usually accompanied by analytical pipelines that are able to transform images into data (Kalogiros et al., 2016;Passot et al., 2018;Falk et al., 2020). ...
... The genotypes used in this study were selected to maximize the phenotypic plasticity for grain yield and its components in response to water and nitrogen deficits in the field. The 14 genotypes were grown in one experiment at UMR LEPSE, Montpellier, France, in three experiments in the Plant Phenotyping Platform for Plant and Microorganism Interactions (4PMI;Jeudy et al., 2016) at UMR Agroecology, Dijon, France, and in two experiments in the RootPhAir aeroponic platform at the Université catholique de Louvain, Louvain-La-Neuve, Belgium (https://uclouvain.be/fr/node/49328). ...
... 4PMI is an automated HTRP platform based on conveyors that transport plants (up to 1560, average plant density of 21 m -2 ) either towards watering stations or to imaging units (Fig. 1E). The set-up and the functioning of 4PMI is described in detail by Jeudy et al. (2016). In brief, plants are grown in RhizoTubes ® , which are cylindrical rhizotrons 0.5 m height with a transparent polymethylmethacrylate outer tube of 17 cm internal diameter. ...
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.
... Traditional nondestructive techniques for studying root growth, such as rhizotrons, typically produce 2D images (Atkinson et al. 2019). In addition to rhizotrons, one of the main tools to assess root phenotypes is represented by Rhi-zoTubes (Jeudy et al. 2016). These tubes are innovative cylindrical rhizotrons designed for dynamic root phenotyping. ...
... These tubes are innovative cylindrical rhizotrons designed for dynamic root phenotyping. They consist of concentric tubes that create separate zones for root growth, substrate, and nutrient solution, with a permeable membrane allowing the exchange of nutrients, water, as well as soil microbes, while preventing root passage (Jeudy et al. 2016). This design confines the root system in two dimensions, facilitating high-quality imaging using a dedicated camera (namely 'RhizoCab'). ...
... This design confines the root system in two dimensions, facilitating high-quality imaging using a dedicated camera (namely 'RhizoCab'). RhizoTubes have proven to be useful also for studying interactions between roots and microbes (Jeudy et al. 2016). The highresolution imaging capabilities of RhizoTubes might allow the assessment of root nodules (symbiosis with rhizobia) as well as the visualization of mycelium in the case of fungi interacting with roots (Jeudy et al. 2016). ...
Plants have evolved various belowground traits to adapt to the changing environments, and root-associated soil microbes play a crucial role in the response, adaptation, and resilience to adverse environmental conditions. This comprehensive review explores the diverse interactions between plants and soil microbes, focusing on the role of root-associated microbiota, with a particular emphasis on arbuscular mycorrhizal fungi, in plant responses to diverse environmental conditions. How plant genotype, root traits, and growth environments influence these interactions, and consequently plant resilience and productivity, are discussed. Recent advances in root phenotyping, including traditional and machine learning-based methods are also presented as an innovative tool to study and characterize root-microbe interactions. Overall, these studies highlight the importance of considering the hidden side of the interactions between roots and microbes to improve plant nutrition and protection in the context of sustainable agriculture in the face of climate change.
... The smallest objects detected using these methods were tree roots with diameters of 5 mm for acoustic imaging [21] and 2.5 mm for GPR [25]. The more direct methods of exposing roots to the camera, such as rhizotrons [28,29], rhizoboxes [30,31], and Rhizotubes [32] have been used to observe fine roots; however, these methods are limited in the field of view and may affect the natural environment of the roots and interfere with the processes being investigated. ...
Crop genetic engineering for better root systems can offer practical solutions for food security and carbon sequestration; however, soil layers prevent the direct visualization of plant roots, thus posing a challenge to effective phenotyping. Here, we demonstrate an original device with a distributed fiber-optic sensor for fully automated, real-time monitoring of underground root development. We show that spatially encoding an optical fiber with a flexible and durable polymer film in a spiral pattern can significantly enhance sensor detection. After signal processing, the resulting device can detect the penetration of a submillimeter-diameter object in the soil, indicating more than a magnitude higher spatiotemporal resolution than previously reported with underground monitoring techniques. Additionally, we also developed computational models to visualize the roots of tuber crops and monocotyledons and then applied them to radish and rice to compare the results with those of X-ray computed tomography. The device’s groundbreaking sensitivity and spatiotemporal resolution enable seamless and laborless phenotyping of root systems that are otherwise invisible underground.
Supplementary Information
The online version contains supplementary material available at 10.1186/s13007-024-01160-z.
... Across the globe, attention to plant root systems has gained momentum with minirhizotrons and 3D root phenotyping platform development which facilitates noninvasive assessments (Fahlgren et al. 2015;Kuijken et al. 2015;Jeudy et al. 2016). Imaging coupled with root system analyzers (e.g., Ez-Rhizo and WinRHIZO™, smart rot and X-ray computed tomography) has increasingly been used (Martins et al. 2020). ...
Arbuscular mycorrhizal fungi (AMF) increase in diversity and abundance in agricultural systems that emphasize soil health practices, including regenerative agriculture and intercropping. Regenerative agriculture in principle includes any practice that increases biodiversity and living roots and integrates livestock while reducing tillage, bare soil, and agrichemical inputs. Intercropping increases biodiversity in an annual system and reduces disease prevalence and weeds while improving soil conditions and yielding more than the equivalent monocrop. These principles and practices simultaneously support AMF proliferation in soils and in turn AMF provide multiple benefits to crops. AMF colonize roots, trading photosynthates for nutrients acquired beyond the reach of the plant root system. While colonizing roots, they trigger innate plant immunity and confer resistance to some insect, fungal, and bacterial pests. Colonized plants hold more water and thus are more resistant to drought. In soils with ample AMF propagules, multiple plants are likely to become connected to their neighbors by a common mycorrhizal network (CMN). Plants connected by a CMN are likely to share beneficial microbes, resistance to disease, and resources. A better understanding of crop root traits and AMF is important to building a wholistic picture of ecological interactions that can be leveraged to maintain agricultural production in intercropped, regenerative, and conventional systems.
... High-throughput time lapse imaging produces data sets that are comparable across organismal types, allowing crosssystem comparisons and the development of generic behavioral metrics. A wide range of technology platforms have been designed for the study of animal movement; however, there exist only a few high throughput imaging devices for plants [13][14][15][16][17]. Some time-lapse studies of plants have been conducted at the field scale covering acres of growing crops as well as in controlled experimental laboratory settings. ...
... Utilizing transparent gel substrates to enable optical access has helped address this challenge; however, the long time scale of root growth has typically restricted throughput. A few high throughput time-lapse imaging systems have been developed to image roots, including the RhizoTube, which allows simultaneous imaging of shoot and root growth [16], the RootArray, which allows imaging of 16 roots with confocal microscopy [21], and robotic gantry systems developed to image multiple petri dishes of growing Arabidopsis seedlings [15]. These imaging systems have enabled greater understanding of plant root growth but are, in general, system specific, and are limited in their generalizability to multiple plant types and experimental conditions. ...
... Other systems designed to systematically image plants are limited by the type of container specified as well as expensive equipment and parts [13][14][15][16][17]. GROOT can be customized based on experimental needs (see Fig 2) and plant types, including the ability to place obstacles such as lattices and angled plates, changing lighting settings and other modifications to container size and materials [23]. ...
The study of plant root growth in real time has been difficult to achieve in an automated, high-throughput, and systematic fashion. Dynamic imaging of plant roots is important in order to discover novel root growth behaviors and to deepen our understanding of how roots interact with their environments. We designed and implemented the Generating Rhizodynamic Observations Over Time (GROOT) robot, an automated, high-throughput imaging system that enables time-lapse imaging of 90 containers of plants and their roots growing in a clear gel medium over the duration of weeks to months. The system uses low-cost, widely available materials. As a proof of concept, we employed GROOT to collect images of root growth of Oryza sativa , Hudsonia montana , and multiple species of orchids including Platanthera integrilabia over six months. Beyond imaging plant roots, our system is highly customizable and can be used to collect time- lapse image data of different container sizes and configurations regardless of what is being imaged, making it applicable to many fields that require longitudinal time-lapse recording.
... On peut, par exemple, citer le développement de moyens d'imagerie spectrale dédiés au phénotypage de système racinaire en Rizhotube® à l'INRAe de Dijon [3]. Cet équipement permet de mieux comprendre les mécanismes de colonisation racinaire et de captation des éléments nutritifs dans les systèmes racinaires. ...
L’imagerie spectrale est un concept d’acquisition optique combinant l’imagerie numérique et la spectroscopie. En constante évolution, cette technique peut être basée sur différentes solutions instrumentales et apporte des solutions à de multiples problématiques, notamment en sciences végétales ou en agriculture de précision.
... For example, 3D imaging methods with X-ray computed tomography and magnetic resonance imaging allow visualization of roots in soil (Mooney et al. 2012;Rascher et al. 2011;Teramoto et al. 2020;van Dusschoten et al. 2016). On the other hand, to observe roots growing adjacent to the culture vessel surface, plant cultivation in soil-filled transparent boxes or tubes is widely used (Bengough et al. 2016;Huck and Taylor 1982;Jeudy et al. 2016;Neufeld et al. 1989;Zhao et al. 2022). These nondestructive methods primarily focus on measuring root size and architecture. ...
Most plants interact with various soil microorganisms as they grow through the soil. Root nodule symbiosis by legumes and rhizobia is a well-known phenomenon of plant-microbe interactions in the soil. Although microscopic observations are useful for understanding the infection processes of rhizobia, nondestructive observation methods have not been established for monitoring interactions between rhizobia and soil-grown roots. In this study, we constructed Bradyrhizobium diazoefficiens strains that constitutively express different fluorescent proteins, which allows identification of tagged rhizobia by the type of fluorophores. In addition, we constructed a plant cultivation device, Rhizosphere Frame (RhizoFrame), which is a soil-filled container made of transparent acrylic plates that allows observation of roots growing along the acrylic plates. Combining fluorescent rhizobia with RhizoFrame, we established a live imaging system, RhizoFrame system, that enabled us to track the nodulation processes with fluorescence stereomicroscope while retaining spatial information about roots, rhizobia, and soil. Mixed inoculation with different fluorescent rhizobia using RhizoFrame enabled the visualization of mixed infection of a single nodule with two strains. In addition, observation of transgenic Lotus japonicus expressing auxin-responsive reporter genes indicated that RhizoFrame system could be used for a real-time and nondestructive reporter assay. Thus, the use of RhizoFrame system is expected to enhance the study of the spatiotemporal dynamics of plant-microbe interactions in the soil.
