Importance of individual root traits to understand crop root system in agronomic and environmental contexts

Identifying genotypes with a greater ability to absorb nitrogen (N) may be important to reducing N loss in the environment and improving the sustainability of agricultural systems. This study extends the knowledge of variability among wheat genotypes in terms of morphological or physiological root traits, N uptake under conditions of low soil N availability, and in the amount and rapidity of the use of N supplied with fertilizer. Nine genotypes of durum wheat were chosen for their different morpho-phenological characteristics and year of their release. The isotopic tracer 15N was used to measure the fertilizer N uptake efficiency. The results show that durum wheat breeding did not have univocal effects on the characteristics of the root system (weight, length, specific root length, etc.) or N uptake capacity. The differences in N uptake among the studied genotypes when grown in conditions of low N availability appear to be related more to differences in uptake efficiency per unit of weight and length of the root system than to differences in the morphological root traits. The differences among the genotypes in the speed and the ability to take advantage of the greater N availability, determined by N fertilization, appear to a certain extent to be related to the development of the root system and the photosynthesizing area. This study highlights some variability within the species in terms of the development, distribution, and efficiency of the root system, which suggests that there may be sufficient grounds for improving these traits with positive effects in terms of adaptability to difficult environments and resilience to climate change.

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Shoot and Root Traits Underlying Genotypic Variation in Early Vigor and Nutrient Accumulation in Spring Wheat Grown in High-Latitude Light Conditions

Plants ◽

10.3390/plants10010174 ◽

2021 ◽

Vol 10 (1) ◽

pp. 174

Author(s):

Hui Liu ◽

Fabio Fiorani ◽

Ortrud Jäck ◽

Tino Colombi ◽

Kerstin A. Nagel ◽

...

Keyword(s):

Root System ◽

Leaf Area ◽

Spring Wheat ◽

High Latitude ◽

Root Length ◽

Nutrient Use Efficiency ◽

Root Traits ◽

Plant Production ◽

Nutrient Accumulation ◽

Early Vigor

Plants with improved nutrient use efficiency are needed to maintain and enhance future crop plant production. The aim of this study was to explore candidate traits for pre-breeding to improve nutrient accumulation and early vigor of spring wheat grown at high latitudes. We quantified shoot and root traits together with nutrient accumulation in nine contrasting spring wheat genotypes grown in rhizoboxes for 20 days in a greenhouse. Whole-plant relative growth rate was here correlated with leaf area productivity and plant nitrogen productivity, but not leaf area ratio. Furthermore, the total leaf area was correlated with the accumulation of six macronutrients, and could be suggested as a candidate trait for the pre-breeding towards improved nutrient accumulation and early vigor in wheat to be grown in high-latitude environments. Depending on the nutrient of interest, different root system traits were identified as relevant for their accumulation. Accumulation of nitrogen, potassium, sulfur and calcium was correlated with lateral root length, whilst accumulation of phosphorus and magnesium was correlated with main root length. Therefore, special attention needs to be paid to specific root system traits in the breeding of wheat towards improved nutrient accumulation to counteract the suboptimal uptake of some nutrient elements.

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

10.1101/2020.10.27.350553 ◽

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.

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Two Wheat Cultivars with Contrasting Post-Embryonic Root Biomass Differ in Shoot Re-Growth after Defoliation: Implications for Breeding Grazing Resilient Forages

Plants ◽

10.3390/plants8110470 ◽

2019 ◽

Vol 8 (11) ◽

pp. 470

Author(s):

Paez-Garcia ◽

Liao ◽

Blancaflor

Keyword(s):

Winter Wheat ◽

Root Growth ◽

Root System ◽

Aboveground Biomass ◽

Root Traits ◽

Shoot Biomass ◽

Wheat Cultivars ◽

Leaf Clipping ◽

The Impact ◽

Embryonic Root

The ability of forages to quickly resume aboveground growth after grazing is a trait that enables farmers to better manage their livestock for maximum profitability. Leaf removal impairs root growth. As a consequence of a deficient root system, shoot re-growth is inhibited leading to poor pasture performance. Despite the importance of roots for forage productivity, they have not been considered as breeding targets for improving grazing resilience due in large part to the lack of knowledge on the relationship between roots and aboveground biomass re-growth. Winter wheat (Triticum aestivum) is extensively used as forage source in temperate climates worldwide. Here, we investigated the impact of leaf clipping on specific root traits, and how these influence shoot re-growth in two winter wheat cultivars (i.e., Duster and Cheyenne) with contrasting root and shoot biomass. We found that root growth angle and post-embryonic root growth in both cultivars are strongly influenced by defoliation. We discovered that Duster, which had less post-embryonic roots before defoliation, reestablished its root system faster after leaf cutting compared with Cheyenne, which had a more extensive pre-defoliation post-embryonic root system. Rapid resumption of root growth in Duster after leaf clipping was associated with faster aboveground biomass re-growth even after shoot overcutting. Taken together, our results suggest that lower investments in the production of post-embryonic roots presents an important ideotype to consider when breeding for shoot re-growth vigor in dual purpose wheat.

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MARSHAL, a novel tool for virtual phenotyping of maize root system hydraulic architectures

in silico Plants ◽

10.1093/insilicoplants/diz012 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 2

Author(s):

Félicien Meunier ◽

Adrien Heymans ◽

Xavier Draye ◽

Valentin Couvreur ◽

Mathieu Javaux ◽

...

Keyword(s):

Root System ◽

Web Application ◽

Root Traits ◽

Root Systems ◽

R Package ◽

Maize Root ◽

Model Parameters ◽

System Modelling ◽

Architecture Model ◽

System Models

Abstract Functional-structural root system models combine functional and structural root traits to represent the growth and development of root systems. In general, they are characterized by a large number of growth, architectural and functional root parameters, generating contrasted root systems evolving in a highly non-linear environment (soil, atmosphere), which makes the link between local traits and functioning unclear. On the other end of the root system modelling continuum, macroscopic root system models associate to each root system a set of plant-scale, easily interpretable parameters. However, as of today, it is unclear how these macroscopic parameters relate to root-scale traits and whether the upscaling of local root traits is compatible with macroscopic parameter measurements. The aim of this study was to bridge the gap between these two modelling approaches. We describe here the MAize Root System Hydraulic Architecture soLver (MARSHAL), a new efficient and user-friendly computational tool that couples a root architecture model (CRootBox) with fast and accurate algorithms of water flow through hydraulic architectures and plant-scale parameter calculations. To illustrate the tool’s potential, we generated contrasted maize hydraulic architectures that we compared with root system architectural and hydraulic observations. Observed variability of these traits was well captured by model ensemble runs. We also analysed the multivariate sensitivity of mature root system conductance, mean depth of uptake, root system volume and convex hull to the input parameters to highlight the key model parameters to vary for virtual breeding. It is available as an R package, an RMarkdown pipeline and a web application.

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Trait-Based Root Phenotyping as a Necessary Tool for Crop Selection and Improvement

Agronomy ◽

10.3390/agronomy10091328 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1328

Author(s):

Rebecca K. McGrail ◽

David A. Van Sanford ◽

David H. McNear

Keyword(s):

Root System ◽

System Architecture ◽

Production Systems ◽

Root Traits ◽

Root System Architecture ◽

Root Decomposition ◽

Crop Breeding ◽

Organic Acid Production ◽

Nutritional Qualities ◽

Chemical Traits

Most of the effort of crop breeding has focused on the expression of aboveground traits with the goals of increasing yield and disease resistance, decreasing height in grains, and improvement of nutritional qualities. The role of roots in supporting these goals has been largely ignored. With the increasing need to produce more food, feed, fiber, and fuel on less land and with fewer inputs, the next advance in plant breeding must include greater consideration of roots. Root traits are an untapped source of phenotypic variation that will prove essential for breeders working to increase yields and the provisioning of ecosystem services. Roots are dynamic, and their structure and the composition of metabolites introduced to the rhizosphere change as the plant develops and in response to environmental, biotic, and edaphic factors. The assessment of physical qualities of root system architecture will allow breeding for desired root placement in the soil profile, such as deeper roots in no-till production systems plagued with drought or shallow roots systems for accessing nutrients. Combining the assessment of physical characteristics with chemical traits, including enzymes and organic acid production, will provide a better understanding of biogeochemical mechanisms by which roots acquire resources. Lastly, information on the structural and elemental composition of the roots will help better predict root decomposition, their contribution to soil organic carbon pools, and the subsequent benefits provided to the following crop. Breeding can no longer continue with a narrow focus on aboveground traits, and breeding for belowground traits cannot only focus on root system architecture. Incorporation of root biogeochemical traits into breeding will permit the creation of germplasm with the required traits to meet production needs in a variety of soil types and projected climate scenarios.

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

Rice ◽

10.1186/s12284-020-00404-5 ◽

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.

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Crop root system response to irrigation

Irrigation Science ◽

10.1007/bf00192280 ◽

1991 ◽

Vol 12 (3) ◽

Cited By ~ 28

Author(s):

B. Klepper

Keyword(s):

Root System ◽

System Response ◽

Crop Root

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Breeding for root yield in alfalfa

Canadian Journal of Plant Science ◽

10.4141/cjps91-106 ◽

1991 ◽

Vol 71 (3) ◽

pp. 727-735 ◽

Cited By ~ 6

Author(s):

G. Saindon ◽

R. Michaud ◽

C. A. St-Pierre

Keyword(s):

Root System ◽

Inorganic Nitrogen ◽

Root Traits ◽

Phenotypic Selection ◽

Nitrogen Fertilizers ◽

Root Yield ◽

Root Branching ◽

Indirect Response ◽

Crown Width ◽

Medicago Sativa L

Winter survival of alfalfa (Medicago sauva L.) has often been associated with the size of the root system but breeding for a larger root system has never received much attention. The objectives of this study were to detect variability for root traits among seven alfalfa entries grown under two nitrogen fertilizer treatments (R- and N-treatments) which consisted of Rhizobium nitrogen fixation and inorganic nitrogen fertilizers, respectively; to select for root yield in two alfalfa cultivars grown under the same two treatments and to measure resulting progress; and to determine which of the two N regimes is more appropriate for root yield selection. Variability for root yield, number of laterals, crown width and top yield was found among R-treated entries whereas only the crown width varied among the N-treated ones. The evaluation under both treatments showed that one cycle of bidirectional phenotypic selection made under both the R- and N-treatments was sufficient to allow the formation of divergent populations for root yield with the exception of Apica-derived populations which showed inconsistent or no responses when evaluated under the N-treatment. Independently of the cultivars and treatments used for selection and evaluation, asymmetries of response were observed. Possible explanations are proposed but additional cycles of selection are needed to provide definitive conclusions. Indirect selection responses observed for top yield, crown width, and root branching should make selection for increasing root yield in alfalfa attractive. Key words: Medicago sativa L., root branching, realized heritability, asymmetry of response, indirect response

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Complete root specimen of plants grown in soil-filled root box: sampling, measuring, and staining method

Plant Methods ◽

10.1186/s13007-021-00798-3 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Takuya Koyama ◽

Shun Murakami ◽

Toshihiko Karasawa ◽

Masato Ejiri ◽

Katsuhiro Shiono

Keyword(s):

Root System ◽

Surface Area ◽

Visual Information ◽

Physiological Function ◽

Physiological Activity ◽

Root Traits ◽

Arbuscular Mycorrhizal ◽

Spatial Arrangement ◽

Root Surface ◽

Root Surface Area

Abstract Background Detailed datasets containing root system and its architecture in soil are required to improve understanding of resource capture by roots. However, most of the root study methods have paid little attention to make and preserve whole root specimens. This study introduces root system sampling equipment that makes the entire root specimen with minimum impairment and without displacement of the spatial arrangement of the root system in root boxes. The objectives are to assess: whether the equipment can rapidly sample the entire root system; whether root surface area is measurable from a scanned digital image of the root specimen; and whether staining of the entire root specimens would provide multidimensional visual information on the interaction between soil and physiological function of root system architecture (RSA). For validation, we examined the root response of two soybean cultivars to arbuscular mycorrhizal (AM) inoculation and the effect of waterlogging stress on the physiological activity of buckwheat RSA. Results The root boxes allowed soybean and buckwheat plants to grow uniformly across the replications. Both species showed significant differences between cultivars and/or among treatments in shoot and root traits. The equipment enabled to sample the whole-root specimens of soybean and buckwheat, where the tips of the fine roots were alive (diameter < 0.2 mm). Also, the whole root specimens of soybean were made in about 7 min. The root surface area calculated from the scanned soybean specimens showed a significant correlation with that calculated from the roots spread out in water (a common method). Staining of the soybean root specimens enabled us to observe the localized root proliferation induced by AM colonization. Moreover, staining of the buckwheat root specimens made it possible to examine the respiratory activity of each root at different depths. Conclusions The present method realized: fast and accurate production of the whole root specimen and precise calculation of the specimens’ root surface area. Moreover, staining of the root specimens enabled analyzing the interaction between soil and physiological function of RSA. The evaluation of root traits, using our methods, will contribute to developing agronomic management and breeding program for sustainable food production.

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