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From lab to field, new approaches to phenotyping root system architecture
Abstract
Plant root system architecture (RSA) is plastic and dynamic, allowing plants to respond to their environment in order to optimize acquisition of important soil resources. A number of RSA traits are known to be correlated with improved crop performance. There is increasing recognition that future gains in productivity, especially under low input conditions, can be achieved through optimization of RSA. However, realization of this goal has been hampered by low resolution and low throughput approaches for characterizing RSA. To overcome these limitations, new methods are being developed to facilitate high throughput and high content RSA phenotyping. Here we summarize laboratory and field approaches for phenotyping RSA, drawing particular attention to recent advances in plant imaging and analysis. Improvements in phenotyping will facilitate the genetic analysis of RSA and aid in the identification of the genetic loci underlying useful agronomic traits.
... The plant roots are essential for its growth, development and strength, and they serve as the shoot support and anchor. They are responsible for nutrition and water absorption and are site of biosynthesis of important hormones necessary for the development and are involved in interactions with the rhizosphere (Zhu et al. 2011). Plant root system consists of four different types of roots, i.e., coarse or taproots (first root to emerge from the seed), lateral roots (any root branching from another root), shoot-borne roots (roots which arise from shoot tissues) and basal roots (roots which develop from the hypocotyl) (Table 1) (Wasaya et al. 2018). ...
... Breeding efforts have traditionally concentrated on enhancing aboveground features with a clear emphasis on yield for practical reasons. While these efforts have been instrumental in increasing crop production to present capacity, future yield increase is likely to be constrained by lower water and fertilizer inputs and the use of marginal lands containing nutrient-poor soils (Zhu et al. 2011). Crop roots system could vary genetically, but crop improvement programs have not yet fully taken advantage of this system, but partly because it is challenging to monitor root growth in soil. ...
... A better understanding of root and rhizosphere processes can therefore essentially contribute to enhancing resource efficiency in crop production and sustainable soil management (Bodner et al. 2018). Due to the heritability of yield tends to decrease under stress conditions but the directed modification of RSA holds promise for improving agricultural productivity under low-input conditions (Zhu et al. 2011;Kephe et al. 2021). ...
Roots are important organs associated with water and nutrient uptake from soil to all the plant parts. Besides plant metabolite storage organ, it also provides anchorage and mechanical support. The root "hidden half" plays a decisive role in root system architecture trait to affect grain yield and abiotic stress tolerance. Genetic study of root trait harbored due to the complex nature of root and unavailability of the rhizosphere. Identification of root system architecture provides a basic understanding of plant fitness, crop performance and grain yield. With increasing interest in root phenotyping, breeders overcome these barriers through the development of advanced phenotyping platforms based on field, laboratories and greenhouses such as soil coring, hydroponics, GLO-roots, rhizotron and mini-rhizotron. The advanced 2-D, 3-D and 4-D root imaging techniques such as magnetic resonance technique, RGB imaging, infrared thermal imaging and X-ray computed tomography are complex , but it gives the most desirable and accurate results to understand the root system architecture. This review focused on root architecture studies methods for root phenotyping using advanced recent techniques.
... Roots, however, are the major route for water and nutrient uptake in plants, and they may also serve as storage organs for carbohydrates, as well as the direct sensing organ of soil stress (Zhu et al., 2011). Root morphology and root physiological functions change under soil stress (Ho et al., 2004;Zhu et al., 2005;Reynolds et al., 2007;York et al., 2013;Al-Tamimi et al., 2016). ...
... Non-soil matrix systems can easily achieve the direct quantification of root morphology and allow the non-invasive imaging analysis of numerous roots in a short time. However, non-soil technology cannot completely mimic the effects of soil on root development (Bengough et al., 2004;Hargreaves et al., 2009) and may even introduce unwanted variables such as hypoxia and bacterial growth (Zhu et al., 2011). To solve these problems, several groups have developed root phenotyping methods specifically designed for soil-grown plants. ...
... Advances in X-ray CT and magnetic resonance imaging (MRI) now allow non-invasive three-dimensional (3D) imaging of crop roots grown in opaque substrates that can quantify root system characteristics (Perret et al., 2007;Tracy et al., 2010;Clark et al., 2011;Mairhofer et al., 2013;Metzner et al., 2015;Pfeifer et al., 2015;Rogers et al., 2016;van Dusschoten et al., 2016). However, the high cost of CT and MRI equipment and the long scanning time needed for individual samples limit the application of these approaches in high-throughput root phenotyping platforms Zhu et al., 2011). Therefore, developing a high-throughput soil cultivation and whole-plant phenotyping system suitable for crop soil stress research remains a largely unfinished task. ...
Soil stress, such as salinity, is a primary cause of global crop yield reduction. Existing crop phenotyping platforms cannot fully meet the specific needs of phenomics studies of plant response to soil stress in terms of throughput, environmental controllability, or root phenotypic acquisition. Here, we report the WinRoots, a low-cost and high-throughput plant soil cultivation and phenotyping system that can provide uniform, controlled soil stress conditions and accurately quantify the whole-plant phenome, including roots. Using soybean seedlings exposed to salt stress as an example, we demonstrate the uniformity and controllability of the soil environment in this system. A high-throughput multiple-phenotypic assay among 178 soybean cultivars reveals that the cotyledon character can serve as a non-destructive indicator of the whole-seedling salt tolerance. Our results demonstrate that WinRoots is an effective tool for high-throughput plant cultivation and soil stress phenomics studies.
... SOPRANA ( 240 241 Figure 3a and 3b) Shoot and root biomass showed highly positive correlation but low to no differences between 270 cultivars, respectively. Thus, an allometric equation could be used to predict root biomasses that 271 remain challenging to measure in field experiments (Zhu et al., 2011). However, shoot and root 272 growth rate showed an average level of plasticity and highly significant differences between cultivars. ...
... Among the identified plastic traits, physiological traits such as the photosynthetic activity recovery 304 (F v /F m .R and SPAD.R) and growth traits such as the shoot growth rate and the TRER appeared 305 suitable to study the difference of plastic response to dark chilling stress between cultivars. Outdoor 306 experiments are required to assess if these results are transposable to the field (Zhu et al., 2011). 307 genotypic difference was observed for photosynthetic traits in our experiment. ...
The expansion of soybean cultivation to high-latitude regions is hindered by the adverse effects of dark chilling stress. This study investigates the phenotypic plasticity of soybean in response to dark chilling stress, aiming to identify traits that contribute to adaptation in northern climates. Five soybean cultivars from early maturity groups (000 and 00) were grown in growth chambers set either at 25/18C or 25/10C (day/night), and a range of performance and functional traits were measured. The relative distance plasticity index highlighted variations in plasticity across traits and genotypes. Photosynthetic activity recovery traits, shoot growth rate, and tap root elongation rate showed high plasticity and significant differences between cultivars, making them suitable for assessing dark chilling tolerance. Moreover, distinct responses to dark chilling stress were exhibited by different soybean cultivars. For instance, cv. SOPRANA displayed a greater phenotypic plasticity in aboveground performance traits, such as shoot growth, while cv. SULTANA exhibited a greater plasticity in physiological traits like photosynthetic activity recovery. These differing strategies may lead to similar biomass production through distinct mechanisms, highlighting the complexity of soybean's adaptive responses to dark chilling stress. These findings provide valuable insights for breeders seeking to develop soybean cultivars adapted to high latitudes, meeting the increasing demand for locally produced protein-based food. However, further research in real field conditions is essential to validate the potential benefits of these plastic traits and their role in improving soybean resilience to dark chilling stress. The identified plastic traits offer a promising avenue for screening a broader range of cultivars and enhancing soybean's suitability for cultivation in northern regions.
... Roots provide anchorage and support for the shoot by taking up water and nutrients from the soil and transporting them to above ground plant parts, storing carbohydrates and other reserves and are a site of biosynthesis of hormones (Zhu et al., 2011). Plants with different root characteristics respond, adapt and survive in different environments. ...
... The results were in accordance with Seiler (1998) demonstrated that the number of lateral roots increased with increased temperature up to 30°C, then declined at 35°C in sunflower. The branching densities response to a broad range of temperatures is a function of the primary root length and number of lateral roots (Zhu et al., 2011). ...
... Evaluating the RSA in the field trials could provide a true representation of root growth in an agriculturally relevant context (Zhu et al. 2011). However, due to the difficulty and intensive labor work to evaluate the root traits directly in the field, most of the root genetic studies have been performed in laboratory experiments at the seedling stage (Jia et al. 2019;Li et al. 2015;Pace et al. 2015Pace et al. , 2014Tuberosa et al. 2002). ...
... However, the changes in root system architecture were neglected. Despite the fact that direct selection for optimal RSA has not been routine Zhu et al. 2011), several root architectural phenes were different between teosinte, landraces and elite maize. Shoot-borne roots of landraces were thicker and steeper than those of teosinte (Burton et al. 2013;Omori and Mano 2007). ...
Key message
A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2–65.0% and 23.7–63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails.
Abstract
Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2–65.0% and 23.7–63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.
... Several studies conducted to evaluate the root system architecture (RSA) in plants have carried out classical and standard experiments in which typically the root is accessed by using a scanner or extracting the soil [15], [16]. In recent years, the rapid development of high-throughput phenomics platforms has opened new paths for the study of complex traits as well as RSA. ...
... In recent years, the rapid development of high-throughput phenomics platforms has opened new paths for the study of complex traits as well as RSA. For instance, the RSA phenotyping methods conducted under laboratory conditions provide controlled environments, allow increased throughput, and require fewer resources; however, they may not accurately reflect RSA under field conditions [15]. To overcome some of the limitations of laboratory and excavation methods, transparent tubes or boxes called minirhizotrons and rhizotrons respectively, have been developed and installed vertically, horizontally, or at various angles in the field or in controlled conditions. ...
... Its fruit was predominantly composed of water (>90%), therefore water and heat stress can significantly affect fruit yield and quality (Hatfield et al., 2008;Paroon et al., 2019). The root system was the major plant organ involved in water and nutrient acquisition and uptake (Zhu et al., 2011). Thus, developing varieties with an improved root system was critical for enhancing plant survival and performance of watermelon crops during periods of reduced water availability (Katuuramu et al., 2020;Luo et al. 2020;Lombardi et al. 2021). ...
... The rhizosphere was defined as the soil region under the influence of root exudates and associated soil microorganisms i.e. root microbiome (Philippot et al., 2013). The establishment of plant-rhizosphere microbiome interaction is highly influenced by the host plant and soil properties (Zhu et al., 2011;Li et al. 2021). Plant microbiota influences both plant health and productivity and is considered nowadays as a second plant genome targeted in many breeding programs (Berendsen et al., 2018). ...
In this study, the microbial community structure in the rhizosphere of 7 watermelon accessions was monitored using the soil dilution plating technique on specific media. All accessions tested were screened for their root growth before planting to select accessions with an improved root system. The fruit production was determined at four months post-planting. The total soluble solids (TSS) content was measured on flesh of sampled fruits. The dendrogram of hierarchical ascending classification clustered watermelon accessions into two main groups. The 1st cluster comprised two accessions P1 and P8 which were characterized by the highest abundance of actinomycetes and Aspergillus spp. communities in their rhizopshere, the highest weight of fruits with sweet taste. The current study clearly demonstrated that the soil microbial community structure has been shaped by Citrullus lanatus accessions. Future watermelon breeding programs will be focused on the selection of accessions that are quite able to exploit these associated beneficial microbial communities for enhanced growth and improved resistance to associated biotic stresses.
... Root system architecture (RSA) refers to the spatial arrangement of roots in soil, which is an essential factor in plant growth and development [3]. Research on root and RSA is a hot area in plant biology [4] as it has important applications in agricultural production and ecological environments [5]. ...
... Discovering root-related genes can help us to understand root system, thereby designing proper scheme to enhance their resistance to stress and increase crop survival [7]. Such investigations are helpful to improve crop production with low input costs [4,8]. However, identification of genes or proteins related to root traits is challenging at present, which is still in an early stage [9]. ...
The root system plays an irreplaceable role in plant growth. Its improvement can increase crop productivity. However, such system is still mysterious for us. The underlying mechanism has not been fully uncovered. The investigation on proteins related to the root system is an important means to complete this task. In the previous time, lack of root-related proteins makes it impossible to adopt machine learning methods for designing efficient models for the discovery of novel root-related proteins. Recently, a public database on root-related proteins was set up and machine learning methods can be applied in this field. In this study, we proposed a machine learning based model, named Graph-Root, for identification of root-related proteins. The features derived from protein sequences and one network were extracted, where the former features were processed by graph convolutional neural network and multi-head attention, and the later features abstracted the linkage between proteins. These features were fed into the fully connected layer to make prediction. The 5-fold cross-validation and independent tests suggested its good performance. It also outperformed the only one previous model, SVM-Root. Furthermore, the importance of each feature type and component in the proposed model was investigated.
... Root traits (i.e. taproot depth, fine root density, number of lateral roots, elongation rate, root length and early root growth) are therefore enhanced under low-N conditions (Svecnjak and Rengel 2006a; Zhu et al., 2011;Koscielny et al., 2012;Aibara and Miwa, 2014;Rao et al., 2016;Li et al., 2016;He et al., 2017). Nevertheless, highlighted that tap root is less sensitive to low-N conditions than the aerial parts. ...
... As reviewed by and Thomas et al. (2016), different root phenotyping methods can be directly used in the field, including root excavations (Oliveira et al., 2000;Bucksch et al., 2014;Arifuzzaman et al., 2019), soil-coring Wasson et al., 2014), and the use of interfaces such as 'windows', trenches (Vepraskas and Hoyt, 1988) and mini-rhizotrons inserted into the soil ( Dupuy et al., 2010). These techniques used to be highly time-consuming and laborious, destructive, prone to inaccuracy because small roots are lost during washing, and not adapted to screening large genetic populations (Zhu et al., 2011;. Therefore, there are inherent difficulties in screening root in plants grown in the field (Laperche et al., 2006). ...
Improving rapeseed yields in a low-Nitrogen (N) agricultural context is a major issue for breeding. It requires a thorough knowledge of the genotypic variation of the processes related to Nitrogen Use Efficiency (NUE, seed yield per unit of N available). This PhD aims at better understanding the ecophysiological processes determining the NUE and its components under low-N availability by identifying and hierarchizing the main traits supporting observed genotypic variation. Six winter oilseed rape genotypes were investigated throughout the crop cycle under semi-controlled conditions and contrasting N-conditions. We proposed NUE_DM (plant dry matter per unit of N available), as a new proxy of NUE at harvest, valid as early as the beginning of stem elongation. This proxy allowed us to dynamically characterize NUE, highlighting NUpE (plant N-amount per unit of N available) as a main contributor of NUE under low-N conditions, which explained up to 80% of the NUE_DM variations before flowering, and more than 30% after. Moreover, NUpE genotypic variability resulted from fine root growth rather than specific N-uptake differences. We developed a whole-plant conceptual modeling framework of carbon and nitrogen absorption and partitioning for winter oilseed rape. This framework, validated up to flowering, highlighted specific carbon assimilation, carbon partitioning between leaves and stems, and fine root ratio as critical traits explaining contrasting genotypic behavior to N-conditions. Our results suggest NUpE and fine root ratio as promising traits for screening larger sets of varieties for NUE breeding purposes.
... De plus, le développement et l'établissement du système racinaire sont corrélés avec la productivité agronomique, en particulier dans la tolérance à certaines conditions défavorables, comme un stress hydrique pour le blé (Reynolds et al., 2007) et pour le maïs (Gao and Lynch, 2016). Sur l'ensemble des cultures, les traits en lien avec les racines sont peu étudiés et leur phénotypage reste un frein pour l'amélioration génétique (Zhu et al., 2011). ...
... Historiquement celles-ci consistaient surtout à déraciner les plants et à réaliser des prélèvements de sol (Böhm, 1979). Elles sont toujours mises en oeuvre aujourd'hui (Zhu et al., 2011). Des techniques non destructives ont également été développées. ...
Le rejet des édulcorants de synthèse par les consommateurs a conduit ces derniers à privilégier les édulcorants naturels comme les glycosides de stéviol (SG). Ces molécules sont accumulées dans les feuilles de Stevia rebaudiana Bertoni, plante pérenne originaire du Paraguay, et aujourd’hui cultivée sur tous les continents. Dans le Sud-Ouest de la France, une filière de production en Agriculture Biologique est en développement, sous l’impulsion de la société Oviatis. Ce travail de thèse sous contrat CIFRE s’intéresse à la caractérisation fine des ressources génétiques cultivées sur les traits d’intérêt, et au développement des connaissances et des outils génétiques sur cette culture. La performance agronomique de la stévia a été évaluée par l’étude des composantes du rendement en SG, de l’architecture de la canopée et de la réponse à un agent fongique. Ces travaux ont permis (1) l’adaptation de l’échelle de stades phénologiques BBCH à la culture de la stévia et sa transmission à la filière, (2) l’évaluation des traits du rendement en SG sur 15 ressources génétiques de Stevia rebaudiana phénotypées pendant quatre années sur une parcelle expérimentale, (3) l’évaluation de la variabilité de la réponse à une infection de septoriose de ces mêmes ressources génétiques en conditions contrôlées et le développement d’un test d’inoculation sur disques foliaires, (4) d’estimer les paramètres génétiques pour les traits du rendement sur quatre populations de stévia cultivées en plein champ pendant trois ans, (5) enfin de construire des idéotypes de stévia dans le contexte local de production. Ces résultats participent au développement de la stévia dans le Sud-Ouest de la France, et alimentent la mise en place d’un programme d’amélioration pour une production en Agriculture Biologique.
... However, only a few studies have reported the potential of root phenomics for crop breeding (Kuijken et al., 2015;Prince et al., 2019;Falk et al., 2020;Liu et al., 2021). This is mostly due to the complexity and large genetic variability of Brassica root systems, the difficulties of accessing intact roots, as well as the tedious and laborious nature of phenotyping Brassica roots (de Dorlodot et al., 2007;Zhu et al., 2011;Meister et al., 2014;Ibrahim et al., 2021;Yang et al., 2024). The main goal of breeding programs that target root traits is to enhance the ability of roots to explore the soil and acquire water and nutrients, and to develop crops with increased stress tolerance and improved yields. ...
The root systems of Brassica species are complex. Eight root system architecture (RSA) traits, including total root length, total root surface area, root average diameter, number of tips, total primary root length, total lateral root length, total tertiary root length, and basal link length, were phenotyped across 379 accessions representing six Brassica species (B. napus, B. juncea, B. carinata, B. oleracea, B. nigra, and B. rapa) using a semi-hydroponic system and image analysis software. The results suggest that, among the assessed species, B. napus and B. oleracea had the most intricate and largest root systems, while B. nigra exhibited the smallest roots. The two species B. juncea and B. carinata shared comparable root system complexity and had root systems with larger root diameters. In addition, 313 of the Brassica accessions were genotyped using a 19K Brassica single nucleotide polymorphism (SNP) array. After filtering by TASSEL 5.0, 6,213 SNP markers, comprising 5,103 markers on the A-genome (covering 302,504 kb) and 1,110 markers on the C-genome (covering 452,764 kb), were selected for genome-wide association studies (GWAS). Two general linear models were tested to identify the genomic regions and SNPs associated with the RSA traits. GWAS identified 79 significant SNP markers associated with the eight RSA traits investigated. These markers were distributed across the 18 chromosomes of B. napus, except for chromosome C06. Sixty-five markers were located on the A-genome, and 14 on the C-genome. Furthermore, the major marker-trait associations (MTAs)/quantitative trait loci (QTLs) associated with root traits were located on chromosomes A02, A03, and A06. Brassica accessions with distinct RSA traits were identified, which could hold functional, adaptive, evolutionary, environmental, pathological, and breeding significance.
... Root systems represent challenging phenotypes to characterise, partly because of the hidden nature of roots into the soil, and also due to their considerable topological complexity (thus hampering the rapid observation of many traits) and permanent interactions with shoot parts (Paez-Garcia et al. 2015;Atkinson et al. 2019) and their abiotic and biotic telluric environment. Platformphenotyped RSA may offer insights into the genetic variability of underlying root traits (Zhu et al. 2011;Colombo et al. 2022). In particular, the process-based characterisation of root growth can offer a framework to break down the development of root systems over time into elementary mechanisms of root production, growth, branching and mortality (Pierret et al. 2007). ...
Background and aims
Root phenotyping and breeding for desirable root traits have been limited in small seed forage species. The objectives of this study were to analyse the degree of within-species variation regarding initial root allocation in two forage legumes and to assess the covariation between root allocation patterns and root and shoot morphogenetic traits involved in carbon source-sink relationships.
Methods
Experiments were carried out at a phenotyping platform to grow alfalfa and red clover plants of five contrasting cultivars under nutrient conditions non-limiting for growth. An automatic image analysis pipeline was used to characterise dynamic root-shoot allocation over 50 days during plant establishment. Measurements were also performed to characterise plant traits related to potential shoot and root development.
Results
In both species, genetic variability was found regarding the allocation of biomass to roots and root morphological traits controlling root elongation and branching. The degree of variability was high for most root traits, within a range similar to that found for the shoot traits usually targeted by breeders. A clear dependency of initial biomass allocation to roots on the shoot traits controlling plant leaf area, and favouring carbon acquisition, was identified. Analysis of covariation between root traits revealed they were largely independent, suggesting considerable potential for their recombination to achieve improved root phenotypes capturing more soil resources at a given biomass.
Conclusion
This study demonstrates the feasibility of direct breeding for root traits in legumes and could help to identify trait combinations that promote their rapid establishment and competitive ability.
... In parallel, a series of artificial, high-throughput root phenotyping (HTRP) platforms have been developed where the root system is accessible non-destructively. These platforms are based on hydroponics (Kuijken et al., 2015b;Guo et al., 2021), transparent cylinders (Jeudy et al., 2016), filter paper (Le Marié et al., 2014;Falk et al., 2020), or aeroponics (Zhu et al., 2011). Such set-ups are usually accompanied by analytical pipelines that are able to transform images into data (Kalogiros et al., 2016;Passot et al., 2018;Falk et al., 2020). ...
Given the difficulties in accessing plant roots in situ, high-throughput root phenotyping (HTRP) platforms under controlled conditions have been developed to meet the growing demand for characterizing root system architecture (RSA) for genetic analyses. However, a proper evaluation of their capacity to provide the same estimates for strictly identical root traits across platforms has never been achieved. In this study, we performed such an evaluation based on six major parameters of the RSA model ArchiSimple, using a diversity panel of 14 bread wheat cultivars in two HTRP platforms that had different growth media and non-destructive imaging systems together with a conventional set-up that had a solid growth medium and destructive sampling. Significant effects of the experimental set-up were found for all the parameters and no significant correlations across the diversity panel among the three set-ups could be detected. Differences in temperature, irradiance, and/or the medium in which the plants were growing might partly explain both the differences in the parameter values across the experiments as well as the genotype × set-up interactions. Furthermore, the values and the rankings across genotypes of only a subset of parameters were conserved between contrasting growth stages. As the parameters chosen for our analysis are root traits that have strong impacts on RSA and are close to parameters used in a majority of RSA models, our results highlight the need to carefully consider both developmental and environmental drivers in root phenomics studies.
... Investigation of root dynamics in response to changing environments has been achieved with image-based root phenotyping techniques [13,14]. Among these, the minirhizotron (MR) technique has been widely used for the nondestructive in situ observation of roots [15]. ...
Image-based root phenotyping technologies, including the minirhizotron (MR), have expanded our understanding of the in-situ root responses to changing environmental conditions. The conventional manual methods used to analyze MR images are time-consuming, limiting their implementation. This study presents an adaptation of our previously developed convolutional neural network (CNN)-based models to estimate the total (cumulative) root length (TRL) per MR image without requiring segmentation. Training data were derived from manual annotations in Rootfly, a commonly-used software for MR image analysis. We compared TRL estimation with two models, a regression-based model and a detection-based model which detects the annotated points along the roots. Notably, the detection-based model can assist in examining human annotations by providing a visual inspection of roots in MR images. The models were trained and tested with 4015 images acquired using two MR system types (manual and automated) and from four crop species (corn, pepper, melon, and tomato) grown under various abiotic stresses. These datasets are made publicly available as part of this publication. The coefficients of determination (R2), between the measurements made using Rootfly and the suggested TRL estimation models were 0.929–0.986 for the main datasets, demonstrating that this tool is accurate and robust. Additional analyses were conducted to examine the effects of (1) the data acquisition system and thus the image quality on the models’ performance, (2) automated differentiation between images with and without roots, and (3) the use of the transfer learning technique. These approaches can support precision agriculture by providing real-time root growth information.
... The mobility of N in the soil-plant system is controlled by factors and complex interactions, including the soil moisture content and the plant root system architecture (RSA; Fageria et al., 2010). Optimization of the RSA, especially under medium input and drought conditions, will significantly improve crop productivity (Xie et al., 2017;Zhu et al., 2011). The root system provides the plant with anchorage, competitiveness, and adaptation to stress. ...
Climate change causes extreme conditions like prolonged drought, which results in yield reductions due to its effects on nutrient balances such as nitrogen uptake and utilization by plants. Nitrogen (N) is a crucial nutrient element for plant growth and productivity. Understanding the mechanistic basis of nitrogen use efficiency (NUE) under drought conditions is essential to improve wheat (Triticum aestivum L.) yield. Here, we evaluated the genetic variation of NUE‐related traits and photosynthesis response in a diversity panel of 200 wheat genotypes under drought and nitrogen stress conditions to uncover the inherent genetic variation and identify quantitative trait loci (QTLs) underlying these traits. The results revealed significant genetic variations among the genotypes in response to drought stress and nitrogen deprivation. Drought impacted plant performance more than N deprivation due to its effect on water and nutrient uptake. GWAS identified a total of 27 QTLs with a significant main effect on the drought‐related traits, while 10 QTLs were strongly associated with the NUE traits. Haplotype analysis revealed two different haplotype blocks within the associated region on chromosomes 1B and 5A. The two haplotypes showed contrasting effects on N uptake and use efficiency traits. The in silico and transcript analyses implicated candidate gene coding for cold shock protein. This gene was the most highly expressed gene under several stress conditions, including drought stress. Upon validation, these QTLs on 1B and 5A could be used as a diagnostic marker for NUE and drought tolerance screening in wheat.
... This is also confirmed by the data of Lu et al. [8], who found a decrease in the concentration of watersoluble and available P in the soil at a distance of 3.5 cm from the monocalcium phosphate granule and 5.5 cm from the diammonium phosphate granule. The formation of powerful lateral roots improves nutrition by covering a larger volume of soil in the upper layer that can be considered as an auxiliary mechanism for plant adaptation to insufficient moisture [53,54]. Kang et al. [55] showed that deep placement of phosphate fertilizers stimulates root growth and has a positive effect on the yield of a drought-tolerant wheat variety. ...
The aim of the research was to study the effect of increasing the depth of mineral fertilizer placement on their agronomic efficiency for crops differed in root system architecture. Available NPK in soil, chlorophyll content in the leaves, and yield of sunflower and soybean were measured in the field small-plot experiments on Luvic Chernozem during three years. It was found a higher efficiency of N60P60K60 placement for sunflower in form of mix of ammonium nitrate, ammophos and potassium chloride on 20-22 cm, and for soybean in form of nitroammophoska by two bands on 10-12 cm and 20-22 cm comparing to the common method of fertilizer applying by one band on the depth 10-12 cm. The maximum yield increase was 15% for soybeans, 36% for sunflower. The content of chlorophyll in leaves might be an additional indicator to optimize the technology of fertilizer application because it has close positive correlation with crops yield. The obtained results prove the need for an individual approach in choosing the optimal fertilizer band placement for each crop separately. In general, increased depth of fertilizer band placement is recommend as a measure for adapting agricultural technology to unstable and insufficient moisture.
... The root is the main organ for nutrient uptake and plays a direct role in N acquisition (Lynch, 2007;Zhu et al., 2011). Root development and activity are responsive to soil N levels (Ju et al., 2015). ...
Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.
... Root responses to nutrient stresses, especially to nitrogen deficiency have been observed in other crops such as Brassica napus and Zea mays (Gao et al., 2015;Guo et al., 2017). However, roots and belowground processes are inherently challenging to study as digging for roots is a destructive process with root losses during washing (Zhu et al., 2011;Freschet et al., 2021). Characterization and quantification of root development without disrupting the root system architecture is an additional challenge, especially in numbers large enough to query natural variation across a plant species. ...
Introduction
Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity.
Methods
Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing).
Results
Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density.
Discussion
These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.
... 3D printed rhizoboxes were used. the past decade, RSA traits have been assessed in the lab noninvasively by 2D and 3D imaging techniques (Heeraman et al., 1997;Tracy et al., 2010;Zhu et al., 2011). 3D imaging techniques such as X-ray computed tomography and magnetic resonance imaging have been used to overcome the low spatial resolution often associated with 2D imaging. ...
Roots are the hidden parts of plants, anchoring their above-ground counterparts in the soil. They are responsible for water and nutrient uptake and for interacting with biotic and abiotic factors in the soil. The root system architecture (RSA) and its plasticity are crucial for resource acquisition and consequently correlate with plant performance while being highly dependent on the surrounding environment, such as soil properties and therefore environmental conditions. Thus, especially for crop plants and regarding agricultural challenges, it is essential to perform molecular and phenotypic analyses of the root system under conditions as near as possible to nature (#asnearaspossibletonature). To prevent root illumination during experimental procedures, which would heavily affect root development, Dark-Root (D-Root) devices (DRDs) have been developed. In this article, we describe the construction and different applications of a sustainable, affordable, flexible, and easy to assemble open-hardware bench-top LEGO® DRD, the DRD-BIBLOX (Brick Black Box). The DRD-BIBLOX consists of one or more 3D-printed rhizoboxes, which can be filled with soil while still providing root visibility. The rhizoboxes sit in a scaffold of secondhand LEGO® bricks, which allows root development in the dark and non-invasive root tracking with an infrared (IR) camera and an IR light-emitting diode (LED) cluster. Proteomic analyses confirmed significant effects of root illumination on barley root and shoot proteomes. Additionally, we confirmed the significant effect of root illumination on barley root and shoot phenotypes. Our data therefore reinforces the importance of the application of field conditions in the lab and the value of our novel device, the DRD-BIBLOX. We further provide a DRD-BIBLOX application spectrum, spanning from investigating a variety of plant species and soil conditions and simulating different environmental conditions and stresses, to proteomic and phenotypic analyses, including early root tracking in the dark.
... The root system is important in the growth, development, and physiology of crop plants, as well as in their responses to various stresses. The roots absorb water and nutrients from the soil and synthesize plant hormones, making them a necessary synthesis site for plant growth and development [7]. Serving as the interface for plant-soil interactions, the roots also play a key role in responding to environmental changes that can affect important traits, such as salt tolerance [8], drought resistance [9], and resistance to other abiotic stressors [10,11]. ...
Alfalfa growth and production in China are negatively impacted by high salt concentrations in soils, especially in regions with limited water supplies. Few reliable genetic markers are currently available for salt tolerance selection. As a result, molecular breeding strategies targeting alfalfa are hindered. Therefore, with the continuous increase in soil salinity in agricultural lands, it is indispensable that a salt-tolerant variety of alfalfa is produced. We collected 220 alfalfa varieties around the world for resequencing and performed genome-wide association studies (GWASs). Alfalfa seeds were germinated in saline water with different concentrations of NaCl, and the phenotypic differences in several key root traits were recorded. In the phenotypic analysis, the breeding status and geographical origin strongly affected the salt tolerance of alfalfa. Forty-nine markers were significantly associated with salt tolerance, and 103 candidate genes were identified based on linkage disequilibrium. A total of 2712 differentially expressed genes were upregulated and 3570 were downregulated based on transcriptomic analyses. Some candidate genes that affected root development in the seed germination stage were identified through the combination of GWASs and transcriptome analyses. These genes could be used for molecular breeding strategies to increase alfalfa’s salt tolerance and for further research on salt tolerance in general.
... Roots play critical role in plant health, growth and survival through water and nutrients uptake (Zhu et al., 2011;Takehisa et al., 2012;Sozzani and Iyer-Pascuzzi, 2014;Bhosale et al., 2018;Giri et al., 2018). Root length, surface area and volume together determine the root system architecture (Smith and De Smet, 2012), which is the spatial arrangement of the root system that is crucial for optimal use of the available resources (Lynch, 1995;Koevoets et al., 2016). ...
Rice (Oryza sativa L.) is one of the most important food crops worldwide. Upland rice growing areas are susceptible to adverse conditions and drought represents the main limiting factor for its production and yield stability. Soil management strategies (e.g., chemical and biological treatments) are often implemented to mitigate drought and improve crop production. However, morpho-physiological responses of upland rice to drought under such management strategies remain poorly understood. Here, we studied the effect of silicon and bioagents pretreatments under water stress on an upland rice landrace, Samambaia Branco. Our results unraveled that these pretreatments improved robustness of the root system in water stressed plants with increase in 40.9%
of surface area, 11.5% on diameter, 53.8% on volume and 30.8% of length density when measured at 45 cm soil depth. Furthermore, these treatments increased the number of thick roots by more than 14.0 and 45.0% at 25 and 45 cm soil depths, respectively; and fine root by more than 25.0% at 45 cm soil depth. Consequently, pretreated water stressed plants exhibited greater yield stability (reduction of 14.6% in grain yield compared to pretreated well-watered plants), root/shoot ratio (26.8%), photosynthesis (50.0%), stomatal conductance (14.4%), leaf
water potential (61.0%) and water use efficiency (49.1%) than untreated water stressed plants. Thus, we conclude that silicon and bioagent pretreatments significantly improve root and shoot performance under water stress. Our results provide a first step towards understanding the relevance of these pretreatments in upland rice for improving adaptive root system as a response to suboptimal environmental conditions.
... While comparing mean values and range for the traits under WW and DT it was observed that mean values of most of the root and shoot traits, except AD, ASI and TE, decreased, whereas range of these traits substantially increased under drought stress. The increased variation observed under drought stress suggests that root system architecture is plastic and dynamic, allowing plants to respond to their environment to optimize acquisition of soil resources such as water and nutrients (Vamerali et al., 2003;Zhu et al., 2011). Maturity group wise analysis showed a significant variation in root traits of three different maturity group of genotypes under drought stress , especially in case of structural traits. ...
Understanding how roots respond to increasing rate of evapotranspiration in warmer days and exposure to dry spells is crucial for saving productivity of rainfed crops, including maize, grown in Asian tropics. In a semi-automatic root phenotyping facility (lysimetric system) a set of 100 elite and diverse tropical maize inbred lines were phenotyped under managed drought stress (DT) and well-watered (WW) conditions. Plants were grown in PVC (Polyvinyl chloride) cylinder of 30.0 cm diameter and 150.0 cm length. In drought experiment, last irrigation was applied based accumulated growing degree days (∑GDD) criteria to achieved reproductive stress DT, whereas optimal moisture was maintained in WW trials. Data recorded on various root structural and function traits in both DT and WW trials. Significant phenotypic variability was observed for various root traits, including both structural and functional traits, under both the moisture regimes. Correlation studies showed that grain yield of early maturity group of genotypes was positively and significantly associated with all the root structural traits under drought, whereas, in case of medium and late maturity group of entries root structural traits showed either weak positive or significant negative correlation with grain yield under drought. Though, root functional traits of all the maturity group of genotypes showed positive and significant correlations with both grain yield and total biomass under both well-watered drought stress. Regression analysis showed that water uptake had significant positive relationship with total biomass in all the three-maturity group of genotypes. However, grain yield seems to be less dependent directly on the total amount of water uptake. We conclude that contribution of various traits in root system architecture under drought or well-watered conditions vary with maturity of genotypes. However, root functional traits, such as water uptake and transpiration efficiency are equally important across maturity groups and water availability regimes.
... The root system has been known to have a great effect on how plants adapt and respond to environmental stress including drought and salinity (Wasaya et al., 2018;Comas et al., 2013;Karahara and Horie, 2021; and the special characters aiding the roots to help plants better adapt to moisture stress are plasticity (Lynch, 2007) and the plasticity is controlled by genetic components triggered by abiotic stress and holds a great potential in stabilizing productivity under suboptimal conditions (Zhu et al., 2011;Gifford et al., 2013). ...
Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.
... Furthermore, the root impedance, the types of competing crops already present, and the amount of growing area available are all strongly correlated with root size [21]. In addition, roots also directly contribute to a plant's health, development and survivability by absorbing moisture and minerals [22,23]. Furthermore, roots serve as a site for hormone production and consumption, which affects the hormonal regulation of the entire plant [24,25]. ...
Citation: Kaysar, M.S.; Sarker, U.K.; Monira, S.; Hossain, M.A.; Mokarroma, N.; Somaddar, U.; Saha, G.; Hossain, S.S.F.; Chaki, A.K.; Uddin, M.R. Water Stress Induced Changes in Root Traits and Yield of Irrigated Rice under Subtropical Condition. Water 2023, 15, 618. Abstract: The presence of water or the degree of soil saturation has a direct impact on the root development and function in rice. In this regard, a pot investigation was performed to test the response of root traits and yield components of boro (irrigated) rice. Three boro rice varieties named Binadhan-10, Hira-2 and BRRI dhan 29 were grown at four irrigation regimes, viz. continuous flooding (CF), saturation (S), 75% S and 50% S at Bangladesh Agricultural University, Mymensingh, Bangladesh, throughout the boro period of 2020-2021. The study was replicated three times by employing a completely randomized design (CRD) method. The study revealed a drastic decline in root attributes at 75% and 50% S. A significant increase in root number (RN), root length (RL), root volume (RV), total dry matter (TDM) and grain yield (GY) under S condition followed by CF was observed. Binadhan-10 exhibited the largest scores of RN (359.00), RL (1577.83 cm) and RV (8.34 cm 3 hill −1) at 80 DAT under S condition. Root attributes and GY were found to be substantially and positively associated in all observations. Binadhan-10 performed best with regard to seed output (26.13 g pot −1) under S condition. S condition increased the yield of Binadhan-10 in CF, 75% S and 50% S by 4.06%, 23.72% and 46.00%, respectively.
... Laboratory phenotyping methods require propagating the sample plant in non-soil media like gels or on paper and supplied with nutrient washes. After growth, root formation features and characteristics are determined by manual measurements or with 2-dimensional imaging [12] [13]. Soil extractions, imaging systems, or combinations of the two are standard field-root phenotyping techniques. ...
... Three-dimensional (3D) analysis is important to accurately assess the structure and function of roots, which develop intricately in the soil. For the 3D analysis of RSA, magnetic resonance imaging (Jahnke et al., 2009;Metzner et al., 2014), neutron imaging (Tumlinson et al., 2007;Leitner et al., 2014), and X-ray computed tomography (CT) (Jenneson et al., 2003;Zhu et al., 2011;Flavel et al., 2012) have recently been used. However, these methods require considerable time to scan and reconstruct the roots. ...
Rice is susceptible to abiotic stresses such as drought stress. To enhance drought resistance, elucidating the mechanisms by which rice plants adapt to intermittent drought stress that may occur in the field is an important requirement. Roots are directly exposed to changes in the soil water condition, and their responses to these environmental changes are driven by photosynthates. To visualize the distribution of photosynthates in the root system of rice plants under drought stress and recovery from drought stress, we combined X-ray computed tomography (CT) with open type positron emission tomography (OpenPET) and positron-emitting tracer imaging system (PETIS) with ¹¹C tracer. The short half-life of ¹¹C (20.39 min) allowed us to perform multiple experiments using the same plant, and thus photosynthate translocation was visualized as the same plant was subjected to drought stress and then re-irrigation for recovery. The results revealed that when soil is drier, ¹¹C-photosynthates mainly translocated to the seminal roots, likely to promote elongation of the root with the aim of accessing water stored in the lower soil layers. The photosynthates translocation to seminal roots immediately stopped after rewatering then increased significantly in crown roots. We suggest that when rice plant experiencing drought is re-irrigated from the bottom of pot, the destination of ¹¹C-photosynthates translocation immediately switches from seminal root to crown roots. We reveal that rice roots are responsive to changes in soil water conditions and that rice plants differentially adapts the dynamics of photosynthates translocation to crown roots and seminal roots depending on soil conditions.
... Increasing our knowledge and understanding of root development in response to environmental stresses is of capital importance for global agricultural production, and has been defined as the pillar of the Second Green Revolution [1]. Many methods are now available to observe RSD and root architecture, yet some of the more advanced techniques such as CT imaging remain expensive and impractical, underlining the need for improved trans-disciplinary phenotyping approaches that can capture and quantify the complexity of RSD and root system architecture [34][35][36]. ...
Purpose
Root system architectures are complex and challenging to characterize effectively for agronomic and ecological discovery.
Methods
We propose a new method, Spatial and Texture Analysis of Root SystEm distribution with Earth mover’s Distance (STARSEED), for comparing root system distributions that incorporates spatial information through a novel application of the Earth Mover’s Distance (EMD).
Results
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.
Conclusion
STARSEED can be 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 .
... Recently, it has been demonstrated that root plasticity is also under genetic control and plastic responses of root phenes are associated with different genetic loci than those controlling expression of root phenes in optimal conditions (Schneider et al. 2020a, b). Consequently, work to uncover the genetic control of root phenes requires special consideration of plant age and production environment, as in some cases, measurements of seedling root systems or plants grown in artificial media may be poor predictors of mature, field-grown root systems (Zhu et al. 2011) and under distinct genetic control (Hochholdinger et al. 2004). Genetic studies of mature plants will be important in unraveling the genetic architecture of root traits for enhanced nutrient efficiency. ...
Issues surrounding soil fertility are fundamental to the productivity and sustainability of diverse agricultural production systems around the world. In developed economies, intensive fertilization is a chief economic, energetic, and environmental cost to crop production, depleting finite resources and causing massive pollution through leaching and runoff. In developing economies where access to, and utilization of soil amendments are rare, degraded soils with low nutrient availability are a primary constraint to yields. The most common challenges surrounding soil fertility in most production systems primarily involve nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), iron (Fe), and zinc (Zn). A chief component of a robust and pragmatic solution to these soil fertility issues lies in the development of more nutrient‐efficient crops. In pursuit of this objective, root phenotypes that improve the efficiency of soil exploration and acquisition of resources offer exceptional opportunities as breeding targets. Natural variation for root phenotypes can have significant effects on soil resource extraction by modifying the placement of roots in soil domains where limiting resources are most available, improving the metabolic efficiency of soil exploration, as well as altering the radial and axial transport of resources. In this chapter, we review root anatomical and architectural phenes that have demonstrated benefit for enhancing acquisition of the most commonly limiting nutrients, and advocate for the consideration of root phenotypes in breeding programs focused on developing crops with greater nutrient efficiency.
... Wheat genotypes with deep root systems and higher root density are considered to better extract soil water mainly from deeper soil layers and to achieve higher yield (Manschadi et al. 2008). We found that the root system architecture of the drought-tolerant Drysdale was more adaptable to the environment, consistent with previous studies (Manschadi et al. 2006;Zhu et al. 2011). ...
Water and nitrogen (N) fertilizer are the two main factors affecting wheat growth and yield. Spring wheat cultivars, Spitfire (drought sensitive) and Drysdale (drought tolerant), were used as materials for studying N metabolism physiological and molecular dynamics under water-deficit treatment at high-N level (180 kg hm−2, i.e., 80 mg kg−1) vs. low-N level (22.5 kg hm−2, i.e., 10 mg kg−1) at heading stage in this experiment. The results showed that the chlorophyll, soluble sugar, soluble protein and free amino acid contents; glutamine synthetase (GS), glutamate synthetase (GOGAT) and phosphoenolpyruvate carboxylase (PEPC) enzyme activities; gene GS1 expression; and grain yield were increased at high-N level compared to low-N level under water-deficient stress at heading stage in both cultivars. Relative expressions of genes GDH, GOGAT and PEPC were down-regulated in Spitfire under water-deficit treatment, but were up-regulated in Drysdale. The indicators of root system architecture, including root surface area, total root volume, root diameter and number of root tips and root branches, were increased at high-N level under water-deficient treatment in both cultivars, whereas total root length decreased. The root–shoot ratio of both cultivars decreased to low-N level under water-deficit treatment. The N transfer rate was significantly increased at high-N level after heading for water-deficit treatment. The grain yields of both cultivars were maintained by the high-N level under water-deficit treatment. Our results suggested a high-N level could alleviate the damage from water deficiency by activating genes/enzymes related to wheat carbon and N metabolism.
... We have updated the list of root phenotyping methods, recently reviewed by Zhu et al. (2011) and Wasaya et al. (2018), by integrating newly published studies in the literature (Tab. 1). ...
... We have updated the list of root phenotyping methods, recently reviewed by Zhu et al. (2011) and Wasaya et al. (2018), by integrating newly published studies in the literature (Tab. 1). ...
Soybean ( Glycine max (L.) Merr.) may contribute to the agro-ecological transition of cropping systems in Europe, but its productivity is severely affected by summer drought. The crop is mainly grown in southern and continental parts of Europe, whereby increasing drought and heat waves are expected in the near future. Agronomic strategies, such as early sowing, require cultivars with enhanced early plant growth traits under suboptimal conditions. Moreover, efficient water uptake by root delays dehydration and promotes drought avoidance. In general, changes in root morphology and root architecture are important pathways for plant adaptation to water stress conditions. This paper reviews the cultivar differences in soybean for root morphological and architectural traits especially during early growth stage. Previous works reported cultivar differences for root traits in soybean but they did not deal with cultivars commonly grown in Europe on which little information is available to date. Genotypic differences in available early-stage root traits can be used as a framework to design soybean ideotypes less vulnerable to drought. To this aim, high-throughput phenotyping supported by digital methods and crop modelling offer new avenues for the exploration of target root traits involved in drought avoidance.
... Biochar provides better aeration, improved water content in soils, plant nutrition, and a boost to plant cultivation [52][53][54][55]. Increasing plant nutrients sourced from biochar can help improve plant cultivation [56]. Abbas et al. [15] evaluated the effect of the application of biochar in combination with the recommended synthetic fertilizer on soil properties, maize (Zea mays L.) plant growth characteristics, and maize grain yield and quality parameters, and they concluded that the potential of biochar application in combination with nitrification inhibitor may be used as the best nutrient management practice for enhanced soil fertility and crop yield. ...
Efficient bioresource management can alter soil biochemistry and soil physical properties, leading to reduced greenhouse gas (GHG) emissions from agricultural fields. The objective of this study was to evaluate the role of organic amendments including biodigestate (BD), biochar (BC), and their combinations with inorganic fertilizer (IF) in increasing carbon sequestration potential and mitigation of GHG emissions from potato (Solanum tuberosum) fields. Six soil amendments including BD, BC, IF, and their combinations BDIF and BCIF, and control (C) were replicated four times under a completely randomized block design during the 2021 growing season of potatoes in Prince Edward Island, Canada. An LI-COR gas analyzer was used to monitor emissions of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) from treatment plots. Analysis of variance (ANOVA) results depicted higher soil moisture-holding capacities in plots at relatively lower elevations and comparatively lesser volumetric moisture content in plots at higher elevations. Soil moisture was also impacted by soil temperature and rainfall events. There was a significant effect of events of data collection, i.e., the length of the growing season (p-value ≤ 0.05) on soil surface temperature, leading to increased GHG emissions during the summer months. ANOVA results also revealed that BD, BC, and BCIF significantly (p-value ≤ 0.05) sequestered more soil organic carbon than other treatments. The six experimental treatments and twelve data collection events had significant effects (p-value ≤ 0.05) on the emission of CO2. However, the BD plots had the least emissions of CO2 followed by BC plots, and the emissions increased with an increase in atmospheric/soil temperature. Results concluded that organic fertilizers and their combinations with inorganic fertilizers help to reduce the emissions from the agricultural soils and enhance environmental sustainability.
... The high heritability ensures the trait's repeatability, which is the fundamental criterion for plant breeders during selection [38]. In accordance with previous reports [23,30,32], strong and positive correlations among different root-related traits indicated that these traits were not expressed independently of one another. ...
Marker-assisted selection enables breeders to quickly select excellent root architectural variations, which play an essential role in plant productivity. Here, ten root-related and shoot biomass traits of a new F6 recombinant inbred line (RIL) population were investigated under hydroponics and resulted in high heritabilities from 0.61 to 0.83. A high-density linkage map of the RIL population was constructed using a Brassica napus 50k Illumina single nucleotide polymorphism (SNP) array. A total of 86 quantitative trait loci (QTLs) explaining 4.16-14.1% of the phenotypic variances were detected and integrated into eight stable QTL clusters, which were repeatedly detected in different experiments. The codominant markers were developed to be tightly linked with three major QTL clusters, qcA09-2, qcC08-2, and qcC08-3, which controlled both root-related and shoot biomass traits and had phenotypic contributions greater than 10%. Among these, qcA09-2, renamed RT.A09, was further fine-mapped to a 129-kb interval with 19 annotated genes in the B. napus reference genome. By integrating the results of real-time PCR and comparative sequencing, five genes with expression differences and/or amino acid differences were identified as important candidate genes for RT.A09. Our findings laid the foundation for revealing the molecular mechanism of root development and developed valuable markers for root genetic improvement in rapeseed.
... Root system architecture must be able to optimize root system and can assess soil conditions to secure and forage nutrient resources while excluding toxic substances for the plant especially under abiotic stress conditions (Mickelbart et al. 2015). Therefore, identifying the root architecture development and its adaptation possesses a great potential for maintaining the productivity gap under adverse conditions of the root environment (Zhu et al. 2011). Taken together, the present chapter summarizes the role of various plant hormones in regulating the root system architecture under changing environmental conditions ( Fig. 9.1). ...
Globally, the continuous changing environment mainly due to the natural or anthropogenic activities has limited the agricultural crop plants productivity. Like aerial plant part, the underground root architecture is also influenced under adverse situations. Root system plays an important role in terms of water, nutrient absorption, and soil anchoring, thus overall affecting the growth and yield. It has been noticed that the plant hormones for instance abscisic acid, auxins, cytokinins, ethylene, and strigolactones played an important role in regulation of root morphology. Therefore, it is believed that the root system engineering offers a new opening for sustainable crop pants production under changing environmental conditions. This chapter focuses on our current understanding of hormones involved in determining the root system architecture under changing environmental conditions.
... To address the challenge of phenotyping RSA, researchers have explored three strategies [19], including (1) well-controlled laboratory methods [20,21], moderately controlled greenhouse methods [22,23], and (3) open field methods [24][25][26]. The significant challenges are the high labor and time costs in RSA field phenotyping [27,28] and the generally low correlation between RSA of plants grown in highly controlled growth chambers or greenhouse experiments and plants grown in dynamic environments in the field experiments [29]. ...
Active breeding programs specifically for root system architecture (RSA) phenotypes remain rare; however, breeding for branch and taproot types in the perennial crop alfalfa is ongoing. Phenotyping in this and other crops for active RSA breeding has mostly used visual scoring of specific traits or subjective classification into different root types. While image-based methods have been developed, translation to applied breeding is limited. This research is aimed at developing and comparing image-based RSA phenotyping methods using machine and deep learning algorithms for objective classification of 617 root images from mature alfalfa plants collected from the field to support the ongoing breeding efforts. Our results show that unsupervised machine learning tends to incorrectly classify roots into a normal distribution with most lines predicted as the intermediate root type. Encouragingly, random forest and TensorFlow-based neural networks can classify the root types into branch-type, taproot-type, and an intermediate taproot-branch type with 86% accuracy. With image augmentation, the prediction accuracy was improved to 97%. Coupling the predicted root type with its prediction probability will give breeders a confidence level for better decisions to advance the best and exclude the worst lines from their breeding program. This machine and deep learning approach enables accurate classification of the RSA phenotypes for genomic breeding of climate-resilient alfalfa.
... Each one of these approaches has its merit and limitations, but systems that are fairly inexpensive and allow the evaluation of a large number of plants are not common. We have developed a non-destructive rhizotron-based system and present the features and validation of our RSA phenotyping platform (Zhu et al., 2011). The rhizotrons, that have a soil capacity of 4.2kg, are constituted of 50x80cm light-proof Aluminium Composite Material (ACM) plates separated from glass plates by a 1.2cm thick spacer. ...
Low yields of cotton are often an outcome of biotic and abiotic
stresses. Among these stresses, cotton leaf curl virus disease (CLCuV) has caused severe threat for cotton production in Pakistan.
A field experiment on cultivar Bt. CRIS-508 was conducted in Central Cotton Research Institute, Sakrand for two consecutive years
to determine response of potassium (K) nutrition to the infestation
of CLCuV and seed cotton yield. Experiment was laid out in randomized complete block design (RCBD) with four replications. Potassium levels were applied 0, 50, 100 and 150 kg K2O ha-1 along
with a basal dose of 170:60 kg N:P205 ha-1. Seed cotton yields
and its components like boll formation plant-1, boll weight and seed index were significantly improved by the addition of K application
and were observed highest with the application of 150 kg K2O ha-1
on both consecutive years. Data for K concentration in different
organs of plant differed significantly due to K –fertilization. Potassium concentration increased linearly with increasing K-levels. The
absorption of K by various plant parts increased with concurrent
increase in varying levels of K-fertilizer. Averaged across levels,
the relative K concentration in plant parts was found in decreasing
in order of leaves > burs > stem > seed > lint. Results for incidence
of CLCuV disease differed significantly due to K levels and seasons. The application of K fertilizer resulted in reduction of spread
of disease at its mild infection level.
Acknowledgments
I am thankful to ICAC, USA and Pakistan Central Cotton Committee for supporting me in participating and presenting research paper in the World Cotton Research Conference-6 at Brazil.
References
Dr. M. Rafiq Chaudhry, Head Technical Information Section International Cotton Advisory Committee
Dr Muhammad Ali Talpur Director Economic Research at Pakistan
Central Cotton Committee, Ministry of Textile Industry,Govtof Pakistan
Dr. Khalid Abdullah Cotton Commissioner/Vice president, Pakistan
Central Cotton Committee (PCCC), Ministry of Textile Industry
Mr. Mushtaq Ali Leghari Director Central Cotton Research Institute Sakrand Sind Pakistan
Keywords: Cotton, Potassium, CLCuV Disease, Seed cotton Yield
... Therefore, insights furnished by this controlled-environment investigation into the interrelatedness of the various phenotypic responses are at least qualitatively relevant. In the future, we plan to quantify the effects of SHS mulching on root growth via noninvasive methods (Brown et al., 1991;Daly et al., 2015;Downie et al., 2012;Zhu et al., 2011), instantaneous leaf gas-exchange, and carbon isotope composition (δ 13 C) (Bednarz et al., 1998;Evans et al., 1986;Monneveux et al., 2006) toward a deeper understanding of above and below-ground processes in controlled environments and field settings. ...
Abstract Irrigated agriculture in arid and semi‐arid regions is a vital contributor to the global food supply. However, these regions endure massive evaporative losses that are compensated by exploiting limited freshwater resources. To increase water‐use efficiency in these giga‐scale operations, plastic mulches are utilized; however, their non‐biodegradability and eventual land‐filling renders them unsustainable. In response, we have developed superhydrophobic sand (SHS) mulching technology that is comprised of sand grains or sandy soils with a nanoscale coating of paraffin wax. Here, we investigate the effects of 1 cm‐thick SHS mulching on the evapotranspiration and phenotypic responses of tomato (Solanum lycopersicum) plants as a model system under normal and reduced irrigation inside controlled growth chambers. Experimental results reveal that under either irrigation scenario, SHS mulching suppresses evaporation and enhances transpiration by 78% and 17%, respectively relative to the unmulched soil. Comprehensive phenotyping revealed that SHS mulching enhanced root xylem vessel diameter, stomatal aperture, stomatal conductance, and chlorophyll content index by 21%, 25%, 28%, and 23%, respectively, in comparison with the unmulched soil. Consequently, total fruit yields, total dry mass, and harvest index increased in SHS‐mulched plants by 33%, 20%, and 16%, respectively compared with the unmulched soil. We also provide mechanistic insights into the effects of SHS mulching on plant physiological processes. These results underscore the potential of SHS for realizing food–water security and greening initiatives in arid regions.
... RSA is plastic and dynamic, allowing plants to optimize acquisition of important soil resources in response to environmental cues (Zhu, Ingram, Benfey, & Elich, 2011). Roots foster a wide range of plant-microbe interactions, such as nodulation in soybean and other legumes, which can be indirectly selected traits in breeding programs, particularly for non-tuber or root crops (York, Galindo-Castañeda, Schussler, & Lynch, 2015). ...
The significance of root system architecture (RSA) to the productivity and adaptation of crops such as soybean (Glycine max (L.) Merr.) is well recognized. RSA is an essential trait in the selection of genotypes with improved resource acquisition and adaptation to environmental stresses. High-throughput phenotyping, imaging of root growth and structure, genomic sequencing and association analysis techniques are useful tools in soybean breeding programs that aim to improve plant performance and productivity. This chapter discusses genetic variability and plasticity in soybean root system morphology, root architecture and root anatomic traits that are relevant to increased soil resource use efficiency and better adaptation to specific soil environments. We consider the importance of soybean/rhizobia and rhizosphere interactions and highlight current challenges and future directions in improving soybean root physiology and morphology for better adaptation to abiotic stresses.
... Other studies reported a lack of throughput by X-ray CT methods for quantitative field studies (Zhu et al., 2011). This study supports previously published work by Tracy et al. (2012), Zappala et al. (2013) and Valentine et al., (2012), proving that modern "fast scanning" technologies demonstrate the ability for X-ray CT to produce medium throughput for large, replicated field trial studies. ...
Winter wheat (Triticum aestivum L.) is an important cereal crop in the temperate climates of western Europe. Root system architecture is a significant contributor to resource capture and plant resilience. However, the impact of soil type on root system architecture (RSA) in field structured soils is yet to be fully assessed. This work studied the development of root growth using deep cultivation (250 mm) during the tillering phase stage (Zadock stage 25) of winter wheat across three soil types. The three sites of contrasting soil types covered a geographical area in the UK and Ireland in October 2018. Root samples were analysed using two methods; X‐ray Computed Tomography (CT) which provides 3D images of the undisturbed roots in the soil, and a WinRHIZOTM scanner used to generate 2D images of washed roots and to measure further root parameters. Important negative relationships existed between soil bulk density and root properties (root length density, root volume, surface area and length) across the three sites. The results revealed that despite reduced root growth, the clay (Southoe) site had a significantly higher crop yield irrespective of root depth. The loamy sand (Harper Adams) site had significantly higher root volume, surface area, root length density compared to the other sites. However, a reduction in grain yield of 2.42 Mt ha‐1 was incurred compared to the clay site and 1.6 Mt ha‐1 compared to the clay loam site. The significantly higher rooting characteristics found in the loamy sand site were a result of the significantly lower soil bulk density compared to the other two sites. The loamy sand site had a lower soil bulk density, but no significant difference in macroporosity between sites (P > 0.05). This suggests that soil type and structure directly influence crop yield to greater extent than root parameters, but the interactions between both need simultaneous assessment in field sites.
... Previous studies reported a similar trend in root phenotyping of other legume crops, such as soybean [22,49]. In addition, the association of root traits (such as TRL) with root mass and root depth, which leads to better adaptation and nutrient uptake in different plant species (including legume species), has also been reported [13,32,50]. Furthermore, longer roots with fine diameters are strongly correlated with stomatal conductance of water vapor, ultimately supporting the water retention capacity of plants [51]. ...
Root system architecture and morphological diversification in wild accessions are important for crop improvement and productivity in adzuki beans. In this study, via analysis using 2-dimensional (2D) root imaging and WinRHIZO Pro software, we described the root traits of 61 ad-zuki bean accessions in their early vegetative growth stage. These accessions were chosen for study because they are used in Korea's crop improvement programs; however, their root traits have not been sufficiently investigated. Analysis of variance revealed a significant difference between the accessions of all measured root traits. Distribution analysis demonstrated that most of the root traits followed normal distribution. The accessions showed up to a 17-fold increase in the values in contrasting accessions for the root traits. For total root length (TRL), the values ranged from 82.43 to 1435 cm, and for surface area (SA), they ranged from 12.30 to 208.39 cm 2. The values for average diameter (AD) ranged from 0.23 to 0.56 mm. Significant differences were observed for other traits. Overall, the results showed that the accession IT 305544 had the highest TRL, SA, and number of tips (NT), whereas IT 262477 and IT 262492 showed the lowest values for TRL, SA, and AD. Principal component analysis showed an 89% variance for PC1 and PC2. K-mean clustering explained 77.4% of the variance in the data and grouped the accessions into three clusters. All six root traits had greater coefficients of variation (≥15%) among the tested accessions. Furthermore, to determine which root traits best distinguished different accessions, the correlation within our set of accessions provided trait-based ranking depending on their contribution. The identified accessions may be advantageous for the development of new crossing combinations to improve root features in adzuki beans during the early growth stage. The root traits assessed in this study could be attributes for future adzuki bean crop selection and improvement.
... However, these methods are unable to track the root growth as they develop in three dimensions in the soil. Therefore, magnetic resonance imaging (MRI) [10][11][12], neutron computerized tomography (CT) [13,14] and X-ray CT [3,[15][16][17] have recently been used as non-invasive methods to analyze three-dimensionally developing root structures. The CT systems, especially, are becoming more widely used by plant researchers because they are cheaper and easier to use than other systems [18]. ...
Roots are essential to plants for uptake of water and nutrients. For the improvement of crop production, it is necessary to understand the elucidation of the root development and its function under the ground. Especially, photosynthate translocation from plant leaves to roots is an important physiological function that affects the root elongation, adaptation to the soil environment and nutrients uptake. To evaluate the translocation dynamics to roots, positron emission tomography (PET) and ¹¹ C tracer have been used. However, the spatial resolution is degraded at roots that develop around the peripheral area of field of view (FOV) due to parallax errors. In this study, to overcome this problem, we developed a small OpenPET prototype applying four-layer depth-of-interaction detectors. We demonstrated the imaging capability of ¹¹ C-photosynthate translocation to rice roots that develop throughout the entire PET field. We also tried to obtain structural information of roots by high-throughput X-ray computerized tomography (CT) system using the same test plant. As a result, we succeeded in visualizing the root structure that developed around the peripheral region of FOV and imaging the accumulation of ¹¹ C-photosynthate to the roots in those areas without degrading the spatial resolution. From obtained images, we also succeeded in evaluating the translocation dynamics varied by roots. The combined use of the high-throughput CT system and the OpenPET prototype was demonstrated to be appropriate for structural and functional analysis of roots.
... Growing in soil-less media allows clear visualization of roots from background, control of environment for treatment evaluation, and measurement of nutrient and root respiration fluxes with methods that are often high-throughput(Paez-Garcia et al. 2015). In contrast, evaluation of plants grown in soil is more representative but comes with the cost of often slower, coarser, and more destructive root analysis techniques(Zhu, Ingram, Benfey & Elich 2011). Pot and tall mesocosm studies often require a root washing step to remove soil before root imaging, but this processing can destroy fine roots and affect the root system architecture. ...
Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical, and biotic properties of soil. However, cover crops, a group of plants that provide ecosystem services, can be utilized during fallow periods or used as an intercrop to restore soil health. The effectiveness of ecosystem services provided by cover crops varies widely as very little breeding has occurred in these species. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. In this review we provide an overview of the range of belowground ecosystem services provided by cover crop roots: (1) soil structural remediation, (2) capture of soil resources, and (3) maintenance of the rhizosphere and building of organic matter content. Based on the ecosystem services described, we outline current and promising phenotyping technologies and breeding strategies in cover crops that can enhance agricultural sustainability through improvement of root traits.
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Вступ. Зміна клімату призвела до частих екстре-мальних погодних явищ, особливо нерегулярних опадів. Це викликає біотичні і абіотичні стреси у сільськогоспо-дарських рослин, що негативно впливають на їх продк-тивність. Результати. Аналіз літературного матеріалу показав, що будова кореневої системи (RSA) є потуж-ним індикатором, що відображає забезпеченість рослин поживними речовинами, а також для визначення її від-повідних реакцій на зовнішні фактори. Вона відіграє жит-тєво важливу роль у продуктивності та адаптації рослин до різних середовищ та їй належить центральна роль у продуктивності та стійкості всіх рослинних екосистем у здатності їх існуванню, взагалі. Тому, зростає визнання того, що майбутні прирости врожайності, можуть бути досягнуті шляхом оптимізації RSA. Основні елементи архітектури RSA це довжина первинного кореня, щіль-ність бічних кореня та під яким кутом по відношенню до стрижневого вони розташовані у ґрунті, діаметр коренів. Зовнішні фактори, такі як доступність води та пожив-них речовин, регулюють формування бічних і додатко-вих коренів та залежно від цього вони можуть поши-рюватися не глибоко поверхнево або заглиблюватись. Генотипи з більшою розгалуженістю, щільністю бічних коренів та довжиною стрижневого кореня й високою врожайністю розглядаються як глибоко вкорінені та придатні для середовища з водним та азотним стресом, а генотипи з меншою щільністю бічних розгалужень, неглибокі придатні для середовищ із низьким вмістом фосфору. На архітектуру кореневої системи вплива-ють мікроорганізми: бактерії та гриби які викликають безліч модифікацій у морфології коренів, залежно від культури, штаму ризобактерій PGPR та виду мікориз-них грибів AMF. Загальною рисою Ризобактерії PGPR є модифікація бічних коренів. Висновок. Використання мікоризних грибів AMF, збільшує ступінь розгалуження коренів, збільшення загальної довжини, площі поверхні та об’єму коренів. Пряме фенотипування залишається актуальною проблемою. Для вирішення цього завдання виділяється наступні методи: добре контрольовані лабо-раторні, які дають змогу автоматично фенотипувати RSA, помірно контрольовані тепличні та польові методи де досліджуються зрілі кореневі системи у реальних ґрунтових умовах у полі із застосуванням інтегрованого способу: візуальна оцінка, ручні вимірювання та аналіз зображення з допомогою 2D, 3D.
Ключові слова: архітектура кореневої системи, про-дуктивність, стрес, вплив зовнішніх факторів, генотипи.
Soil structure has a huge impact on plant root growth, but it is difficult to isolate from other soil properties in field studies, and generally overlooked in laboratory studies that use sieved and homogenised repacked soil. This study aimed to compare root and shoot growth under controlled soil conditions where only soil structure varied. Soil treatments used soil sieved to < 2 mm, packed in uniform layers to create a homogenous structure. A heterogeneous structure was packed from artificially formed aggregates created by breaking apart the homogeneous soil after intense compaction. Barley, peas and Arabidopsis, selected for contrasting root sizes, were grown under three levels of compaction (1.25 g cm−3, 1.40 g cm−3, 1.55 g cm−3) in both homogeneous and heterogeneous structured soils for 10 days. Penetration resistance increased from about 0.4 MPa at 1.25 g cm−3 to 1.3 MPa at 1.55 g cm−3 for either soil structure. Soil structure was quantified from water retention characteristics and X-ray Computed Tomography (CT) as complementary methods to assess the soil's pore size distribution and properties. Heterogenous soil had 50% more macropores at 1.55 g cm−3 when compared to homogenous soils. Pore structure complexity in the heterogeneous structure was found to be beneficial for root growth of peas and barley but not Arabidopsis. Shoot biomass of peas grown in heterogeneous soil at 1.55 g cm−3 increased by 65% when compared to homogenous soil, whereas barley and Arabidopsis shoot biomass did not differ significantly between any treatments. Chlorophyll, flavonoid, and nitrogen content could only be measured on barley or peas due to shoot size, but only minor differences were observed between soil structures. Soil structural heterogeneity influenced many root properties and above-ground biomass, with impacts found to be species-dependent and likely caused by the interaction between root size and preferential growth in macropores.
Root system architecture (RSA) influences the acquisition of heterogeneously dispersed soil nutrients. Cytokinin and C-TERMINALLY ENCODED PEPTIDE (CEP) hormones affect RSA, in part by controlling the angle of lateral root (LR) growth. Both hormone pathways converge on CEP DOWNSTREAM 1 (CEPD1) and CEPD2 to control primary root growth, however, a role for CEPDs in controlling the growth angle of LRs is unknown. Using phenotyping combined with genetic and grafting approaches, we showed that CEP hormone-mediated shallower LR growth required cytokinin synthesis and cytokinin perception in roots via ARABIDOPSIS HISTIDINE KINASE 2 (AHK2) and AHK3. Consistently, cytokinin synthesis and ahk2,3 mutants phenocopied the steeper-root phenotype of cep receptor 1 (cepr1) mutants on agar plates, and CEPR1 was required for trans-Zeatin (tZ)-type cytokinin-mediated shallower LR growth. In addition, cepd1,2 was less sensitive to CEP and tZ and showed basally steeper LRs on agar plates. Cytokinin and CEP pathway mutants were grown in rhizoboxes to define the role of these pathways in controlling RSA. Only cytokinin receptor mutants and cepd1,2 partially phenocopied the steeper-rooted phenotype of cepr1 mutants. These results show CEP and cytokinin signaling intersect to promote shallower LR growth, but additional components contribute to the cepr1 phenotype in soil.
Background and aims
Global wheat production is under threat due to climate change, specifically from heat and drought, which are the major contributors. This study aims to address the response to drought in CIMMYT high temperature wheat lines, specifically analyzing root characteristics and their association with other parameters under water-stressed and well-watered conditions and different culture systems.
Methods
The variability of root traits of CIMMYT High Temperature Wheat Lines (HTWL) previously developed against heat stress and 10 Pakistani approved varieties was assessed under different culture conditions and water availability.
Results
Our findings revealed that the plasticity of the wheat root system is highly pronounced, with the conditions of the rhizosphere exerting a more substantial influence than the genotypic response. Furthermore, a small number of genotypes consistently exhibited desirable traits such as longer root systems and greater root biomass across different conditions. Persistent drought negatively affects root traits and reduces root growth.
Conclusions
The variation in root traits of HTWL against drought indicates their potential for the development of improved genotypes that can withstand multiple stresses. Furthermore, it is crucial to consider rhizosphere conditions when selecting genotypes, as the plasticity of wheat roots may lead to misinterpretations if rhizosphere conditions are disregarded. Therefore, for the selection of root traits under persistent drought conditions, it is recommended to evaluate a broader range of rhizosphere conditions.
This is the annual Report of work done under the India-EU project W4C by a multidisciplinary and multi institutional consortium on the safe use of wastewater.
Because of the variety of genetic components, plants are affected by complex genetic-environment-management interactions that drive phenotypic plasticity. Reliable, automatic, multifunctional, and high-throughput phenotypic technology are more taken into consideration as crucial tools for the speedy development of genetic gain in breeding schemes. With the rapid advancement in high-throughput phenotyping (HTP) technology, a study in this aspect is ingoing a novel era called “phenomics.” The crop phenotyping network now no longer most effective needs to construct a multi-domain, multilevel, and multiscale crop phenotyping large database however additionally to analyze technical structures for phenotypic developments identity and increase bioinformatics technology for statistics extraction from the overpowering quantities of omics data. HTP platforms can monitor phenotypic variation in plants using red, green, and blue (RGB) cameras, hyperspectral sensors, and computed tomography are examples of sensors that can be linked to environmental and genotypic data. Since whole-genome sequencing (WGS) and next-generation sequencing (NGS) of many crops has been achieved, functional genomic studies of crops have divided into the main data and the high-throughput era. However, obtaining large-scale phenotypic data has become one of the most significant roadblocks to crop breeding and functional genomics research. Phenomics can give vast amounts of phenotypic data at a minimal cost because it is an inherently big scale and high throughput. Obtaining high-quality digital phenotypic data with detailed information (e.g., descriptions of protocols, growth conditions, etc., in a standardized format) allows for the examination and quantitative modeling of molecular networks influencing complex features including development, stress tolerance, and metabolism as well as community relationships. In this chapter, we will discuss how image-based HTP can be used to bridge the phenotype–genotype gap for yield prediction, root phenotyping, climate-resilient crop development, pathogen and pest detection, and quantitative trait measurement for long-term food security. Finally, we will discuss some conceptual issues and provide suggestions for bridging the phenotype–genotype divide. There is little question that precise HTP will speed up plant genetic advancements and help to usher in the next crop breeding revolution.
Root morphology and architecture are believed to be important for plant phosphorus (P) efficiency, but their genetic information is relatively scarce. In the present study, a field and a specially designed minirhizotron experiments were conducted using two soybean (Glycine max L. Merr.) genotypes and their 88 recombinant inbred lines (RILs) to elucidate the genetic variability for root morph-architecture traits and root growth dynamics as related to P efficiency in soybean. The results indicated that the root morph-architecture traits were continually segregated in the RILs with a normal distribution, indicating which are possibly controlled by quantitative trait loci. Significantly positive correlations were found between root and P traits, suggesting feasibility of screening P efficient genotype through simple selection of root traits in field. Most root morph-architecture traits were closely correlated, showing a coordinating contribution to P efficiency. Furthermore, root morphological traits always had higher heritability than architecture traits, thus, could serve as more reliable index in field selection. The dynamic parameters of root growth from the minirhizotron experiment showed that the P efficient genotype established longer and larger root system with preferring distribution in surface layer and also kept more active roots, therefore, had a better growth performance in field, than the P-inefficient genotype. Taken together, this is the first report on in situ root growth dynamics and its relation to P efficiency using minirhizotron systems in crops. Our findings help to better understand the relationships between P efficiency and root traits and, thus, facilitate development of P efficient genotypes in crops.
The grass genetic model Brachypodium (Brachypodium distachyon (L.) Beauv., sequenced line Bd 21) was studied from germination,to seed production to assess its potential as a phenotypic,model,for wheat (Triticum aestivum,L.) and other cereal crops. Brachypodium,and wheat shoot and root development,and anatomy,were highly similar. Main stem leaves and tillers (side shoots) emerged,at the same,time in both grasses in four temperature and light environments. Both developed,primary and nodal axile roots at similar leaf stages with the same,number,and arrangement,of vascular xylem trachearyelements(XTEs).Brachypodium,unlikewheat,hadanelongatedamesocotylabovetheseedanddevelopedonly one fineprimary axilerootfromthebase oftheembryo,whilewheatgenerally hasthree to five. Rootsof bothgrassescould develop first, second and third order branches that emerged from phloem poles. Both developed up to two nodal axile roots fromthecoleoptilenodeatleaf3,morethaneightnodalaxilerootsfromstemnodesafterleaf4,andmost(97%)ofthedeepest roots at flowering were branches. In long days Brachypodium flowered 30 days after emergence, and root systems ceased descent 42cm from the soil surface, such that mature roots can be studied readily in much smaller soil volumes than wheat. Brachypodiumhastheoverwhelmingadvantageofasmallsize,fastlifecycleandsmallgenome,andisanexcellentmodelto study cereal root system genetics and function, as well as genes for resource partitioning in whole plants. Additional keywords: Arabidopsis, architecture, genome, monocotyledons, photoperiod, root anatomy, tillering.
Low soil phosphorus availability is a primary constraint for plant growth in many terrestrial ecosystems. Lateral root initiation and elongation may play an important role in the uptake of immobile nutrients, such as phosphorus, by increasing soil exploration and phosphorus solubilisation. The overall objective of this study was to assess the value of lateral rooting for phosphorus,acquisition through assessment of the ‘benefit’ of lateral rooting for phosphorus,uptake and the ‘cost’ of lateral roots in terms of root respiration and phosphorus,investment at low and high phosphorus,availability. Five recombinant inbred lines (RILs) of maize derived from a cross between B73 and Mo17 with contrasting lateral rooting were grown in sand culture in a controlled environment. Genotypes with enhanced or sustained lateral rooting at low phosphorus availability had greater phosphorus acquisition, biomass accumulation, and relative growth rate (RGR) than genotypes with reduced lateral rooting at low phosphorus availability. The association of lateral root development,and plant biomass accumulation,under phosphorus,stress was not caused by allometry. Genotypes varied in the phosphorus investment required for lateral root elongation, owing to genetic differences in specific root length (SRL, which was correlated with root diameter) and phosphorus concentration of lateral roots. Lateral root extension required less biomass and phosphorus,investment than the extension of other root types. Relative growth rate was negatively correlated with specific root respiration, supporting the hypothesis that root carbon costs are an important aspect of adaptation to low phosphorus availability. Two distinct cost–benefit analyses, one with phosphorus acquisition rate as a benefit and root respiration as a cost, the other with plant phosphorus accumulation as a benefit and phosphorus allocation to lateral roots as a cost, both showed that lateral rooting was advantageous,under conditions of low phosphorus,availability. Our data suggest that enhanced lateral rooting under phosphorus,stress may be harnessed as a useful trait for the selection and breeding of more phosphorus-efficient maize genotypes. Keywords: cost–benefit analysis, lateral rooting, maize inbred lines, phosphorus efficiency, root respiration.
Selection for nitrogen (N)-efficient crops is considered to be an effective approach for minimizing the input and the loss of N fertilizers in agricultural fields. This study investigated the hypothesis that nitrate supply may induce changes in root morphology so that N uptake efficiency can be influenced. Different levels of nitrate concentration (0.04, 0.2, 2, and 4 mM) were supplied to five maize (Zea mays L.) inbred lines that had shown different N efficiencies. Possible correlations between N-uptake efficiency and several root parameters of root morphology were evaluated. The two N-efficient varieties, 478 and H21, had higher shoot and root weight and absorbed more N than the two N-inefficient lines, Wu312 and Zong31, especially under low N supply. In general, high nitrate levels (2 and 4 mM) increased the total length of lateral roots (LR), but limited the total length of primary roots (PR) (including seminal and nodal roots) as well as the average length of primary roots. As a result, the total root length (TR) increased with the increasing of nitrate levels. Total N accumulation had significant positive correlations with the root dry weight, TR, and PR at low N supply (0.04-2 mM). At high N supply (4 mM), however, only LR was to some extent correlated to N accumulation. It is concluded that, under N deficient situation, a larger root system (total root length and root surface area) that resulted mainly from the longer primary roots contributed to the efficient N accumulation. At sufficient N supply, longer lateral roots are the main factor contributed to N accumulation.
Conventional wheat (Triticum aestivum L.) cultivars grow slowly in unploughed soil because of physical and biological constraints. Here a conventional cultivar (Janz) is compared with a novel experimental line (Vigour 18), bred for high leaf vigour, to explore the hypothesis that a vigorous wheat grows better in unploughed soil. Roots of both genotypes in unploughed soil were three times more distorted with 30% shorter apices and 60% shorter expansion zones than roots in ploughed soil, because of voids between blocky peds and packed sand particles that impeded root apices. More than half the root length contacted dead, remnant roots. Vigour 18 roots grew 39% faster, were thicker and distorted less than Janz roots in unploughed soil, but developed similarly in ploughed soil. Vigour 18 shoots grew 64% faster in unploughed soil, but 15% faster in ploughed soil. Fumigation of unploughed soil improved the growth of Janz only. We suggest that faster root growth, different exudates promoting a more beneficial rhizosphere microflora, or modified shoot responses are possible mechanisms to explain Vigour 18's superior growth. Vigorous genotypes may present a new opportunity for increased productivity with conservation farming.
On 13 October 1908, Fritz Haber filed his patent on the ``synthesis of ammonia from its elements'' for which he was later awarded the 1918 Nobel Prize in Chemistry. A hundred years on we live in a world transformed by and highly dependent upon Haber-Bosch nitrogen.
Plant organ phenotyping by non-invasive video imaging techniques provides a powerful tool to assess physiological traits and biomass production. We describe here a range of applications of a recently developed plant root monitoring platform (PlaRoM). PlaRoM consists of an imaging platform and a root extension profiling software application.Thisplatformhasbeendevelopedformultiparallelrecordingsofrootgrowthphenotypesofupto50individual seedlings over several days, with high spatial and temporal resolution. PlaRoM can investigate root extension profiles of different genotypes in various growth conditions (e.g. light protocol, temperature, growth media). In particular, we present primary root growth kinetics that was collected over several days. Furthermore, addition of 0.01% sucrose to the growth medium provided sufficient carbohydrates to maintain reduced growth rates in extended nights. Further analysis of records obtained from the imaging platform revealed that lateral root development exhibits similar growth kinetics to the primary root,butthatroothairsdevelopinafasterrate.ThecompatibilityofPlaRoMwithcurrentlyaccessiblesoftwarepackagesfor studyingrootarchitecturewillbediscussed.Weareaimingforaglobalapplicationofourcollectedrootimagestoanalytical tools provided in remote locations.
Several claims have been made about genetic engineering (GE) in comparison with crop domestication and classical plant breeding, including the similarity of genetic changes between those taking place during domestication and by GE, the increased speed and accuracy of GE over classical plant breeding, and the higher level of knowledge about the actual genes being transferred by GE compared with classical breeding. In reviewing evidence pertaining to these claims, I suggest that (i) it is unlikely that changes introduced by GE will make crops weedier, although exceptions have been noted, (ii) changes brought about by GE currently often involve gain-of-function mutations, whereas changes selected during domestication generally involve loss-of-function mutations, (iii) adoption of GE cultivars has been much faster than any previous introduction and spread of agriculture that occurred earlier but has occurred at about the same rate as the spread of cultivars obtained by plant breeding, (iv) introduction of agriculture reduced the health of agriculturists compared with that of hunter-gatherers, suggesting that introduction of innovations do not automatically improve well being, (v) although GE is not a substitute for plant breeding, it can significantly contribute to plant breeding by generating additional genetic diversity, (vi) uncertainties associated with the site of insertion of transgenes in the genome and the expression of transgenes following insertion, makes GE less rapid and precise than originally claimed, and (vii) a potential advantage of GE over classical breeding is the knowledge of the actual gene(s) being inserted, although few cases of unwanted gene introductions through classical plant breeding have been documented. Further advances in GE will increase the precision of the technique, its relevance to consumers, and its environmental friendliness. What is most needed are even-handed, case-by-case assessments of the benefits and potential pitfalls of GE in comparison with other crop improvement techniques. Classical plant breeding may, in the end, also be regulated in the same way as GE.
Traditional methods of measuring tree root biomass are labor intensive and destructive in nature. We studied the utility of ground-penetrating radar (GPR) to measure tree root biomass in situ within a replicated, intensive culture forestry experiment planted with loblolly pine (Pinus taeda L.). The study site was located in Decatur County, Georgia, in an area of the Troup and Lucy (loamy, kaolinitic, thermic Grossarenic Kandiudults and Arenic Kandiudults, respectively) soils. With the aid of a digital signal processing GPR, estimates of root biomass to a depth of 30 cm were correlated to harvested root samples using soil cores. Significant effects of fertilizer application on signal attenuation were observed and corrected. The correlation coefficient between actual root biomass in soil cores and GPR estimates with corrections for fertilizer application were highly significant (r = 0.86, n = 60, p < 0.0001). Where site conditions are favorable to radar investigation, GPR can be a powerful cost-effective tool to measure root biomass. Verification with some destructive harvesting is required since universal calibrations for root biomass are unlikely, even across similar soil types. Use of GPR can drastically reduce the number of soil cores needed to assess tree root biomass and biomass distribution. The quality and quantity of information resulting from a detailed GPR survey, combined with soil cores on a subset of plots, can be used to rapidly estimate root biomass and provide a valuable assessment of lateral root biomass distribution and quantity.
In this study, we assess the possibility of using ground penetrating radar (GPR) and electrical resistivity tomography (ERT) as indirect non-destructive techniques for root detection. Two experimental sites were investigated: a poplar plantation [mean height of plants 25.7 m, diameter at breast height (dbh) 33 cm] and a pinewood forest mainly composed of Pinus pinea L. and Pinus pinaster Ait. (mean height 17 m, dbh 29 cm). GPR measures were taken using antennas of 900 and 1500 MHz applied in square and circular grids. ERT was previously tested along 2-D lines, compared with GPR sections and direct observation of the roots, and then using a complete 3-D acquisition technique. Three-dimensional reconstructions using grids of electrodes centred and evenly spaced around the tree were used in all cases (poplar and pine), and repeated in different periods in the pine forest (April, June and September) to investigate the influence of water saturation on the results obtainable. The investigated roots systems were entirely excavated using AIR-SPADE Series 2000. In order to acquire morphological information on the root system, to be compared with the GPR and ERT, poplar and pine roots were scanned using a portable on ground scanning LIDAR. In test sections analysed around the poplar trees, GPR with a high frequency antenna proved to be able to detect roots with very small diameters and different angles, with the geometry of survey lines ruling the intensity of individual reflectors. The comparison between 3-D images of the extracted roots obtained with a laser scan data point cloud and the GPR profile proved the potential of high density 3-D GPR in mapping the entire system in unsaturated soil, with a preference for sandy and silty terrain, with problems arising when clay is predominant. Clutter produced by gravel and pebbles, mixed with the presence of roots, can also be sources of noise for the GPR signals. The work performed on the pine trees shows that the shape, distribution and volume of roots system, can be coupled to the 3-D electrical resistivity variation of the soil model map. Geophysical surveys can be a useful approach to root investigation in describing both the shape and behaviour of the roots in the subsoil.
Details about the spatiotemporal development of root systems and their influence on ring-width variations in tree stems are still unknown. Furthermore, their size, spread and architecture play an important role in studying tree stability and their stabilizing effect on slopes. A major problem in this regard is the detailed 3D-data acquisition and modeling of its complex structure. The appli -cation of a laser scanner is a step towards the solution of this problem. Scanning the root system of a mature spruce tree facilitated creating a 3D scatter-plot of the root structure (resolution: 2 mm). The subsequent modeling of the structure allowed an automated replication of the coarse root structure down to a size of 0.5 cm of single roots. The resulting model of the root system facilitates cutting the roots for ring-width analysis while tagging the sample points in the model as a base for the further analysis of the root system's development.
Root responses of maize (Zea mays L.) to limited nutrients and water availability were evaluated in two highly productive full-season hybrids, DK585 and Santos (Dekalb – Monsanto), in laboratory, pot and field tests. In the laboratory, under optimal nutrient and water supply, seedlings of DK585 had higher growth (leaves and roots). Under nitrate or sulphate deprivation, DK585 showed better ability in adapting its root/shoot ratio to stress conditions, whereas Santos showed less plastic behaviour. This morphological trait of DK585 was associated with higher sulphate and constitutive nitrate influxes. In pot trials (plants with four to five leaves), DK585 maintained a high transpiration level to very low values (around 0.2) of FTSW (fraction of transpirable soil water), whereas Santos showed a higher response to soil drying. The latter reduced the rate of transpiration starting from a FTSW of about 0.6. In the open field (trial in 2000, Legnaro, NE Italy), in conditions of fluctuating combined water and nitrogen stress, DK585 at flowering reached greater root length density (RLD) than Santos in deep layers (50–100-cm interval depth) of positions further from the plant. However, in these conditions, the yield of DK585 was found to be only slightly higher than that of Santos (8.88 vs. 8.49 t ha–1 d.w.). An overall evaluation of the two hybrids indicates the more conservative strategy towards limited water and nutrient resources in Santos, and a greater tendency towards stress avoidance in DK585.
Variability of fine root (diameter<2mm) distribution was investigated in four 55 to 56-year-old Maritime pine (Pinus pinaster) stands using a combination of trench wall observations and destructive sampling. Our objectives were to assess patterns
of fine root distribution, to estimate tree fine root biomass and to explore interactions with understorey vegetation in a
gradient of relevant site conditions. Results showed that root density decreased with soil depth in all stands, and variability
appeared to be highest in litter and subsoil layers especially where compacted soil layers occurred. Roots were clustered
in patches in the top 0–50cm of the soil or were present as root channels at greater depths. Cluster number, cluster size
and number of root channels were comparable in all four stands. Overall fine root biomass at depths of 0–120cm ranged from
2.7 to 7.2Mgha−1 and was highest for the two driest stands. The use of trench wall records made it possible to reduce the variability of these
estimates. Understorey species represented as much as 90% of the total number of fine roots in the upper layers, and the understorey
formed a considerable proportion of the total ecosystem biomass, suggesting that understorey species are likely competitors
for nutrients in this ecosystem. Further studies should focus on the interaction of the understorey and pine roots and the
ecological significance of clustered roots and nutrient distributions.
Under low-input cropping systems, nitrogen (N) can be a limiting factor in plant growth and yield. Identifying genotypes that
are more efficient at capturing limited N resources and the traits and mechanisms responsible for this ability is important.
Root trait has a substantial influence on N acquisition from soils. Nevertheless, inconsistencies still exist as to the effect
of low N on root length and its architecture in terms of lateral and axial roots. For maize, a crop utilizing heterosis, little
is known about the relationship between parents and their crosses in the response of root architecture to N availability.
Here 7 inbred maize lines and 21 of their crosses created by diallel mating were used to study the effect of N stress on root
morphology as well as the relationship between the inbreds and their crosses. With large genotypic differences, low N generally
suppresses shoot growth and increases the root to shoot ratio with or without increasing root biomass in maize. Maize plants
responded to N deficiency by increasing total root length and altering root architecture by increasing the elongation of individual
axial roots and enhancing lateral root growth, but with a reduction in the number of axial roots. Here, the inbreds showed
weaker responses in root biomass and other root parameters than their crosses. Heterosis of root traits was significant at
both N levels and was attributed to both the general combining ability (GCA) and special combining ability (SCA). Low N had
substantial affects on the pattern of heterosis, GCA and SCA affects on root traits for each of the crosses suggesting that
selection under N stress is necessary in generating low N-tolerant maize genotypes.
Image analysis is used in numerous studies of root system architecture (RSA). To date, fully automatic procedures have not
been good enough to completely replace alternative manual methods. DART (Data Analysis of Root Tracings) is freeware based
on human vision to identify roots, particularly across time-series. Each root is described by a series of ordered links encapsulating
specific information and is connected to other roots. The population of links constitutes the RSA. DART creates a comprehensive
dataset ready for individual or global analyses and this can display root growth sequences along time. We exemplify here individual
tomato root growth response to shortfall in solar radiation and we analyse the global distribution of the inter-root branching
distances. DART helps in studying RSA and in producing structured and flexible datasets of individual root growth parameters.
It is written in JAVA and relies on manual procedures to minimize the risks of errors and biases in datasets.
Food production requires application of fertilizers containing phosphorus, nitrogen and potassium on agricultural fields in order to sustain crop yields. However modern agriculture is dependent on phosphorus derived from phosphate rock, which is a non-renewable resource and current global reserves may be depleted in 50–100 years. While phosphorus demand is projected to increase, the expected global peak in phosphorus production is predicted to occur around 2030. The exact timing of peak phosphorus production might be disputed, however it is widely acknowledged within the fertilizer industry that the quality of remaining phosphate rock is decreasing and production costs are increasing. Yet future access to phosphorus receives little or no international attention. This paper puts forward the case for including long-term phosphorus scarcity on the priority agenda for global food security. Opportunities for recovering phosphorus and reducing demand are also addressed together with institutional challenges.
A newly developed technique based on image sequence analysis allows automatic and precise quantification of the dynamics of
the growth velocity of the root tip, the distribution of expansion growth rates along the entire growth zone and the oscillation
frequencies of the root tip during growth without the need of artificial landmarks. These three major parameters characterizing
expansion growth of primary roots can be analysed over several days with high spatial (20 μm) and temporal resolution (several
minutes) as the camera follows the growing root by an image‐controlled root tracking device. In combination with a rhizotron
set up for hydroponic plant cultivation the impact of rapid changes of environmental factors can be assessed. First applications
of this new system proved the absence of diurnal variation of root growth in Zea mays under constant temperature conditions. The distribution profile of relative elemental growth rate (REGR) showed two maxima
under constant and varying growth conditions. Lateral oscillatory movements of growing root tips were present even under constant
environmental conditions. Dynamic changes in velocity‐ and REGR‐distribution within 1 h could be quantified after a step change
in temperature from 21 °C to 26 °C. Most prominent growth responses were found in the zone of maximal root elongation.
Grafting is a suitable method to control soil-borne diseases in melon (Cucumis melo L.) crops. To date, several Cucurbita species and their inter-specific hybrids have been tested as rootstocks. However, graft-scion incompatibility and lower fruit quality have prevented their commercial use. The wild accession 'Pat 81' ssp. agrestis of C. melo is highly resistant to Monosporascus cannonballus Pollack et Uecker root rot, and develops a root system that is more suitable to withstand infested soils than that of cultivated melon. The potential of 'Pat 81' as a rootstock for melons (e.g., 'Piel de Sapo' type, C. melo ssp. melo) compared with the popular rootstock 'RS 841' (Cucurbita maxima × Cucurbita moschata) has been evaluated here. The response of grafted plants to Monosporascus root rot disease, and rootstock effects on plant performance and fruit quality have been investigated using both classical methods and modern technologies (e.g., root image analysis and real-time PCR). The results indicate that, during infection, the root system of 'Pat 81' adapts to the needs of the aerial part of the 'Piel de Sapo' scion, displays a high level of resistance to M. cannonballus (similar to 'RS 841'), and provides the plant with more healthy roots, with a higher root/vine biomass ratio compared with non-grafted 'Piel de Sapo'. In addition, 'Pat 81' rootstock retains its favourable root structure (i.e., larger total length and root area) to withstand soil stress. In healthy soils, 'Pat 81' rootstocks had less effect on fruit quality than 'RS 841', leading to a lower percentage of non-marketable products. The high resistance of' Pat 81', and its reduced effect on fruit quality, point to it as a good rootstock for the grafting of melons to resist M. Cannonballus infested soils.
The study of the genetic control of natural variation in the root architecture of Cucumis melo L. is complex due to the difficulties of root phenotyping and to the quantitative nature of root traits and their plasticity. A library of near-isogenic lines (NILs), constructed by introgressing the genome of the exotic Korean accession Shongwan Charmi [SC (PI161375)] into the genetic background of the cultivar Piel de Sapo (PS) has recently become available. In this work, we used this population to identify quantitative trait loci (QTLs) controlling variation in root growth and architecture. We studied separately the primary root and the secondary and tertiary root systems during a 15-day period. Heritabilities for the root traits were moderate. Correlation and principal component analysis showed independence among traits measuring root length and root branching level, indicating the possibility of modifying both traits independently. PS and SC clearly differed in plant size. Significant allometric relationships between vine biomass and some root traits were identified. The use of NILs with similar plant size of PS allowed us to avoid the inaccuracies caused by size-dependent variation of root traits. A total of 17 QTLs for root traits in seven linkage groups were identified: three QTLs for primary root length, three QTLs for the diameter of the primary root, three QTLs for secondary root density, three QTLs for the average length of the secondary roots, three QTLs for the percentage of secondary roots bearing tertiary roots, and two QTLs for tertiary root density. In most of these traits, transgressive variation was observed.
A requirement for understanding morphogenesis is being able to quantify expansion at the cellular scale. Here, we present new software (RootflowRT) for measuring the expansion profile of a growing root at high spatial and temporal resolution. The software implements an image processing algorithm using a novel combination of optical flow methods for deformable motion. The algorithm operates on a stack of nine images with a given time interval between each (usually 10 s) and quantifies velocity confidently at most pixels of the image. The root does not need to be marked. The software calculates components of motion parallel and perpendicular to the local tangent of the root's midline. A variation of the software has been developed that reports the overall root growth rate versus time. Using this software, we find that the growth zone of the root can be divided into two distinct regions, an apical region where the rate of motion, i.e. velocity, rises gradually with position and a subapical region where velocity rises steeply with position. In both zones, velocity increases almost linearly with position, and the transition between zones is abrupt. We observed this pattern for roots of Arabidopsis, tomato (Lycopersicon lycopersicum), lettuce (Lactuca sativa), alyssum (Aurinia saxatilis), and timothy (Phleum pratense). These velocity profiles imply that relative elongation rate is regulated in a step-wise fashion, being low but roughly uniform within the meristem and then becoming high, but again roughly uniform, within the zone of elongation. The executable code for RootflowRT is available from the corresponding author on request.
A pressure chamber and a root pressure probe technique have been used to measure hydraulic conductivities of rice roots (root
Lpr per m2 of root surface area). Young plants of two rice (Oryza sativa L.) varieties (an upland variety, cv. Azucena and a lowland variety, cv. IR64) were grown for 31–40 d in 12 h days with 500 μmol m−2 s−1 PAR and day/night temperatures of 27 °C and 22 °C. Root Lpr was measured under conditions of steady‐state and transient water flow. Different growth conditions (hydroponic and aeroponic
culture) did not cause visible differences in root anatomy in either variety. Values of root Lpr obtained from hydraulic (hydrostatic) and osmotic water flow were of the order of 10−8 m s−1 MPa−1 and were similar when using the different techniques. In comparison with other herbaceous species, rice roots tended to have
a higher hydraulic resistance of the roots per unit root surface area. The data suggest that the low overall hydraulic conductivity
of rice roots is caused by the existence of apoplastic barriers in the outer root parts (exodermis and sclerenchymatous (fibre)
tissue) and by a strongly developed endodermis rather than by the existence of aerenchyma. According to the composite transport
model of the root, the ability to adapt to higher transpirational demands from the shoot should be limited for rice because
there were minimal changes in root Lpr depending on whether hydrostatic or osmotic forces were acting. It is concluded that this may be one of the reasons why rice
suffers from water shortage in the shoot even in flooded fields.
One of the most popular systems to study root systems is growing plants in bioassay dishes filled with agar. However these dishes have contamination problems, are expensive as they cannot be autoclaved, are difficult to handle, and are not suitable for big roots of crop plants. In this paper we present a new methacrylate container box that has been successfully used for the study of the melon root system. These new container boxes have several advantages over commercially available boxes and are useful to study the root system of horticultural plants with considerable root growth.
Root phenotyping is a challenging task, mainly because of the hidden nature of this organ. Only recently, imaging technologies have become available that allow us to elucidate the dynamic establishment of root structure and function in the soil. In root tips, optical analysis of the relative elemental growth rates in root expansion zones of hydroponically-grown plants revealed that it is the maximum intensity of cellular growth processes rather than the length of the root growth zone that control the acclimation to dynamic changes in temperature. Acclimation of entire root systems was studied at high throughput in agar-filled Petri dishes. In the present study, optical analysis of root system architecture showed that low temperature induced smaller branching angles between primary and lateral roots, which caused a reduction in the volume that roots access at lower temperature. Simulation of temperature gradients similar to natural soil conditions led to differential responses in basal and apical parts of the root system, and significantly affected the entire root system. These results were supported by first data on the response of root structure and carbon transport to different root zone temperatures. These data were acquired by combined magnetic resonance imaging (MRI) and positron emission tomography (PET). They indicate acclimation of root structure and geometry to temperature and preferential accumulation of carbon near the root tip at low root zone temperatures. Overall, this study demonstrated the value of combining different phenotyping technologies that analyse processes at different spatial and temporal scales. Only such an integrated approach allows us to connect differences between genotypes obtained in artificial high throughput conditions with specific characteristics relevant for field performance. Thus, novel routes may be opened up for improved plant breeding as well as for mechanistic understanding of root structure and function.
Low phosphorus availability is a primary constraint to plant productivity in many natural and agricultural ecosystems. Plants display a wide array of adaptive responses to low phosphorus availability that generally serve to enhance phosphorus mobility in the soil and increase its uptake. One set of adaptive responses is the alteration of root architecture to increase phosphorus acquisition from the soil at minimum metabolic cost. In a series of studies with the common bean, work in our laboratory has shown that architectural traits that enhance topsoil foraging appear to be particularly important for genotypic adaptation to low phosphorus soils (`phosphorus efficiency'). In particular, the gravitropic trajectory of basal roots, adventitious rooting, the dispersion of lateral roots, and the plasticity of these processes in response to phosphorus availability contribute to phosphorus efficiency in this species. These traits enhance the exploration and exploitation of shallow soil horizons, where phosphorus availability is greatest in many soils. Studies with computer models of root architecture show that root systems with enhanced topsoil foraging acquire phosphorus more efficiently than others of equivalent size. Comparisons of contrasting genotypes in controlled environments and in the field show that plants with better topsoil foraging have superior phosphorus acquisition and growth in low phosphorus soils. It appears that many architectural responses to phosphorus stress may be mediated by the plant hormone ethylene. Genetic mapping of these traits shows that they are quantitatively inherited but can be tagged with QTLs that can be used in plant breeding programs. New crop genotypes incorporating these traits have substantially improved yield in low phosphorus soils, and are being deployed in Africa and Latin America.
Root architectural traits that increase topsoil foraging are advantageous,for phosphorus,acquisition but may incur tradeoffs for the acquisition of deep soil resources such as water. To examine this relationship, common bean genotypes contrasting for rooting depth were grown in the field and in the greenhouse with phosphorus stress, water stress and combined phosphorus and water stress. In the greenhouse, water and phosphorus availability were vertically stratified to approximate field conditions, with higher phosphorus in the upper layer and more moisture in the bottom layer. Under phosphorus stress, shallow-rooted genotypes grew best, whereas under drought stress, deep- rooted genotypes grew best. In the combined stress treatment, the best genotype in the greenhouse had a dimorphic root system that permitted vigorous rooting throughout the soil profile. In the field, shallow-rooted genotypes surpassed deep-rooted genotypes under combined,stress. This may reflect the importance of early vegetative growth in terminal drought environments. Our results support the hypothesis that root architectural tradeoffs exist for multiple resource acquisition, particularly when resources are differentially localised in the soil profile. Architectural plasticity and root dimorphism,achieved through complementary,growth of distinct root classes may be important means to optimise acquisition of multiple soil resources. Keywords: drought, functional tradeoffs, multiple resource acquisition, Phaseolus vulgaris (common bean),
Plants develop most organs post-embryonically, which allows the incorporation of environmental information into decisions concerning when and where to produce new organs. This developmental plasticity is evident in the plant root system, which in dicotyledonous plants such as Arabidopsis thaliana is mostly comprised of lateral and adventitious roots that develop along the length of the primary root. The rate of primary root growth and the location, spacing and growth rate of lateral roots are influenced by the availability of environmental cues such as water and nutrients, which can have dramatic effects on the final architecture of the root system. These environmental responses must intersect with the intrinsic developmental programme of the plant, which is responsible for the general formation and maintenance of the root system. The final root system architecture of any plant is then the product of both intrinsic and environmental response pathways. Carbohydrates and plant hormones such as auxin and cytokinins are required for both intrinsic root development and modulating root system architecture in response to different growth conditions, thus facilitating the optimisation of root growth in complex, heterogeneous environments.
Breeding widely adapted wheat ( Triticum aestivum L.) genotypes with stable and high yields across environments is particularly important for developing countries since yield stabilizing inputs are often limited or not available. To evaluate the screening ability of locations for identification of such genotypes, data collected for 19 yr by the International Spring Wheat Yield Nursery (ISWYN) were analyzed; 1221 trials at 268 locations in 69 countries were involved. To compare single‐experiment parameters, i.e., genotypic variance (σ̂ ² g ) k , error variance (σ̂ ² e ) k , heritability (h ² ) k , and coefficient of variation (CV) k , trials without major biotic stresses were divided into three groups according to mean grain yield. Genotypic variance, error variance, and heritability increased and (CV) k decreased with yield. Group means for the four parameters were significantly ( P = 0.01) different. A fourth group containing trials with major biotic stresses had the highest, but not significantly higher, average estimates for (σ̂ ² g ) k , (h ² ) k , and (CV) k . The screening ability for each location was calculated as the correlation, r k , between mean grain yield of genotypes at each location and mean yield across locations. The screening ability was highest for locations with no major abiotic and biotic stress factors apart from leaf rust ( Puccinia recondita Roberge ex Desmaz. f. sp. tritici ) and stem rust ( P. graminis Pers.:Pers. f. sp. tritici Eriks. & E. Henn.). CIMMYT's principal test site, Ciudad Obrégon, Sonora, Mexico, was most suitable for screening, with an average r k of 0.77. Sensitivity to photoperiod, cold tolerance, need for late maturity, tolerance to problem soils, and resistance to diseases other than rusts were the main adaptation‐limiting and location‐specific factors.
The Green Revolution boosted crop yields in developing nations by introducing dwarf genotypes of wheat and rice capable of responding to fertilisation without lodging. We now need a second Green Revolution, to improve the yield of crops grown in infertile soils by farmers with little access to fertiliser, who represent the majority of third-world farmers. Just as the Green Revolution was based on crops responsive to high soil fertility, the second Green Revolution will be based on crops tolerant of low soil fertility. Substantial genetic variation in the productivity of crops in infertile soil has been known for over a century. In recent years we have developed a better understanding of the traits responsible for this variation. Root architecture is critically important by determining soil exploration and therefore nutrient acquisition. Architectural traits under genetic control include basal-root gravitropism, adventitious-root formation and lateral branching. Architectural traits that enhance topsoil foraging are important for acquisition of phosphorus from infertile soils. Genetic variation in the length and density of root hairs is important for the acquisition of immobile nutrients such as phosphorus and potassium. Genetic variation in root cortical aerenchyma formation and secondary development ('root etiolation') are important in reducing the metabolic costs of root growth and soil exploration. Genetic variation in rhizosphere modification through the efflux of protons, organic acids and enzymes is important for the mobilisation of nutrients such as phosphorus and transition metals, and the avoidance of aluminum toxicity. Manipulation of ion transporters may be useful for improving the acquisition of nitrate and for enhancing salt tolerance. With the noteworthy exceptions of rhizosphere modification and ion transporters, most of these traits are under complex genetic control. Genetic variation in these traits is associated with substantial yield gains in low-fertility soils, as illustrated by the case of phosphorus efficiency in bean and soybean. In breeding crops for low-fertility soils, selection for specific root traits through direct phenotypic evaluation or molecular markers is likely to be more productive than conventional field screening. Crop genotypes with greater yield in infertile soils will substantially improve the productivity and sustainability of low-input agroecosystems, and in high-input agroecosystems will reduce the environmental impacts of intensive fertilisation. Although the development of crops with reduced fertiliser requirements has been successful in the few cases it has been attempted, the global scientific effort devoted to this enterprise is small, especially considering the magnitude of the humanitarian, environmental and economic benefits being forgone. Population growth, ongoing soil degradation and increasing costs of chemical fertiliser will make the second Green Revolution a priority for plant biology in the 21st century.
Rice accessions from the International Rice Research Institute (IRRI) germplasm bank were evaluated for root traits of 40-day-old plants grown in soil in the greenhouse. The 136 accessions represented six groups defined on the basis of isozyme classification, with isozyme group six further subdivided on the basis of origin and morphology. An additional 28 rice cultivars were evaluated for seminal root xylem vessel diameter when grown in pots in a growth chamber. Rice groups differed in root thickness, root xylem vessel diameter, root:shoot ratio, and patterns of root distribution. Isozyme group 1, which corresponds generally to the indica subspecies, had thin, superficial roots with narrow vessels and a low root:shoot ratio. The other major isozyme group, group 6, comprising japonica types, was characterized by thick roots with wider vessels, a greater proportion of the root weight below 15cm, and a larger root:shoot ratio. On an average, the bulu and temperate group 6 accessions were similar to the non-bulu types except that their root:shoot ratios and proportion of root weight above 15cm were more similar to group 1. Group 2, with aus types from South Asia, was characterized by intermediate root thickness, but vertical root distribution and root:shoot ratio were more similar to group 6. The minor isozyme groups 3–5 were represented by few accessions, and in general, they had root thickness and root distribution profiles more similar to group 1 than to group 6. While significant differences were observed among isozyme groups for all the traits under study, there was significant variation within groups and groups overlapped for all traits measured. This study highlights the wide range of variability for constitutive root traits in rice. For example, root thickness ranged from 0.68 to 1.04mm, seminal root xylem vessel diameters from 30 to 58μm, root:shoot ratios from 0.05 to 0.21, and accessions had from 44 to 73% of the total root weight concentrated in the surface 15cm of soil. For the 28 cultivars evaluated, root xylem vessel diameter was highly correlated with reported values of leaf epicuticular wax content (r=0.89). These values indicate the range of genetic variation within the rice genome for root morphological traits.
vation of roots growing in soils, minirhizotrons also allow observation of other underground plant organs Root research methods are often tedious, labor intensive, and such as rhizomes, peanut (Arachis hypogaea L.) pods, prone to large variability. Minirhizotron technology has the potential to greatly enhance root research capabilities, but quantifying minirhi- and legume nodules and other soil organisms such as zotron data is very time consuming. This note presents new software insects, worms, and fungi (Lussenhop et al., 1991). that allows rapid, accurate measurement of root length from digital The greatest disadvantage of minirhizotron systems has images—Root Measurement System (RMS). In addition to measuring been the tedious, time-consuming process of translating root lengths and diameters, RMS records number of roots in an image qualitative information from observations to quantita- and calculates their total volume, total surface area, and length density. tive data (Hendrick and Pregitzer, 1996). Until recently, Ten untrained RMS users averaged 654 6 42 s to measure the length most root images have been collected on video, film, or of a 24 mm s-shaped line 10 times. The standard error of the mean overlays traced with a wax pencil. Root length may be for repeated length measurements was ,0.1 mm for all but one of
In soybean and common bean, enhanced topsoil foraging permitted by shallow root architectures is advantageous for phosphorus acquisition from stratified soils. The importance of this phenomenon in graminaceous crops, which have different root architecture and morphology from legumes, is unclear. In this study we evaluated the importance of shallow roots for phosphorus acquisition in maize (Zea mays L.). In a field study, maize genotypes with shallower roots had greater growth in low phosphorus soil than deep-rooted genotypes. For physiological analysis, four maize genotypes differing in root shallowness in the field were grown in solid media with stratified phosphorus availability in a controlled environment. Of the four genotypes, one shallow and one deep genotype were also inoculated with arbuscular mycorrhiza (AM). Shallower genotypes had significantly greater growth and phosphorus accumulation compared with deeper genotypes at low phosphorus availability. Mycorrhizal colonisation altered root shallowness under low phosphorus conditions, increasing shallowness substantially in a deep-rooted genotype but slightly decreasing shallowness in a shallow-rooted genotype. Mycorrhizal colonisation increased phosphorus acquisition under low phosphorus availability. Respiration costs of roots and shoots of phosphorus- efficient genotypes were significantly lower under low phosphorus conditions compared with inefficient genotypes. The physiological efficiency of phosphorus acquisition, expressed as root respiration per unit of phosphorus acquisition, was greater in shallow rooted genotypes. Our results demonstrate that genetic variation for root shallowness exists in maize, that phosphorus and AM can modulate root shallowness independently, and that a shallower root system is beneficial for plant performance in maize at low phosphorus availability. We propose that root architectural traits that enhance topsoil foraging are important traits for improved phosphorus acquisition efficiency of annual grain crops such as maize in addition to legumes.
The root system is essential for the growth and development of plants. In addition to anchoring the plant in the ground, it is the site of uptake of water and minerals from the soil. Plant root systems show an astonishing plasticity in their architecture, which allows for optimal exploitation of diverse soil structures and conditions. The signalling pathways that enable plants to sense and respond to changes in soil conditions, in particular nutrient supply, are a topic of intensive research, and root system architecture (RSA) is an important and obvious phenotypic output. At present, the quantitative description of RSA is labour intensive and time consuming, even using the currently available software, and the lack of a fast RSA measuring tool hampers forward and quantitative genetics studies. Here, we describe EZ-Rhizo: a Windows-integrated and semi-automated computer program designed to detect and quantify multiple RSA parameters from plants growing on a solid support medium. The method is non-invasive, enabling the user to follow RSA development over time. We have successfully applied EZ-Rhizo to evaluate natural variation in RSA across 23 Arabidopsis thaliana accessions, and have identified new RSA determinants as a basis for future quantitative trait locus (QTL) analysis.
summaryTwo components of root architecture (topology and link lengths) were measured in a group of 13 dicotyledon and eight grass species, under both high and low nutrient supply rates. Predictions were made, based on a simulation analysis, that root systems from plants grown in low nutrient conditions and those from plants characteristic of such conditions should have the more herringbone topology (branching principally on main axis) and longer links. Both these predictions were confirmed for the dicots, but data from grasses agreed with the predictions only in terms of geometry (link lengths) and not topology. The ecological character of the species was assessed on the assumption that species of low inherent relative growth rate were characteristic of infertile soils, Taxonomic patterns were also evident, indicating that some variation in root system architecture may be historical rather than adaptive.
Four minirhizotrons were installed in each of three replicate plots in a deciduous forest dominated by Acer saccharum Marsh. The length growth of tree roots along the surface of the minirhizotrons was measured for a period of one year, and the resulting data were analyzed in nested, averaged and pooled arrangements. The analyses of nested data showed that spatial variation in root growth and abundance among minirhizotrons within plots was greater than variation among plots. Averaging data from minirhizotrons within plots prior to analysis reduced variation about plot means, but extensive intraplot variation invalidates this approach on statistical grounds. Both nested and averaged data failed to account for the contribution of individual roots to the mean, and root production rates were consequently overestimated. Pooling the data from the four minirhizotrons reduced variation about the means, and resulted in a more representative estimate of root production rates. The analysis of composited data can be used to incorporate small-scale variation into a single replicate sample in those circumstances where the activity of the root systems of plant communities is the object of study.
To investigate the genetic background of nitrate-induced elongation and initiation of lateral roots in rice (Oryza sativa L.), a doubled haploid (DH) population, derived from a cross between IR64 and Azucena, which showed different responses to local supplied NO3
– in lateral root elongation and initiation, was used in an agar culture experiment with three separated layers. The second agar layer was supplied with 3mM NO3
– or without NO3
– as two treatments. Average lateral root length, lateral root number and surface area of lateral roots in the second agar layers with and without nitrate, respectively, were measured. The ratio of the parameters from the two treatments were calculated as derived parameters. Seven putative Quantitative trait loci (QTLs) for the 6 lateral root traits in nitrate-deficient and nitrate-supplied layers were detected. These QTLs individually explained about 9% to 15% of the total phenotypic variations in the traits. Identical QTLs for root traits from other reports with QTLs detected in this case were found, which suggests that the genetic factors responsive to local supplied NO3
– is involved in root growth and development
The objective of this study was to develop a phenotyping platform for the non-destructive, digital measurement of early root
growth of axile and lateral roots and to evaluate its suitability for identifying maize (Zea mays L.) genotypes with contrasting root development. The system was designed to capture images of the root system within minutes
and to batch process them automatically. For system establishment, roots of the inbred line Ac7729/TZSRW were grown until
nine days after germination on the surface of a blotting paper in pouches. An A4 scanner was used for image acquisition followed
by digital image analysis. Image processing was optimized to enhance the separation between the roots and the background and
to remove image noise. Based on the root length in diameter-class distribution (RLDD), small-diameter lateral roots and large-diameter
axile roots were separated. Root systems were scanned daily to model the growth dynamics of these root types. While the axile
roots exhibited an almost linear growth, total lateral root length increased exponentially. Given the determined exponential
growth, it was demonstrated that two plants, germinated one day apart but with the same growth rates differed in root length
by 100%. From the growth rates we were able to identify contrasting genotypes from 236 recombinant inbred lines (RILs) of
the CML444 x SC-Malawi cross. Differences in the growth of lateral roots of two selected RILs were due to differences in the
final length and linear density of the primary lateral roots, as proven by the manual reanalysis of the digital images. The
high throughput makes the phenotyping platform attractive for routine genetic studies and other screening purposes.
Recognition of chlorine as a plant micronutrient has been extended to include ten species. Acute chlorine deficiencies or decreased yields were produced with lettuce, tomato, cabbage, carrot, sugar beet, barley, alfalfa, buckwheat, corn, and beans. Squash plants showed neither loss in yield nor other deficiency symptoms when cultured at the same time and under the same conditions as the aforementioned species. All plants acquired more chlorine during their growth than can be accounted for from seeds, inorganic salts, or water used in the experiments. Plant species least susceptible to injury when cultured upon low chlorine salt solutions were also the ones most capable of acquiring extrinsic chlorine. Of the species studied, lettuce was the most sensitive to minus chlorine culture solutions and squash, the least sensitive. However, the concentration of chlorine in all of the species cultured under limited chlorine supply was not greatly different. It is inferred that plants such as corn, beans, and squash survived the minus chlorine cultures by reason of greater accretion of extrinsic chlorine from the atmosphere. The form of the atmospherically borne chlorine is not known.
A simple gel chamber is described for measurement of seedling root traits. Seedlings are located between two closely spaced flat layers of transparent gel, on plastic plates (at least one of which is transparent). Root system traits can be non-destructively recorded in two-dimensions using a flatbed scanner. Easily measured rooting traits include root length, elongation rate, longest root, deepest root, seminal root number, and angular spread of roots. Examples of wild, landrace, and cultivated barleys were grown in the gel chambers, between gel layers or in loosely packed soil. Root growth on the gel plates was similar to that in loose soil, with the cultivated barley having the most seminal axes (about7), and widest angular spread of roots (about 120), and wild barley the fewest seminal axes (about3), and narrowest angular spread of roots (about 40). Landrace barley lines tested were intermediate between wild barley and modern cultivars. Separate experiments were performed to study the effect of grain mass and grain size on these rooting traits. These experiments included parents of genetic mapping populations. Seminal root number was most strongly dependent on grain mass in the modern cultivar Chime. Grain size significantly influenced root number in the modern cultivar Derkado, the breeding line B83-12/21/5, and a selection from a landrace Tadmor, suggesting that grain size should be controlled in any screening exercise.
During the last 10years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters
have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these
data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL
analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number,
maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs
detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published
between 1995 and 2007. The physical position on the pseudo-chromosomes of the markers flanking each QTL was determined. An
overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The
32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package
MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information
criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones,
encompassed only a few genes.
We present a method to visually score 10 root architectural traits of the root crown of an adult maize plant in the field
in a few minutes. Phenotypic profiling of three recombinant inbred line (RIL) populations of maize (Zea mays L.; B73xMo17, Oh43xW64a, Ny821xH99) was conducted in 2008 in a silt loam soil in Pennsylvania and in a sandy soil in Wisconsin,
and again in 2009 in Pennsylvania. Numbers, angles and branching pattern of crown and brace roots were assessed visually at
flowering. Depending on the soil type in which plants were grown, sample processing took from three (sand) to 8min (silt-loam).
Visual measurement of the root crown required 2min per sample irrespective of the environment. Visual scoring of root crowns
gave a reliable estimation of values for root architectural traits as indicated by high correlations between measured and
visually scored trait values for numbers (r
2 = 0.46–0.97), angles (r
2 = 0.66–0.76), and branching (r
2 = 0.54–0.88) of brace and crown roots. Based on the visual evaluation of root crown traits it was possible to discriminate
between populations. RILs derived from the cross NY821 x H99 generally had the greatest number of roots, the highest branching
density and the most shallow root angles, while inbred lines from the cross between OH43 x W64a generally had the steepest
root angles. The ranking of genotypes remained the same across environments, emphasizing the suitability of the method to
evaluate genotypes across environments. Scoring of brace roots was better correlated with the actual measurements compared
to crown roots. The visual evaluation of root architecture will be a valuable tool in tailoring crop root systems to specific
environments.
Keywords
Zea mays L.–Root architecture–Crown root–Brace root–High throughput phenotyping–Root angles–Root branching
Root characteristics of seedlings of five different barley genotypes were analysed in 2D using gel chambers, and in 3D using
soil sacs that were destructively harvested and pots of soil that were assessed non-invasively using X-ray microtomography.
After 5days, Chime produced the greatest number of root axes (∼6) and Mehola significantly less (∼4) in all growing methods.
Total root length was longest in GSH01915 and shortest in Mehola for all methods, but both total length and average root diameter
were significantly larger for plants grown in gel chambers than those grown in soil. The ranking of particular growth traits
(root number, root angular spread) of plants grown in gel plates, soil sacs and X-ray pots was similar, but plants grown in
the gel chambers had a different order of ranking for root length to the soil-grown plants. Analysis of angles in soil-grown
plants showed that Tadmore had the most even spread of individual roots and Chime had a propensity for non-uniform distribution
and root clumping. The roots of Mehola were less well spread than the barley cultivars supporting the suggestion that wild
and landrace barleys tend to have a narrower angular spread than modern cultivars. The three dimensional analysis of root
systems carried out in this study provides insights into the limitations of screening methods for root traits and useful data
for modelling root architecture.
The value of germplasm-specific and general indexes of selection based on morphophysiological traits was assessed as an alternative to conventional yield-based selection for grain yield improvement of durum wheat in a semi-arid Mediterranean region. General indexes were developed from the evaluation of a collection of 503 landrace accessions. Specific indexes were also defined for each of the durum wheat types mediterraneum typicum and syriacum as well as for a third germplasm group including mostly Mediterranean material pertaining to neither of these types. Indexes included two or three traits among the following: displacement from optimal heading date (difference in absolute value of days from the mean heading date of three control cultivars), early growth vigour, kernels per spike and kernel weight, the two yield components being alternative to each other. The efficiency of selection criteria was assessed in another set of 64 entries in terms of predicted yield responses and actual yield gains over target environments other than that of selection. Each of the three environments acted by turns as the selection environment and the remaining two as the target environments. These environments allowed for the assessment of selection criteria over a wide range of seasonal rainfall and mean yield levels. Large genotype×environment interaction was observed for yield and early vigour. Ranking of selection indexes for predicted and actual yield responses were fairly consistent, indicating an advantage of general indexes. The best among them, including heading displacement and kernels per spike, was, on the average, 20% and 11% more efficient than yield-based selection in terms of predicted and actual responses, respectively. The advantage of this index was the consequence of the absence of covariation and the moderate to high values of genetic correlation with yield over target environments, heritability and ratio of genotypic to genotype×environment interaction variance of its component traits.
A protocol is described for non-destructive visualization and quantification of roots for relatively large core using computed tomography (CT) and computer codes developed to isolate and analyze the CT matrices. The scanner settings were optimized using a phantom core filled with different soil and materials (including root segments) of known geometry and orientation. CT parameters were optimized (130 kV peak voltage and 480 mAs), using a core 0.23×0.14 m diam. filled with a single grain sand scanned at a voxel resolution of 275×275×1000 μm. Quantitative attributes of the roots of chickpea 21 days after germination such as the number of root laterals, their volume, length, wall area, tortuosity and orientation are presented and compared with results obtained by destructive sampling. Results suggest the CT approach systematically underestimated root length compared to destructive sampling (difference reaching up to 10%). The average root segment length estimated by the non-destructive algorithm was 28.1 mm compared to 36 mm by destructive analysis. However, the non-destructive approach revealed details that are not possible to obtain with invasive techniques. For instance, the root laterals had an average tortuosity of 2.5 indicating that their length was 2.5 greater than the distance between their extremities.
Root complexity is an important factor in the growth and survivability of maize plants under biotic and abiotic stress conditions. To genetically improve root structure in the future, there is a need to identify the genes that govern root complexity. Root complexity itself is ill defined, but indicators derived from images of the root system such as Fractal Dimension can be used as proxies. A disadvantage of using Fractal Dimension as a complexity indicator is that the complexity of the root as seen in the images is captured into a single parameter.This paper describes an alternative method, which translates a root image into a set of parameters. The method consists of computing the intercepts of circles drawn around the centre of the root image with the root branches. This led to characteristic curves from which parameters can be extracted using curve fitting. In addition to the parameters obtained by curve fitting, the density of the root images was included. All parameters were evaluated on their ability to classify the roots among their original genotypes using a method from the realm of Artificial Intelligence, the Support Vector Machine (SVM).The results showed that whilst using merely three parameters originating from the characteristic curves, the SVM algorithm was capable of correctly classifying 99.95% of roots among 235 original genotypes.
We describe a method to reconstruct the root network from a three-dimensional image generated with computed tomography. The X-ray absorption of roots and the interface of the air–soil material is very similar and the contrast extremely low. The method consists of three steps: contrast enhancement using a non-linear diffusion filter, thresholding based on Rosin's method and extraction of the main features using a morphological connectivity algorithm. With this approach, we are also capable of reconstructing fine roots with high fidelity, which is shown with a performance experiment using artificial images with increasing noise. The method is applied to an X-ray microtomography data set of two alder roots, grown for 4 months in a natural moraine soil. To simplify the soil material, the bare roots were transferred into a Plexiglas receptacle filled with quartz sand. The reconstructed image is compared with a photograph of the real roots.
Information on the amount and spatial distribution of plant roots is increasingly needed for understanding and managing crop behaviour. Soil electrical resistivity (ρ) tomography has been proposed as a non-destructive method for root biomass quantification and mapping in trees but evidence is needed on the applicability of the technique at low root density and in herbaceous plants.We produced high-resolution 3D DC soil resistivity tomograms in containers with bare soil (B), and alfalfa (Medicago sativa L.) (A1) on a silt loam soil, and alfalfa on a loam (A2). Root biomass (RMD), root length density (RLD), soil electrical conductivity (EC) and water content (θ) were measured destructively.The pattern of soil resistivity matched the spatial distribution of θ in bare soil and of RMD in rooted soil. Univariate linear relations were found between ρ and θ in bare soil and between ρ, RLD and RMD in rooted soil. Across all data RMD and soil texture (P < 0.01) explained a high proportion of variability in soil resistivity.This allows to conclude that soil resistivity is quantitatively related to root biomass in herbaceous plants even at low root density (biomass < 0.001 Mg m−3), providing a basis for the development of resistivity-founded methods for the non-destructive spatial detection of root mass in situ, but the response in ρ is of the same order of magnitude as the effects of grain size and water content. Therefore in field studies reciprocal masking of low-density roots and other soil features is possible, and the effect of variation in other soil properties should be explicitly addressed.
Root systems play an important role in soil-based resource acquisition. The ability to quantify the structural complexity of a root system should lead to an improved understanding of its many functions, but first of all, root systems must be visualized in the soil medium. Accordingly, the main objective of the reported study was to bring the novel approach based on computed tomography (CT) scanning to the next stage in root system studies, by upgrading the operational and analytical procedures available and reporting concrete results for a given crop species (i.e. maize) in different soil-moisture combinations. We also wanted to quantify the structural complexity of root systems by fractal analysis. Maize (Zea mays L.) was sown in standard plastic pots, 100 mm in top diameter. Sieved and homogenized mineral soils with no or very little organic material were used as growth media. A high-resolution X-ray CT scanner, formerly used for medical purposes, produced series of 500 CT images of 0.1-mm thick cross-sections of the root systems of the seedlings in dry and water-saturated soil conditions. Some seedlings were grown in a homogenous sandy soil, and were CT scanned about 5 days after emergence. Others were grown in loamy sand, and were CT scanned 3 days after emergence, because of their faster growth rate. Data analysis was performed on the 512 × 512 matrices of CT numbers used to construct CT images. Each CT number provided an indirect measure of density for one voxel with dimensions 0.12 × 0.12 × 0.1 mm3. We present the procedures that we used to digitally isolate a root system from the soil medium in 3-D space using CT scan data and to skeletonize the resulting 3-D image. We explain how to estimate the fractal dimension (FD) on such a skeletonized 3-D image of a root system in order to quantify its complexity. For the same root system, once removed from the soil and washed, FD was also estimated from a 2-D photograph. The expected dissimilarities between the FD estimates of the two types are confirmed and discussed. We found that the soil conditions allowing more accurate visualization of maize root systems by CT scanning were dry homogeneous sand and water-saturated loamy sand. The use of sieved and homogenized mineral soils facilitated the presentation of the new methodology here. In future studies, non-homogeneous soils can be used, and the guidelines that we have proposed will then be helpful in analyzing root geometry with respect to soil structure, for example.
Nitrogen is a key element controlling the species composition, diversity, dynamics, and functioning of many terrestrial, freshwater, and marine ecosystems. Many of the original plant species living in these ecosystems are adapted to, and function optimally in, soils and solutions with low levels of available nitrogen. The growth and dynamics of herbivore populations, and ultimately those of their predators, also are affected by N. Agriculture, combustion of fossil fuels, and other human activities have altered the global cycle of N substantially, generally increasing both the availability and the mobility of N over large regions of Earth. The mobility of N means that while most deliberate applications of N occur locally, their influence spreads regionally and even globally. Moreover, many of the mobile forms of N themselves have environmental consequences. Although most nitrogen inputs serve human needs such as agricultural production, their environmental conse- quences are serious and long term. Based on our review of available scientific evidence, we are certain that human alterations of the nitrogen cycle have: 1) approximately doubled the rate of nitrogen input into the terrestrial nitrogen cycle, with these rates still increasing; 2) increased concentrations of the potent greenhouse gas N2O globally, and increased concentrations of other oxides of nitrogen that drive the formation of photochemical smog over large regions of Earth; 3) caused losses of soil nutrients, such as calcium and potassium, that are essential for the long-term maintenance of soil fertility; 4) contributed substantially to the acidification of soils, streams, and lakes in several regions; and 5) greatly increased the transfer of nitrogen through rivers to estuaries and coastal oceans. In addition, based on our review of available scientific evidence we are confident that human alterations of the nitrogen cycle have: 6) increased the quantity of organic carbon stored within terrestrial ecosystems; 7) accelerated losses of biological diversity, especially losses of plants adapted to efficient use of nitrogen, and losses of the animals and microorganisms that depend on them; and 8) caused changes in the composition and functioning of estuarine and nearshore ecosystems, and contributed to long-term declines in coastal marine fisheries.
Abstract Biofuels from crops are emerging as a Jekyll & Hyde – promoted by some as a means to offset fossil fuel emissions, denigrated by others as lacking sustainability and taking land from food crops. It is frequently asserted that plants convert only 0.1% of solar energy into biomass, therefore requiring unacceptable amounts of land for production of fuel feedstocks. The C4 perennial grass Miscanthus×giganteus has proved a promising biomass crop in Europe, while switchgrass (Panicum virgatum) has been tested at several locations in N. America. Here, replicated side-by-side trials of these two crops were established for the first time along a latitudinal gradient in Illinois. Over 3 years of trials, Miscanthus×giganteus achieved average annual conversion efficiencies into harvestable biomass of 1.0% (30 t ha−1) and a maximum of 2.0% (61 t ha−1), with minimal agricultural inputs. The regionally adapted switchgrass variety Cave-in-Rock achieved somewhat lower yields, averaging 10 t ha−1. Given that there has been little attempt to improve the agronomy and genetics of these grasses compared with the major grain crops, these efficiencies are the minimum of what may be achieved. At this 1.0% efficiency, 12 million hectares, or 9.3% of current US cropland, would be sufficient to provide 133 × 109 L of ethanol, enough to offset one-fifth of the current US gasoline use. In contrast, maize grain from the same area of land would only provide 49 × 109 L, while requiring much higher nitrogen and fossil energy inputs in its cultivation.