scholarly journals Spatial and Texture Analysis of Root System Architecture with Earth Mover's Distance

2021 ◽  
Author(s):  
Joshua Peeples ◽  
Weihuang Xu ◽  
Romain Gloaguen ◽  
Diane Rowland ◽  
Alina Zare ◽  
...  
Keyword(s):  
Root System ◽  
Texture Analysis ◽  
System Architecture ◽  
Spatial Information ◽  
Growth Conditions ◽  
Root System Architecture ◽  
Earth Mover’S Distance ◽  
System Architectures ◽  
Earth Mover's Distance ◽  
Experimental Treatments

Root system architectures are complex, multidimensional, and challenging to characterize effectively for agronomic and ecological discovery. We propose a new method, Spatial and Texture Analysis of Root System architEcture with Earth mover's Distance (STARSEED), for comparing root architectures that incorporate spatial information through a novel application of the Earth Mover's Distance (EMD). We illustrate that the approach captures the response of sesame root systems for different genotypes and soil moisture levels. STARSEED provides quantitative and visual insights into changes that occur in root architectures across experimental treatments. STARSEED can be easily generalized to other plants and provides insight into root system architecture development and response to varying growth conditions not captured by existing root architecture metrics and models. The code and data for our experiments are publicly available https://github.com/GatorSense/STARSEED.

scholarly journals Spatial and Texture Analysis of Root System Architecture with Earth Mover's Distance (STARSEED)

2021 ◽  
Author(s):  
Joshua Peeples ◽  
Weihuang Xu ◽  
Romain Gloaguen ◽  
Diane Rowland ◽  
Alina Zare ◽  
...  
Keyword(s):  
Root System ◽  
Texture Analysis ◽  
System Architecture ◽  
Spatial Information ◽  
Growth Conditions ◽  
Root System Architecture ◽  
Earth Mover’S Distance ◽  
System Architectures ◽  
Earth Mover's Distance ◽  
Architecture Development

Abstract Root system architectures are complex, multidimensional, and challenging to characterize effectively for agronomic and ecological discovery. We propose a new method, Spatial and Texture Analysis of Root System architEcture with Earth mover's Distance (STARSEED), for comparing root architectures that incorporate spatial information through a novel application of the Earth Mover's Distance (EMD).We illustrate that the approach captures the response of sesame root systems for different genotypes and soil moisture levels. STARSEED provides quantitative and visual insights into changes that occur in root architectures across experimental treatments.STARSEED can be easily generalized to other plants and provides insight into root system architecture development and response to varying growth conditions not captured by existing root architecture metrics and models. The code and data for our experiments are publicly available: https://github.com/GatorSense/STARSEED.

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 Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Admas Alemu ◽  
Tileye Feyissa ◽  
Marco Maccaferri ◽  
Giuseppe Sciara ◽  
Roberto Tuberosa ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Root System ◽  
System Architecture ◽  
Root Length ◽  
Dry Weight ◽  
Root System Architecture ◽  
High Density ◽  
Soil Conditions ◽  
Root Dry Weight ◽  
Seminal Roots

Abstract Background Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina. Results Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (− log10P ≥ 4) and 34 nominal (− log10P ≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight). Conclusions After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions.

Changes induced by lead in root system architecture of Arabidopsis seedlings are mediated by PDR2-LPR1/2 phosphate dependent way

BioMetals ◽  
2021 ◽  
Author(s):  
Ricardo Ortiz-Luevano ◽  
José López-Bucio ◽  
Miguel Martínez-Trujillo ◽  
Lenin Sánchez-Calderón
Keyword(s):  
Root System ◽  
System Architecture ◽  
Root System Architecture

scholarly journals Root System Architecture Plasticity of Bread Wheat in Response to Oxidative Burst under Extended Osmotic Stress

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 939
Author(s):  
Omar Azab ◽  
Abdullah Al-Doss ◽  
Thobayet Alshahrani ◽  
Salah El-Hendawy ◽  
Adel M. Zakri ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Membrane Potential ◽  
Osmotic Stress ◽  
Root System ◽  
Bread Wheat ◽  
System Architecture ◽  
Mitochondrial Membrane ◽  
Root System Architecture ◽  
Root Tips ◽  
Scavenging Capacity

There is a demand for an increase in crop production because of the growing population, but water shortage hinders the expansion of wheat cultivation, one of the most important crops worldwide. Polyethylene glycol (PEG) was used to mimic drought stress due to its high osmotic potentials generated in plants subjected to it. This study aimed to determine the root system architecture (RSA) plasticity of eight bread wheat genotypes under osmotic stress in relation to the oxidative status and mitochondrial membrane potential of their root tips. Osmotic stress application resulted in differences in the RSA between the eight genotypes, where genotypes were divided into adapted genotypes that have non-significant decreased values in lateral roots number (LRN) and total root length (TRL), while non-adapted genotypes have a significant decrease in LRN, TRL, root volume (RV), and root surface area (SA). Accumulation of intracellular ROS formation in root tips and elongation zone was observed in the non-adapted genotypes due to PEG-induced oxidative stress. Mitochondrial membrane potential (∆Ψm) was measured for both stress and non-stress treatments in the eight genotypes as a biomarker for programmed cell death as a result of induced osmotic stress, in correlation with RSA traits. PEG treatment increased scavenging capacity of the genotypes from 1.4-fold in the sensitive genotype Gemmiza 7 to 14.3-fold in the adapted genotype Sakha 94. The adapted genotypes showed greater root trait values, ∆Ψm plasticity correlated with high scavenging capacity, and less ROS accumulation in the root tissue, while the non-adapted genotypes showed little scavenging capacity in both treatments, accompanied by mitochondrial membrane permeability, suggesting mitochondrial dysfunction as a result of oxidative stress.

scholarly journals Biochar induced improvement in root system architecture enhances nutrient assimilation by cotton plant seedlings

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lei Feng ◽  
Wanli Xu ◽  
Guangmu Tang ◽  
Meiying Gu ◽  
Zengchao Geng
Keyword(s):  
Root System ◽  
System Architecture ◽  
Fine Roots ◽  
Nitrogen Assimilation ◽  
Surface Soil ◽  
Soil Layer ◽  
Root System Architecture ◽  
Seedling Stage ◽  
Agronomic Efficiency ◽  
Surface Soil Layer

Abstract Background Raising nitrogen use efficiency of crops by improving root system architecture is highly essential not only to reduce costs of agricultural production but also to mitigate climate change. The physiological mechanisms of how biochar affects nitrogen assimilation by crop seedlings have not been well elucidated. Results Here, we report changes in root system architecture, activities of the key enzymes involved in nitrogen assimilation, and cytokinin (CTK) at the seedling stage of cotton with reduced urea usage and biochar application at different soil layers (0–10 cm and 10–20 cm). Active root absorption area, fresh weight, and nitrogen agronomic efficiency increased significantly when urea usage was reduced by 25% and biochar was applied in the surface soil layer. Glutamine oxoglutarate amino transferase (GOGAT) activity was closely related to the application depth of urea/biochar, and it increased when urea/biochar was applied in the 0–10 cm layer. Glutamic-pyruvic transaminase activity (GPT) increased significantly as well. Nitrate reductase (NR) activity was stimulated by CTK in the very fine roots but inhibited in the fine roots. In addition, AMT1;1, gdh3, and gdh2 were significantly up-regulated in the very fine roots when urea usage was reduced by 25% and biochar was applied. Conclusion Nitrogen assimilation efficiency was significantly affected when urea usage was reduced by 25% and biochar was applied in the surface soil layer at the seedling stage of cotton. The co-expression of gdh3 and gdh2 in the fine roots increased nitrogen agronomic efficiency. The synergistic expression of the ammonium transporter gene and gdh3 suggests that biochar may be beneficial to amino acid metabolism.

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.

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