scholarly journals Natural Variation and Domestication Selection of ZmCKX5 with Root Morphological Traits at the Seedling Stage in Maize

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 1
Author(s):  
Houmiao Wang ◽  
Hui Sun ◽  
Haofeng Xia ◽  
Tingting Wu ◽  
Pengcheng Li ◽  
...  
Keyword(s):  
Root System ◽  
Root Length ◽  
Root Traits ◽  
Pleiotropic Effect ◽  
Root System Architecture ◽  
Inbred Lines ◽  
Maize Root ◽  
Functional Markers ◽  
Cytokinin Oxidase ◽  
Root Area

Root system architecture plays a crucial role in water and nutrient acquisition in maize. Cytokinins, which can be irreversibly degraded by the cytokinin oxidase/dehydrogenase (CKX), are important hormones that regulate root development in plants. In this study, ZmCKX5 was resequenced in 285 inbred lines, 68 landraces, and 32 teosintes to identify the significant variants associated with root traits in maize. Sequence polymorphisms and nucleotide diversity revealed that ZmCKX5 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 12 variants of ZmCKX5 that were significantly associated with six root traits, including seed root number (SRN), lateral root length (LRL), total root area (RA), root length in 0 to 0.5 mm diameter class (RL005), total root volume (RV), and total root length (TRL). SNP-1195 explained the most (6.01%) phenotypic variation of SRN, and the frequency of this allele G increased from 6.25% and 1.47% in teosintes and landraces, respectively, to 17.39% in inbred lines. Another significant variant, SNP-1406, with a pleiotropic effect, is strongly associated with five root traits, with the frequency of T allele increased from 25.00% and 23.73% in teosintes and landraces, respectively, to 35.00% in inbred lines. These results indicate that ZmCKX5 may be involved in the development of the maize root system and that the significant variants can be used to develop functional markers to accelerate the improvement in the maize root system.

scholarly journals Nucleotide Diversity and Association Analysis of ZmMADS60 with Root Length in the Maize Seedling Stage

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 342
Author(s):  
Pengcheng Li ◽  
Zhenzhen Ge ◽  
Houmiao Wang ◽  
Jie Wei ◽  
Yunyun Wang ◽  
...  
Keyword(s):  
Association Analysis ◽  
Root Length ◽  
Nucleotide Diversity ◽  
Lateral Roots ◽  
Primary Root ◽  
Root System Architecture ◽  
Inbred Lines ◽  
Seedling Stage ◽  
Functional Markers ◽  
Maize Domestication

Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity and natural variations associated with root length. Nucleotide diversity and neutral tests revealed that ZmMADS60 might be selected in domestication and improvement processes. ZmMADS60 in maize retained only 40.1% and 66.9% of the nucleotide diversity found in teosinte and landrace, respectively. Gene-based association analysis of inbred lines identified nine variants that were significantly associated with primary root length (PRL), lateral root length (LRL), root length between 0 mm and 0.5 mm in diameter (RL005) and total root length (TRL). One single-nucleotide polymorphism SNP1357 with pleiotropic effects was significantly associated with LRL, RL005 and TRL. The frequency of the increased allele T decreased from 68.8% in teosintes to 52.9% and 38.9% in the landrace and inbred lines, respectively. The frequency of the increased allele of another significant SNP723 associated with PRL also decreased during the maize domestication and improvement processes. The results of this study reveal that ZmMADS60 may be involved in the elongation of primary and lateral roots in the seedling stage and that significant variants can be used to develop functional markers to improve root length in maize.

scholarly journals Screening of Soybean Genotypes Based on Root Morphology and Shoot Traits Using the Semi-Hydroponic Phenotyping Platform and Rhizobox Technique

Agronomy ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 56
Author(s):  
Mohammad Salim ◽  
Yinglong Chen ◽  
Heng Ye ◽  
Henry T. Nguyen ◽  
Zakaria M. Solaiman ◽  
...  
Keyword(s):  
Root System ◽  
System Architecture ◽  
Root Length ◽  
Specific Root Length ◽  
Root Traits ◽  
Dry Weight ◽  
Root Systems ◽  
Root System Architecture ◽  
Flowering Stage ◽  
Soybean Genotypes

Root-system architecture is vital for improving soybean (Glycine max L.) growth and nutrient uptake. We characterised root-system architecture and shoot traits of 30 soybean genotypes in a semi-hydroponic system 35 days after sowing (DAS) and validated eight genotypes with contrasting root-system architecture in 1.5 m-deep rhizoboxes at the flowering stage. Among them, two genotypes were selected for evaluation through to maturity. Abundant variation (coefficient of variation values ≥ 0.25) was observed in 11 of 13 measured roots and shoot traits during the early growth stage. After late growth stages, strong positive correlations were found between root traits and shoot traits, except for specific root length and diameter. Seed yield and yield traits at final harvest significantly differed between two contrasting soybean genotypes. The large-rooted genotype had a higher harvest index than the small-rooted genotype. Soybean genotypes with larger root systems had a long time to flowering than those with smaller root systems. Genotypes with large-root systems had 106% more leaf area, and 245% more shoot dry weight than those with small systems, presumably due to high canopy photosynthesis to supply the demand for carbon assimilates to roots. Total root length, and root: shoot ratio-traits data collected in the rhizobox study, strongly correlated with the same traits in the semi-hydroponic phenotyping system. We found genetic variation and phenotypic plasticity in other root and shoot traits such as taproot depth, root dry weight, specific root length, and average root diameter among the tested genotypes. Phenology, particularly time to flowering, was associated with root system size. Some root and shoot traits in the semi-hydroponic phenotyping system at the seedling stage produced similar rankings at the later phenological (flowering) stage when grown in the soil-filled rhizoboxes. The soybean genotypes characterised by vastly different root traits could be used for further glasshouse and field studies to improve adaptation to drought and other specific environments.

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.

scholarly journals Shoot and Root Traits Underlying Genotypic Variation in Early Vigor and Nutrient Accumulation in Spring Wheat Grown in High-Latitude Light Conditions

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 174
Author(s):  
Hui Liu ◽  
Fabio Fiorani ◽  
Ortrud Jäck ◽  
Tino Colombi ◽  
Kerstin A. Nagel ◽  
...  
Keyword(s):  
Root System ◽  
Leaf Area ◽  
Spring Wheat ◽  
High Latitude ◽  
Root Length ◽  
Nutrient Use Efficiency ◽  
Root Traits ◽  
Plant Production ◽  
Nutrient Accumulation ◽  
Early Vigor

Plants with improved nutrient use efficiency are needed to maintain and enhance future crop plant production. The aim of this study was to explore candidate traits for pre-breeding to improve nutrient accumulation and early vigor of spring wheat grown at high latitudes. We quantified shoot and root traits together with nutrient accumulation in nine contrasting spring wheat genotypes grown in rhizoboxes for 20 days in a greenhouse. Whole-plant relative growth rate was here correlated with leaf area productivity and plant nitrogen productivity, but not leaf area ratio. Furthermore, the total leaf area was correlated with the accumulation of six macronutrients, and could be suggested as a candidate trait for the pre-breeding towards improved nutrient accumulation and early vigor in wheat to be grown in high-latitude environments. Depending on the nutrient of interest, different root system traits were identified as relevant for their accumulation. Accumulation of nitrogen, potassium, sulfur and calcium was correlated with lateral root length, whilst accumulation of phosphorus and magnesium was correlated with main root length. Therefore, special attention needs to be paid to specific root system traits in the breeding of wheat towards improved nutrient accumulation to counteract the suboptimal uptake of some nutrient elements.

scholarly journals Variability of root traits in common bean genotypes at different levels of phosphorus supply and ontogenetic stages

2014 ◽  
Vol 38 (4) ◽  
pp. 1170-1180 ◽  
Author(s):  
Roberto dos Santos Trindade ◽  
Adelson Paulo Araújo
Keyword(s):  
Common Bean ◽  
Root Length ◽  
Root Traits ◽  
Growth Stages ◽  
Phenotypic Variance ◽  
Root Mass ◽  
Root Area ◽  
Ontogenetic Stages ◽  
Growth Habits ◽  
Selection Of

Selection of common bean (Phaseolus vulgaris L.) cultivars with enhanced root growth would be a strategy for increasing P uptake and grain yield in tropical soils, but the strong plasticity of root traits may compromise their inclusion in breeding programs. The aim of this study was to evaluate the magnitude of the genotypic variability of root traits in common bean plants at two ontogenetic stages and two soil P levels. Twenty-four common bean genotypes, comprising the four growth habits that exist in the species and two wild genotypes, were grown in 4 kg pots at two levels of applied P (20 and 80 mg kg-1) and harvested at the stages of pod setting and early pod filling. Root area and root length were measured by digital image analysis. Significant genotype × P level and genotype × harvest interactions in analysis of variance indicate that the genotypic variation of root traits depended on soil nutrient availability and the stage at which evaluation was made. Genotypes differed for taproot mass, basal and lateral root mass, root area and root length at both P levels and growth stages; differences in specific root area and length were small. Genotypes with growth habits II (upright indeterminate) and III (prostrate indeterminate) showed better adaptation to limited P supply than genotypes of groups I (determinate) and IV (indeterminate climbing). Between the two harvests, genotypes of groups II and III increased the mass of basal and lateral roots by 40 and 50 %, respectively, whereas genotypes of groups I and IV by only 7 and 19 %. Values of the genotypic coefficient of determination, which estimates the proportion of phenotypic variance resulting from genetic effects, were higher at early pod filling than at pod setting. Correlations between shoot mass and root mass, which could indicate indirect selection of root systems via aboveground biomass, were higher at early pod filling than at pod setting. The results indicate that selection for root traits in common bean genotypes should preferentially be performed at the early pod-filling stage.

scholarly journals ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture

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.

scholarly journals MARSHAL, a novel tool for virtual phenotyping of maize root system hydraulic architectures

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Félicien Meunier ◽  
Adrien Heymans ◽  
Xavier Draye ◽  
Valentin Couvreur ◽  
Mathieu Javaux ◽  
...  
Keyword(s):  
Root System ◽  
Web Application ◽  
Root Traits ◽  
Root Systems ◽  
R Package ◽  
Maize Root ◽  
Model Parameters ◽  
System Modelling ◽  
Architecture Model ◽  
System Models

Abstract Functional-structural root system models combine functional and structural root traits to represent the growth and development of root systems. In general, they are characterized by a large number of growth, architectural and functional root parameters, generating contrasted root systems evolving in a highly non-linear environment (soil, atmosphere), which makes the link between local traits and functioning unclear. On the other end of the root system modelling continuum, macroscopic root system models associate to each root system a set of plant-scale, easily interpretable parameters. However, as of today, it is unclear how these macroscopic parameters relate to root-scale traits and whether the upscaling of local root traits is compatible with macroscopic parameter measurements. The aim of this study was to bridge the gap between these two modelling approaches. We describe here the MAize Root System Hydraulic Architecture soLver (MARSHAL), a new efficient and user-friendly computational tool that couples a root architecture model (CRootBox) with fast and accurate algorithms of water flow through hydraulic architectures and plant-scale parameter calculations. To illustrate the tool’s potential, we generated contrasted maize hydraulic architectures that we compared with root system architectural and hydraulic observations. Observed variability of these traits was well captured by model ensemble runs. We also analysed the multivariate sensitivity of mature root system conductance, mean depth of uptake, root system volume and convex hull to the input parameters to highlight the key model parameters to vary for virtual breeding. It is available as an R package, an RMarkdown pipeline and a web application.

scholarly journals Trait-Based Root Phenotyping as a Necessary Tool for Crop Selection and Improvement

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1328
Author(s):  
Rebecca K. McGrail ◽  
David A. Van Sanford ◽  
David H. McNear
Keyword(s):  
Root System ◽  
System Architecture ◽  
Production Systems ◽  
Root Traits ◽  
Root System Architecture ◽  
Root Decomposition ◽  
Crop Breeding ◽  
Organic Acid Production ◽  
Nutritional Qualities ◽  
Chemical Traits

Most of the effort of crop breeding has focused on the expression of aboveground traits with the goals of increasing yield and disease resistance, decreasing height in grains, and improvement of nutritional qualities. The role of roots in supporting these goals has been largely ignored. With the increasing need to produce more food, feed, fiber, and fuel on less land and with fewer inputs, the next advance in plant breeding must include greater consideration of roots. Root traits are an untapped source of phenotypic variation that will prove essential for breeders working to increase yields and the provisioning of ecosystem services. Roots are dynamic, and their structure and the composition of metabolites introduced to the rhizosphere change as the plant develops and in response to environmental, biotic, and edaphic factors. The assessment of physical qualities of root system architecture will allow breeding for desired root placement in the soil profile, such as deeper roots in no-till production systems plagued with drought or shallow roots systems for accessing nutrients. Combining the assessment of physical characteristics with chemical traits, including enzymes and organic acid production, will provide a better understanding of biogeochemical mechanisms by which roots acquire resources. Lastly, information on the structural and elemental composition of the roots will help better predict root decomposition, their contribution to soil organic carbon pools, and the subsequent benefits provided to the following crop. Breeding can no longer continue with a narrow focus on aboveground traits, and breeding for belowground traits cannot only focus on root system architecture. Incorporation of root biogeochemical traits into breeding will permit the creation of germplasm with the required traits to meet production needs in a variety of soil types and projected climate scenarios.

scholarly journals Plasticity of the Root System Architecture and Leaf Gas Exchange Parameters Are Important for Maintaining Bottle Gourd Responses under Water Deficit

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1697
Author(s):  
Dinoclaudio Zacarias Rafael ◽  
Osvin Arriagada ◽  
Guillermo Toro ◽  
Jacob Mashilo ◽  
Freddy Mora-Poblete ◽  
...  
Keyword(s):  
Root System ◽  
Water Deficit ◽  
System Architecture ◽  
Root Length ◽  
Leaf Gas Exchange ◽  
Lateral Roots ◽  
Physiological Responses ◽  
Root System Architecture ◽  
Second Order ◽  
Bottle Gourd

The evaluation of root system architecture (RSA) development and the physiological responses of crop plants grown under water-limited conditions are of great importance. The purpose of this study was to examine the short-term variation of the morphological and physiological plasticity of Lagenaria siceraria genotypes under water deficit, evaluating the changes in the relationship between the root system architecture and leaf physiological responses. Bottle gourd genotypes were grown in rhizoboxes under well-watered and water deficit conditions. Significant genotype-water regime interactions were observed for several RSA traits and physiological parameters. Biplot analyses confirmed that the drought-tolerant genotypes (BG-48 and GC) showed a high net CO2 assimilation rate, stomatal conductance, transpiration rates with a smaller length, and a reduced root length density of second-order lateral roots, whereas the genotypes BG-67 and Osorno were identified as drought-sensitive and showed greater values for average root length and the density of second-order lateral roots. Consequently, a reduced length and density of lateral roots in bottle gourd should constitute a response to water deficit. The root traits studied here can be used to evaluate bottle gourd performance under novel water management strategies and as criteria for breeding selection.

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