Research on the Construction and Visualization of a Three-Dimensional Model of Rice Root Growth

2020 ◽  
Vol 36 (6) ◽  
pp. 847-857
Author(s):  
Le   Yang ◽  
Panpan   Wu ◽  
Suyong   Yang ◽  
Peng   Shao
Keyword(s):  
Root Growth ◽  
Growth Model ◽  
Three Dimensional ◽  
Morphological Characteristics ◽  
Rice Root ◽  
Model Output ◽  
Rice Roots ◽  
L System ◽  
Growth Laws ◽  
Dynamic Growth

HighlightsThis article proposes a three-dimensional rice root growth model based on the differential L-system.We tested the accuracy of the model output, and the measured values and the simulated values were compared.A three-dimensional visualization of the growth simulation system was implemented, and the dynamic growth process of rice roots was visually reproduced.Abstract. Three-dimensional visualization studies on the morphological characteristics of rice root systems are important for improving farmland management and for the selective breeding and genetic improvement of rice. To clarify the rules governing the structure and distribution of rice roots, the three-dimensional (3D) coordinates and morphological parameters of rice roots were measured in hydroponic experiments at different growing periods, and the rice root structure was measured with a high degree of accuracy. The initial position, growth direction, and rate were then determined via statistical analysis of the data. In this article, a 3D rice root growth model based on the differential L-system is proposed; in this system, the biological characteristics based on the topological structure and the actual growth laws of rice roots are quantified. We adopted the growing degree day (GDD) as the driving factor that describes the growth law of rice roots and tested the accuracy of the model output. In this model, a 3D visualization of the growth simulation system of rice roots is implemented via Visual C++ and the OpenGL standard library on the basis of algorithms for the constructed 3D rice root growth model. The model output realistically recreates the dynamic growth process of rice roots under different conditions. A large amount of experimental data and comparative analysis show that the average accuracies achieved by the proposed system concerning total root length, root surface area and root volume are 96.95%, 95.97%, and 93.98%, respectively. These results verify the high reliability of the constructed model and the effective simulation of the morphological characteristics and growth laws of rice roots at different growth periods, laying the foundation for future research on the laws of changes in morphological structure and the physiological and ecological factors of rice roots at different growth stages. Keywords: Differential L-system, Rice roots, Simulation, Three-dimensional growth model, Visualization.

scholarly journals Adaptation Mechanism of Roots to Low and High Nitrogen Revealed by Proteomic Analysis

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Jiping Gao ◽  
Wenzhong Zhang ◽  
Jun Yi ◽  
...  
Keyword(s):  
Root Growth ◽  
Nitrogen Use Efficiency ◽  
Root Morphology ◽  
Nitrogen Availability ◽  
Rice Root ◽  
Global Changes ◽  
High Nitrogen ◽  
Nitrogen Use ◽  
Rice Roots ◽  
Use Efficiency

Abstract Background Nitrogen-based nutrients are the main factors affecting rice growth and development. Root systems play an important role in helping plants to obtain nutrients from the soil. Root morphology and physiology are often closely related to above-ground plant organs performance. Therefore, it is important to understand the regulatory effects of nitrogen (N) on rice root growth to improve nitrogen use efficiency. Results In this study, changes in the rice root traits under low N (13.33 ppm), normal N (40 ppm) and high N (120 ppm) conditions were performed through root morphology analysis. These results show that, compared with normal N conditions, root growth is promoted under low N conditions, and inhibited under high N conditions. To understand the molecular mechanism underlying the rice root response to low and high N conditions, comparative proteomics analysis was performed using a tandem mass tag (TMT)-based approach, and differentially abundant proteins (DAPs) were further characterized. Compared with normal N conditions, a total of 291 and 211 DAPs were identified under low and high N conditions, respectively. The abundance of proteins involved in cell differentiation, cell wall modification, phenylpropanoid biosynthesis, and protein synthesis was differentially altered, which was an important reason for changes in root morphology. Furthermore, although both low and high N can cause nitrogen stress, rice roots revealed obvious differences in adaptation to low and high N. Conclusions These results provide insights into global changes in the response of rice roots to nitrogen availability and may facilitate the development of rice cultivars with high nitrogen use efficiency through root-based genetic improvements.

scholarly journals An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability

2019 ◽  
Vol 20 (23) ◽  
pp. 5893 ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Wenzhong Zhang ◽  
Jiping Gao ◽  
Jun Yi ◽  
...  
Keyword(s):  
Root Growth ◽  
Differentially Expressed Genes ◽  
Nitrogen Availability ◽  
Rice Root ◽  
Integrated Analysis ◽  
High Nitrogen ◽  
Rice Roots ◽  
Regulation Mechanisms ◽  
Low Nitrogen ◽  
Nitrogen Conditions

Nitrogen is an essential nutrient for plant growth and basic metabolic processes. Root systems play an important role in the ability of plants to obtain nutrients from the soil, and are closely related to the growth and development of above-ground plants. Root morphology analysis showed that root growth was induced under low-nitrogen conditions and inhibited under high-nitrogen conditions. To better understand the molecular mechanisms and metabolic basis underlying the rice root response to nitrogen availability, an integrated analysis of the rice root transcriptome and metabolome under three environmental conditions (low-, control, and high-nitrogen conditions) was conducted. A total of 262 and 262 differentially level metabolites were identified under low- and high-nitrogen conditions, respectively. A total of 696 and 808 differentially expressed genes were identified under low- and high-nitrogen conditions, respectively. For both the differentially expressed genes and metabolites, KEGG pathway analysis indicated that amino acid metabolism, carbon and nitrogen metabolism, phenylpropanoid metabolism, and phytohormones’ signal transduction were significantly affected by nitrogen availability. Additionally, variable levels of 65 transcription factors (TFs) were identified in rice leaves exposed to high and low nitrogen, covering 22 TF families. These results also indicate that there is a significant difference in the transcriptional regulation mechanisms of rice roots between low and high nitrogen. In summary, our study provides new information for a further understanding of the response of rice roots to low-nitrogen and high-nitrogen conditions.

scholarly journals Modeling and Visualization of Rice Root Based on Morphological Parameters

2019 ◽  
Author(s):  
Le Yang ◽  
Peng Shao
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Morphological Structure ◽  
Growth Function ◽  
Growth Characteristics ◽  
Rice Root ◽  
Morphological Parameters ◽  
Rice Roots ◽  
Spline Curves ◽  
Growth Change

AbstractTo clarify the morphological distributional characteristic of rice roots, the “root box” experiments are conducted to extract various morphological parameters of roots. On the basis of experiments, in this paper, the rice root model based on morphological parameters is constructed with B-spline curves by analyzing the topological structure of rice roots, quantifying their biological characteristics, summarizing the morphological structure and growth characteristics and improving the Cubic growth function to describe the growth change of rice roots. Meanwhile, the output accuracy of the model is tested. Finally, the dynamic simulation of rice root growth characteristics in three-dimensional space is implemented by using Visual C++ and OpenGL standard graphics library. The compared results demonstrate that the model could faithfully simulate the dynamic growing process of rice roots, and help to enrich the methods of digitization and visualization for roots of other crops.

scholarly journals A novel missense variant of the GNAI3 gene and recognisable morphological characteristics of the mandibula in ARCND1

2021 ◽  
Author(s):  
Kumiko Yanagi ◽  
Noriko Morimoto ◽  
Manami Iso ◽  
Yukimi Abe ◽  
Kohji Okamura ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Morphological Characteristics ◽  
Missense Variant ◽  
Nucleotide Binding ◽  
Sequencing Analysis ◽  
Guanine Nucleotide ◽  
Guanine Nucleotide Binding Protein ◽  
Computer Tomography Scan ◽  
Novel Variant ◽  
Guanine Nucleotide Binding

AbstractAuriculocondylar syndrome (ARCND) is an autosomal monogenic disorder characterised by external ear abnormalities and micrognathia due to hypoplasia of the mandibular rami, condyle and coronoid process. Genetically, three subtypes of ARCND (ARCND1, ARCND2 and ARCND3) have been reported. To date, five pathogenic variants of GNAI3 have been reported in ARCND1 patients. Here, we report a novel variant of GNAI3 (NM_006496:c.807C>A:p.(Asn269Lys)) in a Japanese girl with micrognathia using trio-based whole exome sequencing analysis. The GNAI3 gene encodes a heterotrimeric guanine nucleotide-binding protein. The novel variant locates the guanine nucleotide-binding site, and the substitution was predicted to interfere with guanine nucleotide-binding by in silico structural analysis. Three-dimensional computer tomography scan, or cephalogram, displayed severely hypoplastic mandibular rami and fusion to the medial and lateral pterygoid plates, which have been recognised in other ARCND1 patients, but have not been described in ARCND2 and ARCND3, suggesting that these may be distinguishable features in ARCND1.

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