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 ◽  
...  

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.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Admas Alemu ◽  
Tileye Feyissa ◽  
Marco Maccaferri ◽  
Giuseppe Sciara ◽  
Roberto Tuberosa ◽  
...  

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.


Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 645 ◽  
Author(s):  
Kumbirai Ivyne Mateva ◽  
Hui Hui Chai ◽  
Sean Mayes ◽  
Festo Massawe

Characterizing the morphological variability in root system architecture (RSA) during the sensitive pre-flowering growth stage is important for crop performance. To assess this variation, eight bambara groundnut single genotypes derived from landraces of contrasting geographic origin were selected for root system architecture and rooting distribution studies. Plants were grown in a polyvinyl chloride (PVC) column system under controlled water and nutrient availability in a rainout shelter. Days to 50% plant emergence was characterized during the first two weeks after sowing, while taproot length (TRL), root length (RL), root length density (RLD), branching number (BN), branching density (BD) and intensity (BI), surface area (SA), root volume (RV), root diameter (RDia), root dry weight (RDW), shoot dry weight (SDW), and shoot height (SH) were determined at the end of the experiment, i.e., 35 days after emergence. Genotypes S19-3 and DipC1 sourced from drier regions of sub-Saharan Africa generally had longer taproots and greater root length distribution in deeper (60 to 90 cm) soil depths. In contrast, bambara groundnut genotypes from wetter regions (i.e., Gresik, Lunt, and IITA-686) in Southeast Asia and West Africa exhibited relatively shallow and highly branched root growth closer to the soil surface. Genotypes at the pre-flowering growth stage showed differential root foraging patterns and branching habits with two extremes, i.e., deep-cheap rooting in the genotypes sourced from dry regions and a shallow-costly rooting system in genotypes adapted to higher rainfall areas with shallow soils. We propose specific bambara groundnut genotype as donors in root trait driven breeding programs to improve water capture and use efficiency.


2020 ◽  
Author(s):  
◽  
Sulaiman Ahmed Ali

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI-COLUMBIA AT REQUEST OF AUTHOR.] Soybean (Glycine max (L.) is currently grown throughout the world because it has been adapted to many environments and because of the high protein and oil content of the seeds. Water scarcity is responsible for the biggest crop losses worldwide and this is expected to worsen; thus, much attention is directed towards the development of drought tolerant crops. The root system is fundamentally important for plant growth and survival because of its role in water and nutrient uptake. Crops with deep roots can capture more soil resources, particularly water, to support shoot growth and yield formation. However, the investigation of root systems is difficult and remains challenging, especially under field conditions. Nonetheless, a better understanding of root system form and function is critical to develop strategies to breed for more stress-resilient crops for local production environments. Studies of soybean root systems in general, and rooting depth in particular have been limited. Thus, the aims of the research described in this dissertation were to (i) identify genotypic diversity in rooting depth and distribution of roots in the soil profile and relate these traits to above ground characteristics including yield under rainfed field conditions in a wide range of soybean genotypes, (ii) characterize, compare and contrast root systems of selected soybean genotypes grown under field- and greenhouse-conditions, and (iii) explore the influence of scion and rootstock genotype on root growth of contrasting soybean genotypes under well-watered and water deficit stress conditions. In the first series of experiments, a set of five soybean genotypes that represented contrasting root rooting depths and root elongation rates were selected based on greenhouse experiment and grown under rainfed field conditions. The core break method was used to assess root distributions of these genotypes in two years. The main goals of this experiment were to confirm genotypic variation for key root traits, including rooting depth and distribution, and to determine whether rooting depth is related to seed yield and selected shoot traits. This study confirmed significant variation among genotypes regarding their rooting depth and root distribution in the soil profile. Genotypes with greater maximum rooting depth also exhibited greater numbers of roots in the lower soil strata than shallower rooting genotypes, and rooting depth was positively correlated with seed yield. Confirmation of differences in rooting depth among these genotypes and the relationship with seed yield under field conditions establishes the suitability of the selected genotypes for physiological studies, studies of genetic mechanisms underpinning maximum rooting depth in soybean, and to confirm the potential for yield increase as a result of selection for deep rooting. A second study consisted of two greenhouse experiments to evaluate the effect of water availability on the rooting depth plasticity of deep- and shallow-rooted genotypes. Six contrasting genotypes were grown in PVC pipes under well-watered and dry-down conditions. The soil media was a mixture of soil and sand with a ratio of 4:1, respectively. Significant genotype, water treatment, and genotype by water treatment interaction effects were observed for maximum rooting depth. Maximum rooting depth increased in the dry-down compared to the well-watered treatment and induced a reallocation of root length from shallow strata to deeper regions in the profile for all genotypes. The extent of the difference in rooting depth between well-watered and dry-down treatments, measured as plasticity, was significantly different among genotypes. Thus, plasticity in maximum rooting depth appears to be under genetic control in soybean and may be a suitable target for breeding efforts aimed at increasing yields under drought. In a final study, the influence of scion and rootstock genotype on shoot growth and root system characteristics was examined in deep tubes in an automated rainout shelter. Plants were sown into 1.5- m deep tubes filled with a soil-sand mix (4:1) and grown under well-watered and dry-down conditions. Nine days after sowing, self and reciprocal grafts were made using the wedge grafting method. The dry-down treatment resulted in significantly increased rooting depth for all grafted as well as the non-grafted treatments compared to well-watered treatment. As expected, root length densities in the top 30 cm of the soil were greater for well-watered plants than plants in the dry-down treatment whereas the opposite was true for root length density at depth. Overall, whether self-grafted or serving as rootstock only, the deep-rooted genotype had a stimulatory effect on root growth in most soil strata, particularly under dry-down conditions. In general, limited differences observed among the grafting treatments suggest a small influence of the scion or rootstock genotype on the rooting depth and root distribution in the soil profile. However, grafting studies with additional genotypes should be conducted to explore whether this observation is specific to the genotype combination used in this study or whether it applies more generally for soybean. The experiments described in this dissertation lay the foundation for additional physiological and genetic studies. Further research is needed to ascertain the physiological mechanism behind the responses of contrasting genotypes, and to identify molecular markers and/or genes to facilitate incorporation of desirable root traits into a breeding program to increase yields and/or yield stability under drought conditions.


2020 ◽  
Author(s):  
Nicolás Gaggion ◽  
Federico Ariel ◽  
Vladimir Daric ◽  
Éric Lambert ◽  
Simon Legendre ◽  
...  

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.


2018 ◽  
Vol 28 (5) ◽  
pp. 629-636 ◽  
Author(s):  
Matthew B. Bertucci ◽  
David H. Suchoff ◽  
Katherine M. Jennings ◽  
David W. Monks ◽  
Christopher C. Gunter ◽  
...  

Grafting of watermelon (Citrullus lanatus) is an established production practice that provides resistance to soilborne diseases or tolerance to abiotic stresses. Watermelon may be grafted on several cucurbit species (interspecific grafting); however, little research exists to describe root systems of these diverse rootstocks. A greenhouse study was conducted to compare root system morphology of nine commercially available cucurbit rootstocks, representing four species: pumpkin (Cucurbita maxima), squash (Cucurbita pepo), bottle gourd (Lagenaria siceraria), and an interspecific hybrid squash (C. maxima × C. moschata). Rootstocks were grafted with a triploid watermelon scion (‘Exclamation’), and root systems were compared with nongrafted (NG) and self-grafted (SG) ‘Exclamation’. Plants were harvested destructively at 1, 2, and 3 weeks after transplant (WAT), and data were collected on scion dry weight, total root length (TRL), average root diameter, root surface area, root:shoot dry-weight ratio, root diameter class proportions, and specific root length. For all response variables, the main effect of rootstock and rootstock species was significant (P < 0.05). The main effect of harvest was significant (P < 0.05) for all response variables, with the exception of TRL proportion in diameter class 2. ‘Ferro’ rootstock produced the largest TRL and root surface area, with observed values 122% and 120% greater than the smallest root system (‘Exclamation’ SG), respectively. Among rootstock species, pumpkin produced the largest TRL and root surface area, with observed values 100% and 82% greater than those of watermelon, respectively. These results demonstrate that substantial differences exist during the initial 3 WAT in root system morphology of rootstocks and rootstock species available for watermelon grafting and that morphologic differences of root systems can be characterized using image analysis.


Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 173
Author(s):  
Vijaya Singh ◽  
Marisa Collins ◽  
Colin Andrew Douglas ◽  
Michael Bell

In recent years phosphorus application methods have become an important management strategy for optimising the uptake of the immobile nutrient phosphorus (P). Root system architecture (RSA) could play a particularly important role in the uptake of P by grain legumes, due to their relatively coarse root systems. The objective of this study was to understand the response of mungbean root systems to P application methods. Four mungbean varieties were grown in purpose-built soil filled root chambers that received five P application methods. Phosphorus treatments consisted of a control (no application of P) compared with 30 mg P/kg soil throughout the soil volume (high P treatment) or restricted to 10cm deep layers in the topsoil or in a layer from 20-30cm deep. A fifth treatment consisted of the same amount of P as applied in deeper dispersed layer applied in a concentrated band at 25cm depth. After 50 days of growth, plant were destructively harvested and shoot and root parameters were measured. Mungbean varieties responded differently to P application methods, with Jade and Berken varieties showing greater root proliferation at depth and greater shoot growth in response to banded and deeper dispersed P applications, relative to the late maturing variety Putland. Shallow dispersed P and the no-P control both resulted in poor root growth in all the genotypes except Celera II, which did not respond to P application from any placement strategy. Results suggest that P application strategies may need to vary with variety to maximize the uptake of P.


Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1328
Author(s):  
Rebecca K. McGrail ◽  
David A. Van Sanford ◽  
David H. McNear

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.


Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1697
Author(s):  
Dinoclaudio Zacarias Rafael ◽  
Osvin Arriagada ◽  
Guillermo Toro ◽  
Jacob Mashilo ◽  
Freddy Mora-Poblete ◽  
...  

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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