Modeling root system growth around obstacles

Abstract State-of-the-Art models of Root System Architecture (RSA) do not allow simulating root growth around rigid obstacles. Yet, the presence of obstacles can be highly disruptive to the root system. We grew wheat seedlings in sealed petri dishes without obstacle and in custom 3D-printed rhizoboxes containing obstacles. Time-lapse photography was used to reconstruct the wheat root morphology network. We used the reconstructed wheat root network without obstacle to calibrate an RSA model implemented in the R-SWMS software. The root network with obstacles allowed calibrating the parameters of a new function that models the influence of rigid obstacles on wheat root growth. Experimental results show that the presence of a rigid obstacle does not affect the growth rate of the wheat root axes, but that it does influence the root trajectory after the main axis has passed the obstacle. The growth recovery time, i.e. the time for the main root axis to recover its geotropism-driven growth, is proportional to the time during which the main axis grows along the obstacle. Qualitative and quantitative comparisons between experimental and numerical results show that the proposed model successfully simulates wheat RSA growth around obstacles. Our results suggest that wheat roots follow patterns that could inspire the design of adaptive engineering flow networks.

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Transcriptomic Analysis Reveals the Contribution of QMrl-7B to Wheat Root Growth and Development

10.21203/rs.3.rs-124839/v1 ◽

2020 ◽

Author(s):

Jiajia Liu ◽

Hanwen Li ◽

Na Zhang ◽

Deyuan Meng ◽

Liya Zhi ◽

...

Keyword(s):

Root Growth ◽

Root System ◽

Root Traits ◽

Wheat Root ◽

Root System Architecture ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Yield Potential ◽

Trait Locus ◽

Normal Nitrogen

Abstract Backgound: Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for increasing yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), strongly contributes to an improved root system in wheat. Results: To further analyse the biological functions of QMrl-7B in root development, two types of Triticum aestivum near isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411), were subjected to transcriptomic analysis. Among all the mapped genes analysed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that include mainly NO3- transporters, phytohormone signalling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this assay, 4308 were specifically expressed in the A-NIL which brings superior alleles, and 2463 were expressed specifically in the B-NIL which brings inferior alleles. These DEGs reflect different responses of the two types of NILs to varying N supplies, which likely involve LN-induced root growth. Conclusions: These results explain the better-developed root system and increased root vitality provided by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.

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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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Root growth of lupins is more sensitive to waterlogging than wheat

Functional Plant Biology ◽

10.1071/fp11148 ◽

2011 ◽

Vol 38 (11) ◽

pp. 910 ◽

Cited By ~ 12

Author(s):

Helen Bramley ◽

Stephen D. Tyerman ◽

David W. Turner ◽

Neil C. Turner

Keyword(s):

Root Growth ◽

Oxygen Deficiency ◽

Triticum Aestivum L ◽

Wheat Root ◽

Lupinus Luteus ◽

Apical Region ◽

Basal Region ◽

Yellow Lupin ◽

Wheat Roots ◽

Root Death

In south-west Australia, winter grown crops such as wheat and lupin often experience transient waterlogging during periods of high rainfall. Wheat is believed to be more tolerant to waterlogging than lupins, but until now no direct comparisons have been made. The effects of waterlogging on root growth and anatomy were compared in wheat (Triticum aestivum L.), narrow-leafed lupin (Lupinus angustifolius L.) and yellow lupin (Lupinus luteus L.) using 1 m deep root observation chambers. Seven days of waterlogging stopped root growth in all species, except some nodal root development in wheat. Roots of both lupin species died back progressively from the tips while waterlogged. After draining the chambers, wheat root growth resumed in the apical region at a faster rate than well-drained plants, so that total root length was similar in waterlogged and well-drained plants at the end of the experiment. Root growth in yellow lupin resumed in the basal region, but was insufficient to compensate for root death during waterlogging. Narrow-leafed lupin roots did not recover; they continued to deteriorate. The survival and recovery of roots in response to waterlogging was related to anatomical features that influence internal oxygen deficiency and root hydraulic properties.

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Root plasticity under abiotic stress

Plant Physiology ◽

10.1093/plphys/kiab392 ◽

2021 ◽

Author(s):

Rumyana Karlova ◽

Damian Boer ◽

Scott Hayes ◽

Christa Testerink

Keyword(s):

Abiotic Stress ◽

Root Growth ◽

Root System ◽

System Architecture ◽

Root System Architecture ◽

Root Anatomy ◽

Soil Conditions ◽

Root Plasticity ◽

Cellular Mechanisms ◽

Aerenchyma Formation

Abstract Abiotic stresses increasingly threaten existing ecological and agricultural systems across the globe. Plant roots perceive these stresses in the soil and adapt their architecture accordingly. This review provides insights into recent discoveries showing the importance of root system architecture and plasticity for the survival and development of plants under heat, cold, drought, salt, and flooding stress. In addition, we review the molecular regulation and hormonal pathways involved in controlling root system architecture plasticity, main root growth, branching and lateral root growth, root hair development and formation of adventitious roots. Several stresses affect root anatomy by causing aerenchyma formation, lignin and suberin deposition, and Casparian strip modulation. Roots can also actively grow towards favourable soil conditions and avoid environments detrimental to their development. Recent advances in understanding the cellular mechanisms behind these different root tropisms are discussed. Understanding root plasticity will be instrumental for the development of crops that are resilient in the face of abiotic stress.

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Chickpea (Cicer arietinum L.) root system architecture adaptation to initial soil moisture improves seed development in dry-down conditions

10.1101/2020.09.24.311753 ◽

2020 ◽

Author(s):

Thibaut Bontpart ◽

Ingrid Robertson ◽

Valerio Giuffrida ◽

Cristobal Concha ◽

Livia C. T. Scorza ◽

...

Keyword(s):

Soil Moisture ◽

Root Growth ◽

Root System ◽

Seed Development ◽

Water Use ◽

System Architecture ◽

Adaptive Strategies ◽

Root System Architecture ◽

Initial Soil Moisture ◽

Initial Soil

AbstractSoil water deficit (WD) impacts vascular plant phenology, morpho-physiology, and reproduction. Chickpea, which is mainly grown in semi-arid areas, is a good model plant to dissect mechanisms involved in drought resistance.We used a rhizobox-based phenotyping system to simultaneously and non-destructively characterise root system architecture (RSA) dynamics and water use (WU) patterns. We compared the drought-adaptive strategies of ‘Teketay’ to the drought-sensitive genotype ICC 1882 in high and low initial soil moisture without subsequent irrigation.WD restricted vegetative and reproductive organ biomass for both genotypes. Teketay displayed greater adaptability for RSA dynamics and WU patterns and revealed different drought adaptive strategies depending on initial soil moisture: escape when high, postponement when low. These strategies were manifested in distinct RSA dynamics: in low initial soil moisture, its reduced root growth at the end of the vegetative phase was followed by increased root growth in deeper, wetter soil strata, which facilitated timely WU for seed development and produced better-developed seeds.We demonstrate that RSA adaptation to initial soil moisture is one mechanism by which plants can tolerate WD conditions and ensure reproduction by producing well-developed seeds. Our approach will help in identifying the genetic basis for large plasticity of RSA dynamics which enhances the resilience with which crops can optimally adapt to various drought scenarios.HighlightRoot system architecture and water use patterns change dynamically for distinct drought adaptation strategies in chickpea.

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Root growth and root system architecture of field-grown maize in response to high planting density

Plant and Soil ◽

10.1007/s11104-018-3720-8 ◽

2018 ◽

Vol 430 (1-2) ◽

pp. 395-411 ◽

Cited By ~ 18

Author(s):

Hui Shao ◽

Tingting Xia ◽

Dali Wu ◽

Fanjun Chen ◽

Guohua Mi

Keyword(s):

Root Growth ◽

Root System ◽

System Architecture ◽

Root System Architecture ◽

Planting Density

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Genetic Bases of Root System Architecture in Durum Wheat Seedlings

International Journal of Life Sciences ◽

10.3126/ijls.v10i1.14504 ◽

2016 ◽

Vol 10 (1) ◽

pp. 25-28

Author(s):

Ghasemali Nazemi ◽

Silvio Salvi

Keyword(s):

Durum Wheat ◽

Root System ◽

System Architecture ◽

Root Length ◽

Recombinant Inbred Lines ◽

Primary Root ◽

Root System Architecture ◽

Total Root Length ◽

Wheat Seedlings ◽

Significant Difference

Root system architecture (RSA) traits are characterized by constitutive genetic inheritance components which may enable to predict the root phenotypes based on genetic information. The research presented in this study aimed at the identification of traits and genes that underlie root system architecture (RSA) in a population of 176 recombinant inbred lines (RILs) derived from the cross between two durum wheat cvs. Meridiana and Claudio, in order to eventually contribute to the genetic improvement of this species. The following seedling-stage RSA traits were: primary root length, seminal root length, total root length, diameter of primary and seminal roots. Results of ANOVA showed a significant difference among durum wheat cultivars for all traits and the largest heritability was observed for total root length (30.7%). In total, 14 novel QTLs for RSA traits were identified, and both parents contributed favorable alleles to the population.International Journal of Life Sciences 10 (1) : 2016; 25-28

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Alleviatory effects of Silicon on the morphology, physiology, and antioxidative mechanisms of wheat (Triticum aestivum L.) roots under cadmium stress in acidic nutrient solutions

Scientific Reports ◽

10.1038/s41598-020-80808-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shafeeq ur Rahman ◽

Qi Xuebin ◽

Zhijuan Zhao ◽

Zhenjie Du ◽

Muhammad Imtiaz ◽

...

Keyword(s):

Root Growth ◽

Nutrient Solution ◽

Essential Element ◽

Cadmium Stress ◽

Wheat Seedling ◽

Triticum Aestivum L ◽

Wheat Root ◽

Vital Role ◽

Acidic Ph ◽

Wheat Roots

AbstractSilicon (Si), as a quasi-essential element, has a vital role in alleviating the damaging effects of various environmental stresses on plants. Cadmium (Cd) stress is severe abiotic stress, especially in acidic ecological conditions, and Si can demolish the toxicity induced by Cd as well as acidic pH on plants. Based on these hypotheses, we demonstrated 2-repeated experiments to unfold the effects of Si as silica gel on the root morphology and physiology of wheat seedling under Cd as well as acidic stresses. For this purpose, we used nine treatments with three levels of Si nanoparticles (0, 1, and 3 mmol L−1) derived from sodium silicate (Na2SiO3) against three concentrations of Cd (0, 50, and 200 µmol L−1) in the form of cadmium chloride (CdCl2) with three replications were arranged in a complete randomized design. The pH of the nutrient solution was adjusted at 5. The averages of three random replications showed that the mutual impacts of Si and Cd in acidic pH on wheat roots depend on the concentrations of Si and Cd. The collective or particular influence of low or high levels of Si (1 or 3 mM) and acidic pH (5) improved the development of wheat roots, and the collective influence was more significant than that of a single parallel treatment. The combined effects of low or high concentrations of Cd (50 or 200 µM) and acidic pH significantly reduced root growth and biomass while increased antioxidants, and reactive oxygen species (ROS) contents. The incorporation of Si (1 or 3 mmol L−1) in Cd-contaminated acidic nutrient solution promoted the wheat root growth, decreased ROS contents, and further increased the antioxidants in the wheat roots compared with Cd single treatments in acidic pH. The demolishing effects were better with a high level of Si (3 mM) than the low level of Si (1 Mm). In conclusion, we could suggest Si as an effective beneficial nutrient that could participate actively in several morphological and physiological activities of roots in wheat plants grown under Cd and acidic pH stresses.

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Understanding Root Biology for Enhancing Cotton Production

10.5772/intechopen.95547 ◽

2021 ◽

Author(s):

Jayant H. Meshram ◽

Sunil S. Mahajan ◽

Dipak Nagrale ◽

Nandini Gokte-Narkhedkar ◽

Harish Kumbhalkar

Keyword(s):

Root Growth ◽

Root System ◽

Abiotic Stresses ◽

Root Length Density ◽

Plant Root ◽

Root System Architecture ◽

Cotton Production ◽

Tap Root ◽

Commercial Crop ◽

Environmental Responses

Cotton is an important commercial crop grown in India. It occupies an area of about 12.7 million hectares and is grown both in irrigated as well as rainfed tracts. In such situations, roots are very important organ for plant growth and development, since they act as anchors, providing mechanical support, and chemical extractors for the growing plant. Root length density sets the proportion of water uptake both under wet conditions and dry soils. Cotton plants with efficient root system capture water and nutrients from soil having these features of longer tap root. It is widely accepted that breeding efforts on aboveground traits are not sufficient to the necessary yield advantage. Shifting the emphasis to analyzing the root system would provide an additional means to enhance yield under changing climatic condition. Belowground image analysis studies point to the importance of root system architecture for optimizing roots and rhizosphere dynamics for sustainable cotton production. In this review, we describe the cotton root biological context in which root-environment interactions providing an overview of the root growth morphology species wise, phytohormone action that control root growth, root anatomical significance in drying soils, biotic and abiotic stresses involved in controlling root growth and environmental responses.

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Disruption of CYCLOPHILIN 38 function reveals a photosynthesis-dependent systemic signal controlling lateral root emergence

10.1101/2020.03.11.985820 ◽

2020 ◽

Author(s):

Lina Duan ◽

Juan Manuel Pérez-Ruiz ◽

Francisco Javier Cejudo ◽

José R. Dinneny

Keyword(s):

Root Growth ◽

Root System ◽

Lateral Root ◽

System Development ◽

Lateral Roots ◽

Primary Root ◽

Root System Architecture ◽

Minor Effect ◽

Low Light ◽

Primary Root Growth

AbstractPhotosynthesis in leaves generates the fixed-carbon resources and essential metabolites that support sink tissues, such as roots [1]. One of these products, sucrose, is known to promote primary root growth, but it is not clear what other molecules may be involved and whether other stages of root system development are affected by photosynthate levels [2]. Through a mutant screen to identify pathways regulating root system architecture, we identified a mutation in the CYCLOPHILIN 38 (CYP38) gene, which causes an accumulation of pre-emergent stage lateral roots, with a minor effect on primary root growth. CYP38 was previously reported to maintain the stability of Photosystem II (PSII) in chloroplasts [3]. CYP38 expression is enriched in the shoot and grafting experiments show that the gene acts non-cell autonomously to promote lateral root emergence. Growth of wild-type plants under low light conditions phenocopied the cyp38 lateral root emergence phenotype as did the inhibition of PSII-dependent electron transport or NADPH production. Importantly, the cyp38 root phenotype is not rescued by exogenous sucrose, suggesting the involvement of another metabolite. Auxin (IAA) is an essential hormone promoting root growth and its biosynthesis from tryptophan is dependent on reductant generated during photosynthesis [4,5]. Both WT seedlings grown under low light and cyp38 mutants have highly diminished levels of IAA in root tissues. The cyp38 lateral root defect is rescued by IAA treatment, revealing that photosynthesis promotes lateral root emergence partly through IAA biosynthesis. Metabolomic profiling shows that the accumulation of several defense-related metabolites are also photosynthesis-dependent, suggesting that the regulation of a number of energy-intensive pathways are down-regulated when light becomes limiting.

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