Root architecture simulation improves the inference from seedling root phenotyping towards mature root systems

AbstractBackgroundBreeding towards resilient rice varieties is often constrained by the limited data on root system architecture obtained from relevant agricultural environments. Knowledge on the genotypic differences and responses of root architecture to environmental factors is limited due the difficulty of analysing soil-grown rice roots. An improved method using imaging is thus needed, but the existing methods were never proven successful for rice. Here, we aimed to evaluate and improve a higher throughput method of image-based root phenotyping for rice grown under field conditions. Rice root systems from seven experiments were phenotyped based on the “shovelomics” method of root system excavation followed by manual root phenotyping and digital root analysis after root imaging. Analyzed traits were compared between manual and image-based root phenotyping systems using Spearman rank correlations to evaluate whether both methods similarly rank the phenotypes. For each trait, the relative phenotypic variation was calculated. A principal component analysis was then conducted to assess patterns in root architectural variation.ResultsSeveral manually collected and image-based root traits were identified as having a high potential of differentiating among contrasting phenotypes, while other traits are found to be inaccurate and thus unreliable for rice. The image-based traits projected area, root tip thickness, stem diameter, and root system depth successfully replace the manual determination of root characteristics, however attention should be paid to the lower accuracy of the image-based methodology, especially when working with older and larger root systems.ConclusionsThe challenges and opportunities of rice root phenotyping in field conditions are discussed for both methods. We therefore propose an integrated protocol adjusted to the complexity of the rice root structure combining image analysis in a water bath and the manual scoring of three traits (i.e. lateral density, secondary branching degree, and nodal root thickness at the root base). The proposed methodology ensures higher throughput and enhanced accuracy during root phenotyping of soil grown rice in fields or pots compared to manual scoring only, it is cheap to develop and operate, it is valid in remote environments, and it enables fast data extraction.

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Contemporary Concepts of Root System Architecture of Urban Trees

Arboriculture & Urban Forestry ◽

10.48044/jauf.2010.020 ◽

2010 ◽

Vol 36 (4) ◽

pp. 149-159

Author(s):

Susan Day ◽

P. Eric Wiseman ◽

Sarah Dickinson ◽

J. Roger Harris

Keyword(s):

Built Environment ◽

Root Growth ◽

Root System ◽

Root Architecture ◽

Root Systems ◽

Growth Patterns ◽

Urban Trees ◽

Rooting Depth ◽

Similar Species ◽

Urban Settings

Knowledge of the extent and distribution of tree root systems is essential for managing trees in the built environment. Despite recent advances in root detection tools, published research on tree root architecture in urban settings has been limited and only partially synthesized. Root growth patterns of urban trees may differ considerably from similar species in forested or agricultural environments. This paper reviews literature documenting tree root growth in urban settings as well as literature addressing root architecture in nonurban settings that may contribute to present understanding of tree roots in built environments. Although tree species may have the genetic potential for generating deep root systems (>2 m), rooting depth in urban situations is frequently restricted by impenetrable or inhospitable soil layers or by underground infrastructure. Lateral root extent is likewise subject to restriction by dense soils under hardscape or by absence of irrigation in dry areas. By combining results of numerous studies, the authors of this paper estimated the radius of an unrestricted root system initially increases at a rate of approximately 38 to 1, compared to trunk diameter; however, this ratio likely considerably declines as trees mature. Roots are often irregularly distributed around the tree and may be influenced by cardinal direction, terrain, tree lean, or obstacles in the built environment. Buttress roots, tap roots, and other root types are also discussed.

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Toward Marker-assisted Breeding for Root Architecture Traits in Southern Highbush Blueberry

Journal of the American Society for Horticultural Science ◽

10.21273/jashs03798-16 ◽

2016 ◽

Vol 141 (5) ◽

pp. 414-424 ◽

Cited By ~ 4

Author(s):

Gerardo H. Nunez ◽

Hilda Patricia Rodríguez-Armenta ◽

Rebecca L. Darnell ◽

James W. Olmstead

Keyword(s):

Root Growth ◽

Root Architecture ◽

Root Systems ◽

Vaccinium Corymbosum ◽

Lower Percentage ◽

Soil Conditions ◽

Growth Substrate ◽

Family Pedigree ◽

Southern Highbush ◽

Trait Associations

Root growth and root system architecture (RSA) are affected by edaphic and genetic factors and they can impact plant growth and farm profitability. Southern highbush blueberries [SHBs (Vaccinium corymbosum hybrids)] develop shallow, fibrous root systems, and exhibit a preference for acidic soils where water and ammonium are readily available. The amendments used to create these soil conditions negatively affect the profitability of SHB plantations. Hence, breeding for RSA traits has been suggested as an alternative to soil amendments. Vaccinium arboreum is a wild species that is used in SHB breeding. V. arboreum exhibits greater drought tolerance and broader soil pH adaptation than SHB, and—according to anecdotal evidence—it develops deep, taproot-like root systems. The present study constitutes the first in-depth study of the RSA of Vaccinium species with the intention of facilitating breeding for RSA traits. Root systems were studied in rhizotron-grown seedling families. In separate experiments, we tested the effect that growth substrate and family pedigree can have on root growth and RSA. Subsequently, a genotyping by sequence approach was used to develop single nucleotide polymorphism (SNP) markers that could be used along with the phenotyping method to investigate the heritability of RSA traits and look for marker-trait associations. We found that RSA is affected by growth substrate and family pedigree. In addition, we found that V. arboreum exhibited greater maximum root depth and a lower percentage of roots in the top 8 cm of soil than SHB, and interspecific hybrids generally exhibited intermediate phenotypes. Also, we found that RSA traits exhibit moderate to low heritability and genetic correlations among them. Finally, we found 59 marker-trait associations. Among these markers, 37 were found to be located in exons, and 16 of them were annotated based on protein homology with entries in National Center for Biotechnology Information (NCBI) GenBank. Altogether, the present study provides tools that can be used to breed for root architecture traits in SHB.

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A rapid method for detecting cold injury in conifer seedling root systems

Canadian Journal of Forest Research ◽

10.1139/x90-004 ◽

1990 ◽

Vol 20 (1) ◽

pp. 26-30 ◽

Cited By ~ 8

Author(s):

Gary A. Ritchie

Keyword(s):

Weight Loss ◽

Root Systems ◽

Douglas Fir ◽

Cold Injury ◽

Percent Weight Loss ◽

Seedling Root ◽

Seedling Roots ◽

Temperature Exposure ◽

Low Temperature Exposure ◽

Conifer Seedling

A method is described for rapidly determining the extent of cold injury to Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) seedling root systems. It is based upon pressure:volume theory but short-cuts the tedious pressure:volume method. Injured root systems were brought to full hydration, then weighed and placed into a pressure chamber. A pressure of 1.5 MPa was applied for a 5-min period, then the root system was removed from the chamber and reweighed. The percent weight loss was then calculated. Percent weight loss was closely related to degree of low temperature exposure in Douglas-fir seedling roots. Percent weight loss values were near 5 in uninjured controls, whereas freeze-injured seedlings had percent weight loss values of 7 or greater. Percent weight loss values measured on seedlings just before planting were closely correlated with seedling vigor and mortality 3 months following planting in both a field test and a greenhouse pot trial.

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

Functional Plant Biology ◽

10.1071/fp16128 ◽

2017 ◽

Vol 44 (1) ◽

pp. 76 ◽

Cited By ~ 22

Author(s):

Tania Gioia ◽

Anna Galinski ◽

Henning Lenz ◽

Carmen Müller ◽

Jonas Lentz ◽

...

Keyword(s):

High Throughput ◽

Phenotypic Diversity ◽

Crop Improvement ◽

Root Traits ◽

Root Systems ◽

Non Invasive ◽

Large Sets ◽

High Throughput Phenotyping ◽

Improvement Programs ◽

Root Phenotyping

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

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The Influence of Growing Temperature on the Growth and Morphology of Cereal Seedling Root Systems

Journal of Experimental Botany ◽

10.1093/jxb/34.12.1720 ◽

1983 ◽

Vol 34 (12) ◽

pp. 1720-1730 ◽

Cited By ~ 33

Author(s):

M. K. ABBAS AL-ANI ◽

R. K. M. HAY

Keyword(s):

Root Systems ◽

Seedling Root

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Curled root hairs are a site of entry for Bradyrhizobium infecting hydroponically grown soybean plants with mature root systems

Canadian Journal of Botany ◽

10.1139/b88-098 ◽

1988 ◽

Vol 66 (4) ◽

pp. 683-686 ◽

Cited By ~ 1

Author(s):

Jeanne M. L. Selker ◽

John Imsande ◽

Eldon H. Newcomb

Keyword(s):

Glycine Max ◽

Root Hair ◽

Bradyrhizobium Japonicum ◽

Root Hairs ◽

Root Systems ◽

Glycine Max L ◽

Soybean Plants ◽

A Site ◽

Hydroponically Grown ◽

Mature Root

Early emergent nodules on roots of hydroponically grown soybean plants (Glycine max (L.) Merr.) were sectioned serially to locate the site of infection by Bradyrhizobium japonicum. The plants had been inoculated only after their root systems had produced numerous higher order branches. The hydroponic solutions contained all required nutrients, including either a suboptimal concentration of nitrate (0.5 mM) or an excess of nitrate (4.0 mM). In all six nodules examined, three with suboptimal nitrate and three with excess nitrate, we found a centrally located root hair containing an infection thread. We conclude that mature root systems of soybean grown in aqueous culture can undergo infection through root hairs in the way that is typical of young seedlings grown either in pots of vermiculite or pouches.

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A microcomputer based method for the rapid and detailed measurement of seedling root systems

Plant and Soil ◽

10.1007/bf02374528 ◽

1982 ◽

Vol 69 (2) ◽

pp. 305-309 ◽

Cited By ~ 9

Author(s):

P. A. Costigan ◽

J. A. Rose ◽

T. McBurney

Keyword(s):

Root Systems ◽

Detailed Measurement ◽

Seedling Root

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Simulating rhizodeposition patterns around growing and exuding root systems

10.1101/2021.02.25.432851 ◽

2021 ◽

Author(s):

Magdalena Landl ◽

Adrian Haupenthal ◽

Daniel Leitner ◽

Eva Kroener ◽

Doris Vetterlein ◽

...

Keyword(s):

Root Architecture ◽

Three Dimensional ◽

Temporal Distribution ◽

Root Systems ◽

Distribution Patterns ◽

Three Dimensions ◽

Root Branching ◽

Architecture Model ◽

Spatio Temporal ◽

Model Approach

1AbstractIn this study, we developed a novel model approach to compute the spatio-temporal distribution patterns of rhizodeposits around growing root systems in three dimensions. This model approach allows us for the first time to study the evolution of rhizodeposition patterns around complex three-dimensional root systems. Root systems were generated using the root architecture model CPlantBox. The concentration of rhizodeposits at a given location in the soil domain was computed analytically. To simulate the spread of rhizodeposits in the soil, we considered rhizodeposit release from the roots, rhizodeposit diffusion into the soil, rhizodeposit sorption to soil particles, and rhizodeposit degradation by microorganisms. To demonstrate the capabilities of our new model approach, we performed simulations for the two example rhizodeposits mucilage and cit-rate and the example root system Vicia faba. The rhizodeposition model was parameterized using values from the literature. Our simulations showed that the rhizosphere soil volume with rhizodeposit concentrations above a defined threshold value (i.e., the rhizodeposit hotspot volume), exhibited a maximum at intermediate root growth rates. Root branching allowed the rhizospheres of individual roots to overlap, resulting in a greater volume of rhizodeposit hotspots. This was particularly important in the case of citrate, where overlap of rhizodeposition zones accounted for more than half of the total rhizodeposit hotspot volumes. Coupling a root architecture model with a rhizodeposition model allowed us to get a better understanding of the influence of root architecture as well as rhizodeposit properties on the evolution of the spatio-temporal distribution patterns of rhizodeposits around growing root systems.

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A technological approach to the morphofunctional classification of seedlings of 50 Brazilian forest species

Journal of Seed Science ◽

10.1590/s2317-15372014000100011 ◽

2014 ◽

Vol 36 (1) ◽

pp. 87-93 ◽

Cited By ~ 1

Author(s):

Gabriela Alves Lobo ◽

Denise Garcia de Santana ◽

Antonieta Nassif Salomão ◽

Luciana Salazar Rehbein ◽

Angélica Polenz Wielewicki

Keyword(s):

Primary Root ◽

Root Systems ◽

Forest Species ◽

Seedling Root ◽

Technological Approach ◽

Shoot System ◽

Normal Seedling ◽

Long Life ◽

Great Mass

A technological approach to the morphofunctional classification of forest species seedlings defines the essential structures in the evaluation of germination testing and identifies changes in this structures that suggest abnormalities. The objective was to associate morphofunctional seedling classification to seed germination testing using official germination methods for 50 forest species from Amazon, Caatinga, Cerrado, Atlantic Forest and Pantanal biomes. Morphofunctional classification and abnormalities were defined using seedlings from 232 germination pre-tests and 1,160 samples that were formed for each species using seeds from distinct locations and with at least three levels of vigor. The phanero-epigeal germination with a non-developed epicotyl predominated among species (84%). Common in hypogeal germination, the development of the epicotyl occurred only in seedlings of Anadenanthera colubrina and Erythrina speciosa, both with epigeal germination. The need to supply and sustain the great mass produced in its long life cycle, the presence of the primary root was considered essential for the normal seedling classification of these forest species. Curled, stunted, necrotic, bifurcated primary root and those retained in the seed coat or in the fruit structures, were the main abnormalities of the seedling root systems. Damages to the shoot system were uncommon.

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