scholarly journals Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number

2018 ◽  
Vol 42 (1) ◽  
pp. 212-229 ◽  
Author(s):  
Silvas J. Prince ◽  
Babu Valliyodan ◽  
Heng Ye ◽  
Ming Yang ◽  
Shuaishuai Tai ◽  
...  
Keyword(s):  
Root System ◽  
Genetic Control ◽  
System Architecture ◽  
Lateral Root ◽  
Genetic Basis ◽  
Root System Architecture ◽  
Root Number

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals Morphological Characterization of Root System Architecture in Diverse Tomato Genotypes during Early Growth

2018 ◽  
Vol 19 (12) ◽  
pp. 3888 ◽  
Author(s):  
Aurora Alaguero-Cordovilla ◽  
Francisco Gran-Gómez ◽  
Sergio Tormos-Moltó ◽  
José Pérez-Pérez
Keyword(s):  
Root System ◽  
System Architecture ◽  
Lateral Root ◽  
Morphological Plasticity ◽  
Root System Architecture ◽  
Morphological Characterization ◽  
Early Growth ◽  
Soil Conditions ◽  
Wild Tomato Species ◽  
Local Soil

Plant roots exploit morphological plasticity to adapt and respond to different soil environments. We characterized the root system architecture of nine wild tomato species and four cultivated tomato (Solanum lycopersicum L.) varieties during early growth in a controlled environment. Additionally, the root system architecture of six near-isogenic lines from the tomato ‘Micro-Tom’ mutant collection was also studied. These lines were affected in key genes of ethylene, abscisic acid, and anthocyanin pathways. We found extensive differences between the studied lines for a number of meaningful morphological traits, such as lateral root distribution, lateral root length or adventitious root development, which might represent adaptations to local soil conditions during speciation and subsequent domestication. Taken together, our results provide a general quantitative framework for comparing root system architecture in tomato seedlings and other related species.

scholarly journals AT-HOOK MOTIF NUCLEAR LOCALISED PROTEIN 18 as a Novel Modulator of Root System Architecture

2020 ◽  
Author(s):  
Marek Šírl ◽  
Tereza Šnajdrová ◽  
Dolores Gutiérrez-Alanís ◽  
Joseph G. Dubrovsky ◽  
Jean Phillipe Vielle-Calzada ◽  
...  
Keyword(s):  
Root System ◽  
System Architecture ◽  
Lateral Root ◽  
Apical Meristem ◽  
Lateral Roots ◽  
Primary Root ◽  
Root System Architecture ◽  
Root Apical Meristem ◽  
Root Initiation ◽  
Lateral Root Initiation

The AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN (AHL) gene family encodes embryophyte-specific nuclear proteins with DNA binding activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and growth. AHL18 regulates the length of the proliferation domain and number of dividing cells in the root apical meristem and thereby, cell production. Both primary root growth and lateral root development respond according to AHL18 transcription level. The ahl18 knock-out plants show reduced root systems due to a shorter primary root and a lower number of lateral roots. This change results from a higher number of arrested and non-developing lateral root primordia (LRP) rather than from decreased initiation. Overexpression of AHL18 results in a more extensive root system, longer primary roots, and increased density of lateral root initiation events. Formation of lateral roots is affected during the initiation of LRP and later development. AHL18 regulate root apical meristem activity, lateral root initiation and emergence, which is in accord with localization of its expression.

scholarly journals Genotypic diversity and plasticity of root system architecture to nitrogen availability in oilseed rape

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0250966
Author(s):  
Christophe Lecarpentier ◽  
Loïc Pagès ◽  
Céline Richard-Molard
Keyword(s):  
Root System ◽  
Oilseed Rape ◽  
System Architecture ◽  
Lateral Root ◽  
Nitrogen Availability ◽  
Root System Architecture ◽  
Root Diameter ◽  
Root Density ◽  
Model Parameters ◽  
New Varieties

In the emerging new agricultural context, a drastic reduction in fertilizer usage is required. A promising way to maintain high crop yields while reducing fertilizer inputs is to breed new varieties with optimized root system architecture (RSA), designed to reach soil resources more efficiently. This relies on identifying key traits that underlie genotypic variability and plasticity of RSA in response to nutrient availability. The aim of our study was to characterize the RSA plasticity in response to nitrogen limitation of a set of contrasted oilseed rape genotypes, by using the ArchiSimple model parameters as screening traits. Eight accessions of Brassica napus were grown in long tubes in the greenhouse, under two contrasting levels of nitrogen availability. After plant excavation, roots were scanned at high resolution. Six RSA traits relative to root diameter, elongation rate and branching were measured, as well as nine growth and biomass allocation traits. The plasticity of each trait to nitrogen availability was estimated. Nitrogen-limited plants were characterized by a strong reduction in total biomass and leaf area. Even if the architecture traits were shown to be less plastic than allocation traits, significant nitrogen and genotype effects were highlighted on each RSA trait, except the root minimal diameter. Thus, the RSA of nitrogen-limited plants was primarily characterised by a reduced lateral root density, a smaller primary root diameter, associated with a stronger root dominance. Among the RSA traits measured, the inter-branch distance showed the highest plasticity with a level of 70%, in the same range as the most plastic allocation traits. This work suggests that lateral root density plays the key role in the adaptation of the root system to nitrogen availability and highlights inter-branch distance as a major target trait for breeding new varieties, better adapted to low input systems.

Plant density modifies root system architecture in spring barley (Hordeum vulgare L.) through a change in nodal root number

2018 ◽  
Vol 439 (1-2) ◽  
pp. 179-200 ◽  
Author(s):  
V. L. Hecht ◽  
V. M. Temperton ◽  
K. A. Nagel ◽  
U. Rascher ◽  
R. Pude ◽  
...  
Keyword(s):  
Hordeum Vulgare ◽  
Root System ◽  
System Architecture ◽  
Plant Density ◽  
Spring Barley ◽  
Root System Architecture ◽  
Root Number ◽  
Hordeum Vulgare L ◽  
Nodal Root

scholarly journals Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 633 ◽  
Author(s):  
Muhammad Asim ◽  
Zia Ullah ◽  
Fangzheng Xu ◽  
Lulu An ◽  
Oluwaseun Olayemi Aluko ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Root System ◽  
Root Development ◽  
System Architecture ◽  
Lateral Root ◽  
Transcriptional Regulatory Network ◽  
Primary Root ◽  
Root System Architecture ◽  
Nitrate Transporter ◽  
Nitrate Transporters

Root system architecture (RSA) is required for the acquisition of water and mineral nutrients from the soil. One of the essential nutrients, nitrate (NO3−), is sensed and transported by nitrate transporters NRT1.1 and NRT2.1 in the plants. Nitrate transporter 1.1 (NRT1.1) is a dual-affinity nitrate transporter phosphorylated at the T101 residue by calcineurin B-like interacting protein kinase (CIPKs); it also regulates the expression of other key nitrate assimilatory genes. The differential phosphorylation (phosphorylation and dephosphorylation) strategies and underlying Ca2+ signaling mechanism of NRT1.1 stimulate lateral root growth by activating the auxin transport activity and Ca2+-ANR1 signaling at the plasma membrane and the endosomes, respectively. NO3− additionally functions as a signal molecule that forms a signaling system, which consists of a vast array of transcription factors that control root system architecture that either stimulate or inhibit lateral and primary root development in response to localized and high nitrate (NO3−), respectively. This review elucidates the so-far identified nitrate transporters, nitrate sensing, signal transduction, and the key roles of nitrate transporters and its downstream transcriptional regulatory network in the primary and lateral root development in Arabidopsis thaliana under stress conditions.

scholarly journals A split supply of bio-organic and chemical fertilizer synergistically affects root system architecture and improves above-ground growth in pear tree (Pyrus pyrifolia Nakai)

2020 ◽  
Author(s):  
Yalong Kang ◽  
Xiangrui An ◽  
Yanwei Ma ◽  
Yan Li ◽  
Wenli Wu ◽  
...  
Keyword(s):  
Root System ◽  
System Architecture ◽  
Root Length ◽  
Lateral Root ◽  
Organic Fertilizer ◽  
Root System Architecture ◽  
Chemical Fertilizer ◽  
Root Tissue ◽  
Tissue Density ◽  
Root Tissue Density

Abstract Background: Root system architecture (RSA) is highly plastic, responding to nutrient availability and the heterogeneity of the soil environment. However, the linkage of root morphology to anatomy and root nutrient, and its implication for root function at the heterogeneous application of bio-organic and chemical fertilizer have not yet been defined, especially for pear trees.Results: In this study, a split-root experiment was conducted using 1-year old ‘Cuiguan’ trees. No fertilizer (NF), chemical fertilizer (CF), and bio-organic fertilizer (BIO) were paired to test six combinations: NF-NF, NF-CF, NF-BIO, CF-CF, BIO-BIO, and BIO-CF. Root morphological, anatomical traits and root nutrient concentrations, and their relationships were determined. Trees receiving BIO had significantly higher lateral root numbers, activity, total lateral root length, and specific root length than trees receiving no BIO, while the effects on root tissue density were the direct opposite. Compared with CF-CF treatment, root xylem thickness, stele diameter, vessel diameter, and number of vessels all increased in response to BIO-CF treatment. Root growth was synergistically promoted in BIO-CF, with increased special root length and root nitrogen concentration, but root tissue density and the carbon:nitrogen ratio were reduced. Intriguingly, the synergistic effect resulted in greater trunk girth without sacrificing height, compared to trees receiving CF or BIO alone.Conclusions: The combination of BIO and CF improves root traits and tree growth, suggesting that using bio-organic fertilizer as a supplement to reduce the application rate of chemical fertilizer is beneficial to orchard ecosystems.

scholarly journals At-Hook Motif Nuclear Localised Protein 18 as a Novel Modulator of Root System Architecture

2020 ◽  
Vol 21 (5) ◽  
pp. 1886 ◽  
Author(s):  
Marek Širl ◽  
Tereza Šnajdrová ◽  
Dolores Gutiérrez-Alanís ◽  
Joseph G. Dubrovsky ◽  
Jean Phillipe Vielle-Calzada ◽  
...  
Keyword(s):  
Root System ◽  
System Architecture ◽  
Lateral Root ◽  
Apical Meristem ◽  
Lateral Roots ◽  
Primary Root ◽  
Root System Architecture ◽  
Root Apical Meristem ◽  
Root Initiation ◽  
Lateral Root Initiation

The At-Hook Motif Nuclear Localized Protein (AHL) gene family encodes embryophyte-specific nuclear proteins with DNA binding activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and growth. AHL18 is involved in regulation of the length of the proliferation domain and number of dividing cells in the root apical meristem and thereby, cell production. Both primary root growth and lateral root development respond according to AHL18 transcription level. The ahl18 knock-out plants show reduced root systems due to a shorter primary root and a lower number of lateral roots. This change results from a higher number of arrested and non-developing lateral root primordia (LRP) rather than from a decreased LRP initiation. The over-expression of AHL18 results in a more extensive root system, longer primary roots, and increased density of lateral root initiation events. AHL18 is thus involved in the formation of lateral roots at both LRP initiation and their later development. We conclude that AHL18 participates in modulation of root system architecture through regulation of root apical meristem activity, lateral root initiation and emergence; these correspond well with expression pattern of AHL18.

scholarly journals TopoRoot: A method for computing hierarchy and fine-grained traits of maize roots from X-ray CT images

2021 ◽  
Author(s):  
Dan Zeng ◽  
Mao Li ◽  
Ni Jiang ◽  
Yiwen Ju ◽  
Hannah Schreiber ◽  
...  
Keyword(s):  
Root System ◽  
System Architecture ◽  
State Of The Art ◽  
Root System Architecture ◽  
Ct Images ◽  
Maize Root ◽  
Root Number ◽  
X Ray ◽  
Fine Grained ◽  
Maize Roots

Background: 3D imaging, such as X-ray CT and MRI, has been widely deployed to study plant root structures. Many computational tools exist to extract coarse-grained features from 3D root images, such as total volume, root number and total root length. However, methods that can accurately and efficiently compute fine-grained root traits, such as root number and geometry at each hierarchy level, are still lacking. These traits would allow biologists to gain deeper insights into the root system architecture (RSA). Results: We present TopoRoot, a high-throughput computational method that computes fine-grained architectural traits from 3D X-ray CT images of field-excavated maize root crowns. These traits include the number, length, thickness, angle, tortuosity, and number of children for the roots at each level of the hierarchy. TopoRoot combines state-of-the-art algorithms in computer graphics, such as topological simplification and geometric skeletonization, with customized heuristics for robustly obtaining the branching structure and hierarchical information. TopoRoot is validated on both real and simulated root images, and in both cases it was shown to improve the accuracy of traits over existing methods. We also demonstrate TopoRoot in differentiating a maize root mutant from its wild type segregant using fine-grained traits. TopoRoot runs within a few minutes on a desktop workstation for volumes at the resolution range of 400^3, without need for human intervention. Conclusions: TopoRoot improves the state-of-the-art methods in obtaining more accurate and comprehensive fine-grained traits of maize roots from 3D CT images. The automation and efficiency makes TopoRoot suitable for batch processing on a large number of root images. Our method is thus useful for phenomic studies aimed at finding the genetic basis behind root system architecture and the subsequent development of more productive crops.

scholarly journals Phenotyping Root System Architecture of Cotton (Gossypium barbadense L.) Grown Under Salinity

2017 ◽  
Vol 63 (4) ◽  
pp. 142-150 ◽  
Author(s):  
Shady A. Mottaleb ◽  
Essam Darwish ◽  
Menna Mostafa ◽  
Gehan Safwat
Keyword(s):  
Root System ◽  
System Architecture ◽  
Root Length ◽  
Lateral Root ◽  
Lateral Roots ◽  
Root System Architecture ◽  
Gossypium Barbadense ◽  
Shoot Biomass ◽  
Peat Moss ◽  
Main Root

Abstract Soil salinity causes an annual deep negative impact to the global agricultural economy. In this study, the effects of salinity on early seedling physiology of two Egyptian cotton (Gossypium barbadense L.) cultivars differing in their salinity tolerance were examined. Also the potential use of a low cost mini-rhizotron system to measure variation in root system architecture (RSA) traits existing in both cultivars was assessed. Salt tolerant cotton cultivar ‘Giza 90’ produced significantly higher root and shoot biomass, accumulated lower Na+/K+ ratio through a higher Na+ exclusion from both roots and leaves as well as synthesized higher proline contents compared to salt sensitive ‘Giza 45’ cultivar. Measuring RSA in mini-rhizotrons containing solid MS nutrient medium as substrate proved to be more precise and efficient than peat moss/sand mixture. We report superior values of main root growth rate, total root system size, main root length, higher number of lateral roots and average lateral root length in ‘Giza 90’ under salinity. Higher lateral root density and length together with higher root tissue tolerance of Na+ ions in ‘Giza 90’ give it an advantage to be used as donor genotype for desirable root traits to other elite cultivars.

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