Root phenotyping: important and minimum information required for root modeling in crop plants

Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes

Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.

Analysis of Phosphorus Use Efficiency Traits in Coffea Genotypes Reveals Coffea arabica and Coffea canephora Have Contrasting Phosphorus Uptake and Utilization Efficiencies

BACKGROUND AND AIMS

Phosphate (Pi) is one of the most limiting nutrients for agricultural production in Brazilian soils due to low soil Pi concentrations and rapid fixation of fertilizer Pi by adsorption to oxidic minerals and/or precipitation by iron and aluminum ions. The objectives of this study were to quantify phosphorus (P) uptake and use efficiency in cultivars of the species Coffea arabica L. and Coffea canephora L., and group them in terms of efficiency and response to Pi availability.

METHODS

Plants of 21 cultivars of C. arabica and four cultivars of C. canephora were grown under contrasting soil Pi availabilities. Biomass accumulation, tissue P concentration and accumulation and efficiency indices for P use were measured.

KEY RESULTS

Coffee plant growth was significantly reduced under low Pi availability, and P concentration was higher in cultivars of C. canephora. The young leaves accumulated more P than any other tissue. The cultivars of C. canephora had a higher root/shoot ratio and were significantly more efficient in P uptake, while the cultivars of C. arabica were more efficient in P utilization. Agronomic P use efficiency varied among coffee cultivars and E16 Shoa, E22 Sidamo, Iêmen and Acaiá cultivars were classified as the most efficient and responsive to Pi supply. A positive correlation between P uptake efficiency and root to shoot ratio was observed across all cultivars at low Pi supply. These data identify Coffea genotypes better adapted to low soil Pi availabilities, and the traits that contribute to improved P uptake and use efficiency. These data could be used to select current genotypes with improved P uptake or utilization efficiencies for use on soils with low Pi availability and also provide potential breeding material and targets for breeding new cultivars better adapted to the low Pi status of Brazilian soils. This could ultimately reduce the use of Pi fertilizers in tropical soils, and contribute to more sustainable coffee production.

Evolving technologies for growing, imaging and analyzing 3D root system architecture of crop plants

A plant's ability to maintain or improve its yield under limiting conditions, such as nutrient deficiency or drought, can be strongly influenced by root system architecture (RSA), the three-dimensional distribution of the different root types in the soil. The ability to image, track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying RSA. We have designed a hydroponic growth system which retains the three-dimensional RSA of the plant root system, while allowing for aeration, solution replenishment and the imposition of nutrient treatments, as well as high-quality imaging of the root system. The simplicity and flexibility of the system allows for modifications tailored to the RSA of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity (detection of fine roots and other root details), higher efficiency, and a broad array of growing conditions for plants that more closely mimic those found under field conditions.

The effects of nitrogen form on root morphological and physiological adaptations of maize, white lupin and faba bean under phosphorus deficiency

Root morphological/physiological modifications are important for phosphorus (P) acquisition of plants under P deficiency, but strategies differ among plant species. Detailed studies on the response of maize roots to P deficiency are limited. Nitrogen (N) form influences root morphology/physiology, and thus may influence root responses to P deficiency. This work investigated adaptive mechanisms of maize roots to low P by comparison with white lupin and faba bean supplied with two N forms. Plants were grown for 7-16 days in hydroponics with sufficient (250 µmol L(-1)) and deficient P supply (1 µmol L(-1)) under supply of NH4NO3 or Ca(NO3)2 Plant growth and P uptake were measured, and release of protons and organic acid anions, and acid phosphatase activity in the root were monitored. The results showed that P deficiency significantly decreased shoot growth while increased root growth and total root length of maize and faba bean, but not white lupin. It enhanced the release of protons and organic acid anions, and acid phosphatase activity, from the roots of both legumes but not maize. Compared with Ca(NO3)2, NH4NO3 dramatically increased proton release by roots but did not alter root morphology or physiology of the three species in response to low P. It is concluded that the N form did not fundamentally change root morphological/physiological responses of the three species to P deficiency. Morphological variation in maize and morpho-physiological modifications in white lupin and faba bean were the main adaptive strategies to P deficiency.

Rapid Crown Root Development Confers Tolerance to Zinc Deficiency in Rice

Zinc (Zn) deficiency is one of the leading nutrient disorders in rice (Oryza sativa). Many studies have identified Zn-efficient rice genotypes, but causal mechanisms for Zn deficiency tolerance remain poorly understood. Here, we report a detailed study of the impact of Zn deficiency on crown root development of rice genotypes, differing in their tolerance to this stress. Zn deficiency delayed crown root development and plant biomass accumulation in both Zn-efficient and inefficient genotypes, with the effects being much stronger in the latter. Zn-efficient genotypes had developed new crown roots as early as 3 days after transplanting (DAT) to a Zn deficient field and that was followed by a significant increase in total biomass by 7 DAT. Zn-inefficient genotypes developed few new crown roots and did not increase biomass during the first 7 days following transplanting. This correlated with Zn-efficient genotypes retranslocating a higher proportion of shoot-Zn to their roots, compared to Zn-inefficient genotypes. These latter genotypes were furthermore not efficient in utilizing the limited Zn for root development. Histological analyses indicated no anomalies in crown tissue of Zn-efficient or inefficient genotypes that would have suggested crown root emergence was impeded. We therefore conclude that the rate of crown root initiation was differentially affected by Zn deficiency between genotypes. Rapid crown root development, following transplanting, was identified as a main causative trait for tolerance to Zn deficiency and better Zn retranslocation from shoot to root was a key attribute of Zn-efficient genotypes.

Arabidopsis EDT1/HDG11 improves drought and salt tolerance in cotton and poplar and increases cotton yield in the field

Drought and salinity are two major environmental factors limiting crop production worldwide. Improvement of drought and salt tolerance of crops with transgenic approach is an effective strategy to meet the demand of the ever-growing world population. Arabidopsis ENHANCED DROUGHT TOLERANCE1/HOMEODOMAIN GLABROUS11 (AtEDT1/HDG11), a homeodomain-START transcription factor, has been demonstrated to significantly improve drought tolerance in Arabidopsis, tobacco, tall fescue and rice. Here we report that AtHDG11 also confers drought and salt tolerance in upland cotton (Gossypium hirsutum) and woody plant poplar (Populus tomentosa Carr.). Our results showed that both the transgenic cotton and poplar exhibited significantly enhanced tolerance to drought and salt stress with well-developed root system. In the leaves of the transgenic cotton plants, proline content, soluble sugar content and activities of reactive oxygen species-scavenging enzymes were significantly increased after drought and salt stress compared with wild type. Leaf stomatal density was significantly reduced, whereas stomatal and leaf epidermal cell size were significantly increased in both the transgenic cotton and poplar plants. More importantly, the transgenic cotton showed significantly improved drought tolerance and better agronomic performance with higher cotton yield in the field both under normal and drought conditions. These results demonstrate that AtHDG11 is not only a promising candidate for crops improvement but also for woody plants.

N-fixation in legumes--An assessment of the potential threat posed by ozone pollution

The growth, development and functioning of legumes are often significantly affected by exposure to tropospheric ozone (O3) pollution. However, surprisingly little is known about how leguminous Nitrogen (N) fixation responds to ozone, with a scarcity of studies addressing this question in detail. In the last decade, ozone impacts on N-fixation in soybean, cowpea, mung bean, peanut and clover have been shown for concentrations which are now commonly recorded in ambient air or are likely to occur in the near future. We provide a synthesis of the existing literature addressing this issue, and also explore the effects that may occur on an agroecosystem scale by predicting reductions in Trifolium (clovers) root nodule biomass in United Kingdom (UK) pasture based on ozone concentration data for a "high" (2006) and "average" ozone year (2008). Median 8% and 5% reductions in clover root nodule biomass in pasture across the UK were predicted for 2006 and 2008 respectively. Seasonal exposure to elevated ozone, or short-term acute concentrations >100 ppb, are sufficient to reduce N-fixation and/or impact nodulation, in a range of globally-important legumes. However, an increasing global burden of CO2, the use of artificial fertiliser, and reactive N-pollution may partially mitigate impacts of ozone on N-fixation.

Iodine and Selenium Biofortification with Additional Application of Salicylic Acid Affects Yield, Selected Molecular Parameters and Chemical Composition of Lettuce Plants (Lactuca sativa L. var. capitata)

Iodine (I) and selenium (Se) are included in the group of beneficial elements. They both play important roles in humans and other animals, particularly in the regulation of thyroid functioning. A substantial percentage of people around the world suffer from health disorders related to the deficiency of these elements in the diet. Salicylic acid (SA) is a compound similar to phytohormones and is known to improve the efficiency of I biofortification of plants. The influence of SA on Se enrichment of plants has not, however, been recognized together with its effect on simultaneous application of I and Se to plants. Two-year studies (2014-2015) were conducted in a greenhouse with hydroponic cultivation of lettuce in an NFT (nutrient film technique) system. They included the application of I (as KIO₃), Se (as Na₂SeO₃) and SA into the nutrient solution. KIO₃ was used at a dose of 5 mg I⋅dm^-3 (i.e., 39.4 μM I), while Na₂SeO₃ was 0.5 mg Se⋅dm^-3 (i.e., 6.3 μM Se). SA was introduced at three doses: 0.1, 1.0, and 10.0 mg⋅dm^-3 nutrient solutions, equivalent to 0.724, 7.24, and 72.4 μM SA, respectively. The tested combinations were as follows: (1) control, (2) I + Se, (3) I + Se + 0.1 mg SA⋅dm^-3, (4) I + Se + 1.0 mg SA⋅dm^-3 and (5) I + Se + 10.0 mg SA⋅dm^-3. The applied treatments had no significant impact on lettuce biomass (leaves and roots). Depending on the dose, a diverse influence of SA was noted with respect to the efficiency of I and Se biofortification; chemical composition of leaves; and mineral nutrition of lettuce plants, including the content of macro- and microelements and selenocysteine methyltransferase (SMT) gene expression. SA application at all tested doses comparably increased the level of selenomethionine (SeMet) and decreased the content of SA in leaves.

Arabidopsis: An Adequate Model for Dicot Root Systems?

The Arabidopsis root system is frequently considered to have only three classes of root: primary, lateral, and adventitious. Research with other plant species has suggested up to eight different developmental/functional classes of root for a given plant root system. If Arabidopsis has only three classes of root, it may not be an adequate model for eudicot plant root systems. Recent research, however, can be interpreted to suggest that pre-flowering Arabidopsis does have at least five (5) of these classes of root. This then suggests that Arabidopsis root research can be considered an adequate model for dicot plant root systems.

Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics

BACKGROUND

Plant root systems are key drivers of plant function and yield. They are also under-explored targets to meet global food and energy demands. Many new technologies have been developed to characterize crop root system architecture (CRSA). These technologies have the potential to accelerate the progress in understanding the genetic control and environmental response of CRSA. Putting this potential into practice requires new methods and algorithms to analyze CRSA in digital images. Most prior approaches have solely focused on the estimation of root traits from images, yet no integrated platform exists that allows easy and intuitive access to trait extraction and analysis methods from images combined with storage solutions linked to metadata. Automated high-throughput phenotyping methods are increasingly used in laboratory-based efforts to link plant genotype with phenotype, whereas similar field-based studies remain predominantly manual low-throughput.

DESCRIPTION

Here, we present an open-source phenomics platform "DIRT", as a means to integrate scalable supercomputing architectures into field experiments and analysis pipelines. DIRT is an online platform that enables researchers to store images of plant roots, measure dicot and monocot root traits under field conditions, and share data and results within collaborative teams and the broader community. The DIRT platform seamlessly connects end-users with large-scale compute "commons" enabling the estimation and analysis of root phenotypes from field experiments of unprecedented size.

CONCLUSION

DIRT is an automated high-throughput computing and collaboration platform for field based crop root phenomics. The platform is accessible at http://www.dirt.iplantcollaborative.org/ and hosted on the iPlant cyber-infrastructure using high-throughput grid computing resources of the Texas Advanced Computing Center (TACC). DIRT is a high volume central depository and high-throughput RSA trait computation platform for plant scientists working on crop roots. It enables scientists to store, manage and share crop root images with metadata and compute RSA traits from thousands of images in parallel. It makes high-throughput RSA trait computation available to the community with just a few button clicks. As such it enables plant scientists to spend more time on science rather than on technology. All stored and computed data is easily accessible to the public and broader scientific community. We hope that easy data accessibility will attract new tool developers and spur creative data usage that may even be applied to other fields of science.

Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii

Using GWAS, 13 significant SNPs distributed on six of the seven Aegilops tauschii chromosomes (all but 5D) were identified, and several candidate P-deficiency-responsive genes were proposed from searches of public databases. Aegilops tauschii, the wheat (Triticum aestivum) D-genome progenitor, possesses numerous genes for stress resistance, including genes for tolerance of phosphorus (P) deficiency. Investigation of the genetic architecture of A. tauschii will help in developing P-deficiency-tolerant varieties of wheat. We evaluated nine traits in a population of 380 A. tauschii specimens under conditions with and without P application, and we performed genome-wide association studies for these traits using single nucleotide polymorphism (SNP) chips containing 7185 markers. Using a general linear model, we identified 119 SNPs that were significantly associated with all nine traits, and a mixed linear model revealed 18 SNPs associated with all traits. Both models detected 13 significant markers distributed on six of the seven A. tauschii chromosomes (all but 5D). Searches of public databases revealed several candidate/flanking genes related to P-deficiency tolerance. These genes were grouped in five categories by the types of proteins they encoded: defense response proteins, enzymes, promoters and transcription factors, storage proteins, or proteins triggered by P deficiency. The identified SNPs and genes contain essential information for cloning genes related to P-deficiency tolerance in A. tauschii and wheat, and they provide a foundation for breeding P-deficiency tolerant wheat cultivars.

Beneficial Bacteria Isolated from Grapevine Inner Tissues Shape Arabidopsis thaliana Roots

We investigated the potential plant growth-promoting traits of 377 culturable endophytic bacteria, isolated from Vitis vinifera cv. Glera, as good biofertilizer candidates in vineyard management. Endophyte ability in promoting plant growth was assessed in vitro by testing ammonia production, phosphate solubilization, indole-3-acetic acid (IAA) and IAA-like molecule biosynthesis, siderophore and lytic enzyme secretion. Many of the isolates were able to mobilize phosphate (33%), release ammonium (39%), secrete siderophores (38%) and a limited part of them synthetized IAA and IAA-like molecules (5%). Effects of each of the 377 grapevine beneficial bacteria on Arabidopsis thaliana root development were also analyzed to discern plant growth-promoting abilities (PGP) of the different strains, that often exhibit more than one PGP trait. A supervised model-based clustering analysis highlighted six different classes of PGP effects on root architecture. A. thaliana DR5::GUS plantlets, inoculated with IAA-producing endophytes, resulted in altered root growth and enhanced auxin response. Overall, the results indicate that the Glera PGP endospheric culturable microbiome could contribute, by structural root changes, to obtain water and nutrients increasing plant adaptation and survival. From the complete cultivable collection, twelve promising endophytes mainly belonging to the Bacillus but also to Micrococcus and Pantoea genera, were selected for further investigations in the grapevine host plants towards future application in sustainable management of vineyards.

Root-type-specific plasticity in response to localized high nitrate supply in maize (Zea mays)

BACKGROUND AND AIMS

Shoot-borne roots contribute to most of the nutrient uptake throughout the life cycle of maize (Zea mays). Compared with numerous studies with embryonic roots, detailed information on the phenotypic plasticity of shoot-borne roots in response to a heterogeneous nitrogen supply is scarce. The present study therefore provides a comprehensive profile of fine-scale plastic responses of distinct root types to localized high nitrate supply.

METHODS

Seedlings of the maize inbred line B73 were grown in split-root systems. The anatomy and morphological plasticity of the primary root and the roots initiated from the 2nd, 5th and 7th shoot nodes, and their lateral roots, were studied in response to local high nitrate supply to one side of the root system.

KEY RESULTS

In contrast to the insensitivity of axial roots, local high nitrate supply increased the length of 1st-order lateral roots on the primary root and the three whorls of shoot-borne roots at different growth stages, and increased the density of 1st-order lateral roots on the 7th shoot-borne root after silking. The length and density of 2nd-order lateral roots on the three whorls of shoot-borne roots displayed a more flexible response to local high nitrate than 1st-order lateral roots. Root diameter and number, and total area and diameter of metaxylem vessels increased from the primary root to early and then later developed shoot-borne roots, which showed a positive relationship with shoot growth and N accumulation.

CONCLUSIONS

Maize axial roots and lateral roots responded differently to local high nitrate, and this was related to their function. The extent of morphological plasticity of lateral roots in response to local high nitrate depended on the initiation time of the shoot-borne roots on which the lateral roots developed. Morphological plasticity was higher on 2nd-order than on 1st-order lateral roots. The results suggest that higher order lateral root branching might be a potential target for genetic improvement in future maize breeding.

Genetic approaches to enhancing nitrogen-use efficiency (NUE) in cereals: challenges and future directions

Over 100million tonnes of nitrogen (N) fertiliser are applied globally each year to maintain high yields in agricultural crops. The rising price of N fertilisers has made them a major cost for farmers. Inefficient use of N fertiliser leads to substantial environmental problems through contamination of air and water resources and can be a significant economic cost. Consequently, there is considerable need to improve the way N fertiliser is used in farming systems. The efficiency with which crops use applied N fertiliser - the nitrogen-use efficiency (NUE) - is currently quite low for cereals. This is the case in both high yielding environments and lower yielding environments characteristic of cereal growing regions of Australia. Multiple studies have attempted to identify the genetic basis of NUE, but the utility of the results is limited because of the complex nature of the trait and the magnitude of genotype by environment interaction. Transgenic approaches have been applied to improve plant NUE but with limited success, due, in part, to a combination of the complexity of the trait but also due to lack of accurate phenotyping methods. This review documents these two approaches and suggests future directions in improving cereal NUE with a focus on the Australian cereal industry.

Root phenes that reduce the metabolic costs of soil exploration: opportunities for 21st century agriculture

Crop genotypes with reduced metabolic costs of soil exploration would have improved water and nutrient acquisition. Three strategies to achieve this goal are (1) production of the optimum number of axial roots; (2) greater biomass allocation to root classes that are less metabolically demanding; and (3) reduction of the respiratory requirement of root tissue. An example of strategy 1 is the case of reduced crown root number in maize, which is associated with greater rooting depth, N capture and yield in low N soil. An example of strategy 2 is the case of increased hypocotyl-borne rooting in bean, which decreases root cost and increases P capture from low P soil. Examples of strategy 3 are the cases of increased formation of root cortical aerenchyma, decreased cortical cell file number and increased cortical cell size in maize, which decrease specific root respiration, increase rooting depth and increase water capture and yield under water stress. Root cortical aerenchyma also increases N capture and yield under N stress. Root phenes that reduce the metabolic cost of soil exploration are promising, underexploited avenues to the climate-resilient, resource-efficient crops that are urgently needed in global agriculture.

Interactions among cluster-root investment, leaf phosphorus concentration, and relative growth rate in two Lupinus species

PREMISE OF THE STUDY

Cluster-root (CR) formation is a desirable trait to improve phosphorus (P) acquisition as global P resources are dwindling. CRs in some lupine species are suppressed at higher P status. Whether increased growth rate enhances CR formation due to a "dilution" of leaf P concentration is unknown. We investigated interactive effects of leaf P status and relative growth rate (RGR) on CR formation in two Lupinus species, which differ in their CR biomass investment. Variation in RGR was imposed by varying day length.

METHODS

Lupinus albus and L. pilosus were grown hydroponically with KH2PO4 at a day length of 6, 10, or 14 h. We used a slightly higher P supply at longer day lengths to avoid a decline in leaf P concentration, which would induce CRs. Cluster-root percentage, leaf P concentrations, and RGR were determined at 22, 38, and 52 d after sowing.

KEY RESULTS

Lupinus species grown at similar root P availability, but with a faster growth rate, as dependent on day length, showed a greater CR percentage. Because our aim to achieve exactly the same leaf P concentrations at different day lengths was only partially achieved, we carried out a multiple regression analysis. This analysis showed the CR percentage was strongly and negatively correlated with plant P status and only marginally and positively correlated with RGR.

CONCLUSIONS

The two Lupinus species invariably formed fewer cluster roots at higher leaf P status, irrespective of RGR. Differences in RGR or leaf P concentration cannot explain the species-specific variation in cluster-root investment.

Intensive field phenotyping of maize (Zea mays L.) root crowns identifies phenes and phene integration associated with plant growth and nitrogen acquisition

Root architecture is an important regulator of nitrogen (N) acquisition. Existing methods to phenotype the root architecture of cereal crops are generally limited to seedlings or to the outer roots of mature root crowns. The functional integration of root phenes is poorly understood. In this study, intensive phenotyping of mature root crowns of maize was conducted to discover phenes and phene modules related to N acquisition. Twelve maize genotypes were grown under replete and deficient N regimes in the field in South Africa and eight in the USA. An image was captured for every whorl of nodal roots in each crown. Custom software was used to measure root phenes including nodal occupancy, angle, diameter, distance to branching, lateral branching, and lateral length. Variation existed for all root phenes within maize root crowns. Size-related phenes such as diameter and number were substantially influenced by nodal position, while angle, lateral density, and distance to branching were not. Greater distance to branching, the length from the shoot to the emergence of laterals, is proposed to be a novel phene state that minimizes placing roots in already explored soil. Root phenes from both older and younger whorls of nodal roots contributed to variation in shoot mass and N uptake. The additive integration of root phenes accounted for 70% of the variation observed in shoot mass in low N soil. These results demonstrate the utility of intensive phenotyping of mature root systems, as well as the importance of phene integration in soil resource acquisition.

Genetic diversity and population structure of wheat in India and Turkey

Genetic diversity among plant species offers prospects for improving the plant characteristics. Its assessment is necessary to help tackle the threats of environmental fluctuations and for the effective exploitation of genetic resources in breeding programmes. Although wheat is one of the most thoroughly studied crops in terms of genetic polymorphism studies, phylogenetic affinities of Indian and Turkish Triticum species have not been assessed to date. In this study, genetic association of 95 tetraploid and hexaploid wheat genotypes originating from India and Turkey was determined for the first time. Combined analysis of random amplified polymorphic DNA and inter-simple sequence repeat markers disclosed 177 polymorphic bands, and both the dendrogram and two-dimensional scatterplot showed similar groupings of the wheat genotypes. Turkish hexaploid varieties were basically divided into two clusters, one group showed its close association with Indian hexaploid varieties and the other with Indian tetraploid varieties. Analysis of molecular variance revealed high (77 %) genetic variation within Indian and Turkish populations. Population structure analysis elucidated distinct clustering of wheat genotypes on the basis of both geographical origin and ploidy. The results revealed in this study will support worldwide wheat breeding programmes and assist in achieving the target of sustainable wheat production.

Multiple interval QTL mapping and searching for PSTOL1 homologs associated with root morphology, biomass accumulation and phosphorus content in maize seedlings under low-P

BACKGROUND

Modifications in root morphology are important strategies to maximize soil exploitation under phosphorus starvation in plants. Here, we used two multiple interval models to map QTLs related to root traits, biomass accumulation and P content in a maize RIL population cultivated in nutrient solution. In addition, we searched for putative maize homologs to PSTOL1, a gene responsible to enhance early root growth, P uptake and grain yield in rice and sorghum.

RESULTS

Based on path analysis, root surface area was the root morphology component that most strongly contributed to total dry weight and to P content in maize seedling under low-P availability. Multiple interval mapping models for single (MIM) and multiple traits (MT-MIM) were combined and revealed 13 genomic regions significantly associated with the target traits in a complementary way. The phenotypic variances explained by all QTLs and their epistatic interactions using MT-MIM (23.4 to 35.5 %) were higher than in previous studies, and presented superior statistical power. Some of these QTLs were coincident with QTLs for root morphology traits and grain yield previously mapped, whereas others harbored ZmPSTOL candidate genes, which shared more than 55 % of amino acid sequence identity and a conserved serine/threonine kinase domain with OsPSTOL1. Additionally, four ZmPSTOL candidate genes co-localized with QTLs for root morphology, biomass accumulation and/or P content were preferentially expressed in roots of the parental lines that contributed the alleles enhancing the respective phenotypes.

CONCLUSIONS

QTL mapping strategies adopted in this study revealed complementary results for single and multiple traits with high accuracy. Some QTLs, mainly the ones that were also associated with yield performance in other studies, can be good targets for marker-assisted selection to improve P-use efficiency in maize. Based on the co-localization with QTLs, the protein domain conservation and the coincidence of gene expression, we selected novel maize genes as putative homologs to PSTOL1 that will require further validation studies.

Phosphorus and magnesium interactively modulate the elongation and directional growth of primary roots in Arabidopsis thaliana (L.) Heynh

A balanced supply of essential nutrients is an important factor influencing root architecture in many plants, yet data related to the interactive effects of two nutrients on root growth are limited. Here, we investigated the interactive effect between phosphorus (P) and magnesium (Mg) on root growth of Arabidopsis grown in pH-buffered agar medium at different P and Mg levels. The results showed that elongation and deviation of primary roots were directly correlated with the amount of P added to the medium but could be modified by the Mg level, which was related to the root meristem activity and stem-cell division. High P enhanced while low P decreased the tip-focused fluorescence signal of auxin biosynthesis, transport, and redistribution during elongation of primary roots; these effects were greater under low Mg than under high Mg. The altered root growth in response to P and Mg supply was correlated with AUX1, PIN2, and PIN3 mRNA abundance and expression and the accumulation of the protein. Application of either auxin influx inhibitor or efflux inhibitor inhibited the elongation and increased the deviation angle of primary roots, and decreased auxin level in root tips. Furthermore, the auxin-transport mutants aux1-22 and eir1-1 displayed reduced root growth and increased the deviation angle. Our data suggest a profound effect of the combined supply of P and Mg on the development of root morphology in Arabidopsis through auxin signals that modulate the elongation and directional growth of primary root and the expression of root differentiation and development genes.

Soil Tillage Management Affects Maize Grain Yield by Regulating Spatial Distribution Coordination of Roots, Soil Moisture and Nitrogen Status

The spatial distribution of the root system through the soil profile has an impact on moisture and nutrient uptake by plants, affecting growth and productivity. The spatial distribution of the roots, soil moisture, and fertility are affected by tillage practices. The combination of high soil density and the presence of a soil plow pan typically impede the growth of maize (Zea mays L.).We investigated the spatial distribution coordination of the root system, soil moisture, and N status in response to different soil tillage treatments (NT: no-tillage, RT: rotary-tillage, SS: subsoiling) and the subsequent impact on maize yield, and identify yield-increasing mechanisms and optimal soil tillage management practices. Field experiments were conducted on the Huang-Huai-Hai plain in China during 2011 and 2012. The SS and RT treatments significantly reduced soil bulk density in the top 0–20 cm layer of the soil profile, while SS significantly decreased soil bulk density in the 20–30 cm layer. Soil moisture in the 20–50 cm profile layer was significantly higher for the SS treatment compared to the RT and NT treatment. In the 0-20 cm topsoil layer, the NT treatment had higher soil moisture than the SS and RT treatments. Root length density of the SS treatment was significantly greater than density of the RT and NT treatments, as soil depth increased. Soil moisture was reduced in the soil profile where root concentration was high. SS had greater soil moisture depletion and a more concentration root system than RT and NT in deep soil. Our results suggest that the SS treatment improved the spatial distribution of root density, soil moisture and N states, thereby promoting the absorption of soil moisture and reducing N leaching via the root system in the 20–50 cm layer of the profile. Within the context of the SS treatment, a root architecture densely distributed deep into the soil profile, played a pivotal role in plants’ ability to access nutrients and water. An optimal combination of deeper deployment of roots and resource (water and N) availability was realized where the soil was prone to leaching. The correlation between the depletion of resources and distribution of patchy roots endorsed the SS tillage practice. It resulted in significantly greater post-silking biomass and grain yield compared to the RT and NT treatments, for summer maize on the Huang-Huai-Hai plain.

Root Traits and Phenotyping Strategies for Plant Improvement

Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs.

Replace, reuse, recycle: improving the sustainable use of phosphorus by plants

The 'phosphorus problem' has recently received strong interest with two distinct strands of importance. The first is that too much phosphorus (P) is entering into waste water, creating a significant economic and ecological problem. Secondly, while agricultural demand for phosphate fertilizer is increasing to maintain crop yields, rock phosphate reserves are rapidly declining. Unravelling the mechanisms by which plants sense, respond to, and acquire phosphate can address both problems, allowing the development of crop plants that are more efficient at acquiring and using limited amounts of phosphate while at the same time improving the potential of plants and other photosynthetic organisms for nutrient recapture and recycling from waste water. In this review, we attempt to synthesize these important but often disparate parts of the debate in a holistic fashion, since solutions to such a complex problem require integrated and multidisciplinary approaches that address both P supply and demand. Rapid progress has been made recently in our understanding of local and systemic signalling mechanisms for phosphate, and of expression and regulation of membrane proteins that take phosphate up from the environment and transport it within the plant. We discuss the current state of understanding of such mechanisms involved in sensing and responding to phosphate stress. We also discuss approaches to improve the P-use efficiency of crop plants and future direction for sustainable use of P, including use of photosynthetic organisms for recapture of P from waste waters.

A large and deep root system underlies high nitrogen-use efficiency in maize production

Excessive N fertilization results in low N-use efficiency (NUE) without any yield benefits and can have profound, long-term environmental consequences including soil acidification, N leaching and increased production of greenhouse gases. Improving NUE in crop production has been a longstanding, worldwide challenge. A crucial strategy to improve NUE is to enhance N uptake by roots. Taking maize as a model crop, we have compared root dry weight (RDW), root/shoot biomass ratio (R/S), and NUE of maize grown in the field in China and in western countries using data from 106 studies published since 1959. Detailed analysis revealed that the differences in the RDW and R/S of maize at silking in China and the western countries were not derived from variations in climate, geography, and stress factors. Instead, NUE was positively correlated with R/S and RDW; R/S and NUE of maize varieties grown in western countries were significantly greater than those grown in China. We then testified this conclusion by conducting field trials with representative maize hybrids in China (ZD958 and XY335) and the US (P32D79). We found that US P32D79 had a better root architecture for increased N uptake and removed more mineral N than Chinese cultivars from the 0-60 cm soil profile. Reported data and our field results demonstrate that a large and deep root, with an appropriate architecture and higher stress tolerance (higher plant density, drought and N deficiency), underlies high NUE in maize production. We recommend breeding for these traits to reduce the N-fertilizer use and thus N-leaching in maize production and paying more attention to increase tolerance to stresses in China.

The effect of impedance to root growth on plant architecture in wheat

BACKGROUND AND AIMS

We were interested in the effect of impedance to root growth on root and shoot architecture of wheat. It is known that Rht-1 semi-dwarfing alleles decrease the degree of leaf stunting due to root impedance. We compared commercial wheat cultivars containing different Rht-1 alleles to determine whether leaf stunting caused by root impedance differed between cultivars. We investigated effects of impedance to root growth on the angular spread of roots.

METHODS

The wheat cultivars Avalon, Robigus and Battalion, carrying semi-dwarfing alleles of Rht-1, and cv. Cadenza, carrying the tall, wild-type allele, were grown under two levels of soil strength in a sand culture system designed to allow the mechanical impedance of the root growth environment to be adjusted independently of water and nutrient availability.

RESULTS

Impeded roots grew more steeply than non-impeded roots: the angular spread of roots decreased from 55° to 43° from the vertical, but the genotypic effects were weak. Root impedance reduced leaf elongation and the number of tillers. Leaf area and total root length provided a common relationship across all genotype x treatment combinations. Leaf stunting in Cadenza was more severe.

CONCLUSION

Our data support the hypothesis that the severity of leaf stunting due to root impedance is related to the Rht allele. Impeded roots had a smaller angular spread.

Opportunities and challenges in the subsoil: pathways to deeper rooted crops

Greater exploitation of subsoil resources by annual crops would afford multiple benefits, including greater water and N acquisition in most agroecosystems, and greater sequestration of atmospheric C. Constraints to root growth in the subsoil include soil acidity (an edaphic stress complex consisting of toxic levels of Al, inadequate levels of P and Ca, and often toxic levels of Mn), soil compaction, hypoxia, and suboptimal temperature. Multiple root phenes under genetic control are associated with adaptation to these constraints, opening up the possibility of breeding annual crops with root traits improving subsoil exploration. Adaptation to Al toxicity, hypoxia, and P deficiency are intensively researched, adaptation to soil hardness and suboptimal temperature less so, and adaptations to Ca deficiency and Mn toxicity are poorly understood. The utility of specific phene states may vary among soil taxa and management scenarios, interactions which in general are poorly understood. These traits and issues merit research because of their potential value in developing more productive, sustainable, benign, and resilient agricultural systems.

A comprehensive analysis of root morphological changes and nitrogen allocation in maize in response to low nitrogen stress

The plasticity of root architecture is crucial for plants to acclimate to unfavourable environments including low nitrogen (LN) stress. How maize roots coordinate the growth of axile roots and lateral roots (LRs), as well as longitudinal and radial cell behaviours in response to LN stress, remains unclear. Maize plants were cultivated hydroponically under control (4 mm nitrate) and LN (40 μm) conditions. Temporal and spatial samples were taken to analyse changes in the morphology, anatomical structure and carbon/nitrogen (C/N) ratio in the axile root and LRs. LN stress increased axile root elongation, reduced the number of crown roots and decreased LR density and length. LN stress extended cell elongation zones and increased the mature cell length in the roots. LN stress reduced the cell diameter and total area of vessels and increased the amount of aerenchyma, but the number of cell layers in the crown root cortex was unchanged. The C/N ratio was higher in the axile roots than in the LRs. Maize roots acclimate to LN stress by optimizing the anatomical structure and N allocation. As a result, axile root elongation is favoured to efficiently find available N in the soil.

Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat

Seedling root traits of wheat (Triticum aestivum L.) have been shown to be important for efficient establishment and linked to mature plant traits such as height and yield. A root phenotyping pipeline, consisting of a germination paper-based screen combined with image segmentation and analysis software, was developed and used to characterize seedling traits in 94 doubled haploid progeny derived from a cross between the winter wheat cultivars Rialto and Savannah. Field experiments were conducted to measure mature plant height, grain yield, and nitrogen (N) uptake in three sites over 2 years. In total, 29 quantitative trait loci (QTLs) for seedling root traits were identified. Two QTLs for grain yield and N uptake co-localize with root QTLs on chromosomes 2B and 7D, respectively. Of the 29 root QTLs identified, 11 were found to co-localize on 6D, with four of these achieving highly significant logarithm of odds scores (>20). These results suggest the presence of a major-effect gene regulating seedling root vigour/growth on chromosome 6D.

Biofortification and phytoremediation of selenium in China

Selenium (Se) is an essential trace element for humans and animals but at high concentrations, Se becomes toxic to organisms due to Se replacing sulfur in proteins. Selenium biofortification is an agricultural process that increases the accumulation of Se in crops, through plant breeding, genetic engineering, or use of Se fertilizers. Selenium phytoremediation is a green biotechnology to clean up Se-contaminated environments, primarily through phytoextraction and phytovolatilization. By integrating Se phytoremediation and biofortification technologies, Se-enriched plant materials harvested from Se phytoremediation can be used as Se-enriched green manures or other supplementary sources of Se for producing Se-biofortified agricultural products. Earlier studies primarily aimed at enhancing efficacy of phytoremediation and biofortification of Se based on natural variation in progenitor or identification of unique plant species. In this review, we discuss promising approaches to improve biofortification and phytoremediation of Se using knowledge acquired from model crops. We also explored the feasibility of applying biotechnologies such as inoculation of microbial strains for improving the efficiency of biofortification and phytoremediation of Se. The key research and practical challenges that remain in improving biofortification and phytoremediation of Se have been highlighted, and the future development and uses of Se-biofortified agricultural products in China has also been discussed.

Hierarchical traits distances explain grassland Fabaceae species' ecological niches distances

Fabaceae species play a key role in ecosystem functioning through their capacity to fix atmospheric nitrogen via their symbiosis with Rhizobium bacteria. To increase benefits of using Fabaceae in agricultural systems, it is necessary to find ways to evaluate species or genotypes having potential adaptations to sub-optimal growth conditions. We evaluated the relevance of phylogenetic distance, absolute trait distance and hierarchical trait distance for comparing the adaptation of 13 grassland Fabaceae species to different habitats, i.e., ecological niches. We measured a wide range of functional traits (root traits, leaf traits, and whole plant traits) in these species. Species phylogenetic and ecological distances were assessed from a species-level phylogenetic tree and species' ecological indicator values, respectively. We demonstrated that differences in ecological niches between grassland Fabaceae species were related more to their hierarchical trait distances than to their phylogenetic distances. We showed that grassland Fabaceae functional traits tend to converge among species with the same ecological requirements. Species with acquisitive root strategies (thin roots, shallow root systems) are competitive species adapted to non-stressful meadows, while conservative ones (coarse roots, deep root systems) are able to tolerate stressful continental climates. In contrast, acquisitive species appeared to be able to tolerate low soil-P availability, while conservative ones need high P availability. Finally we highlight that traits converge along the ecological gradient, providing the assumption that species with similar root-trait values are better able to coexist, regardless of their phylogenetic distance.

"Rhizoponics": a novel hydroponic rhizotron for root system analyses on mature Arabidopsis thaliana plants

BACKGROUND

Well-developed and functional roots are critical to support plant life and reach high crop yields. Their study however, is hampered by their underground growth and characterizing complex root system architecture (RSA) therefore remains a challenge. In the last few years, several phenotyping methods, including rhizotrons and x-ray computed tomography, have been developed for relatively thick roots. But in the model plant Arabidopsis thaliana, in vitro culture remains the easiest and preferred method to study root development, which technically limits the analyses to young seedlings.

RESULTS

We present here an innovative design of hydroponic rhizotrons (rhizoponics) adapted to Arabidopsis thaliana. The setup allows to simultaneously characterize the RSA and shoot development from seedling to adult stages, i.e. from seed to seed. This system offers the advantages of hydroponics such as control of root environment and easy access to the roots for measurements or sampling. Being completely movable and low cost, it can be used in controlled cabinets. We chose the case of cadmium treatment to illustrate potential applications, from cell to organ levels.

CONCLUSIONS

Rhizoponics makes possible, on the same plants of Arabidopsis, RSA measurements, root sampling and characterization of aerial development up to adult size. It therefore provides a valuable tool for addressing fundamental questions in whole plant physiology.

How changing root system architecture can help tackle a reduction in soil phosphate (P) levels for better plant P acquisition

The readily available global rock phosphate (P) reserves may run out within the next 50-130 years, causing soils to have a reduced P concentration which will affect plant P uptake. Using a combination of mathematical modelling and experimental data, we investigated potential plant-based options for optimizing crop P uptake in reduced soil P environments. By varying the P concentration within a well-mixed agricultural soil, for high and low P (35.5-12.5 mg L(-1) respectively using Olsen's P index), we investigated branching distributions within a wheat root system that maximize P uptake. Changing the root branching distribution from linear (evenly spaced branches) to strongly exponential (a greater number of branches at the top of the soil) improves P uptake by 142% for low-P soils when root mass is kept constant between simulations. This causes the roots to emerge earlier and mimics topsoil foraging. Manipulating root branching patterns, to maximize P uptake, is not enough on its own to overcome the drop in soil P from high to low P. Further mechanisms have to be considered to fully understand the impact of P reduction on plant development.

Role of ethylene in responses of plants to nitrogen availability

Ethylene is a plant hormone involved in several physiological processes and regulates the plant development during the whole life. Stressful conditions usually activate ethylene biosynthesis and signaling in plants. The availability of nutrients, shortage or excess, influences plant metabolism and ethylene plays an important role in plant adaptation under suboptimal conditions. Among the plant nutrients, the nitrogen (N) is one the most important mineral element required for plant growth and development. The availability of N significantly influences plant metabolism, including ethylene biology. The interaction between ethylene and N affects several physiological processes such as leaf gas exchanges, roots architecture, leaf, fruits, and flowers development. Low plant N use efficiency (NUE) leads to N loss and N deprivation, which affect ethylene biosynthesis and tissues sensitivity, inducing cell damage and ultimately lysis. Plants may respond differently to N availability balancing ethylene production through its signaling network. This review discusses the recent advances in the interaction between N availability and ethylene at whole plant and different organ levels, and explores how N availability induces ethylene biology and plant responses. Exogenously applied ethylene seems to cope the stress conditions and improves plant physiological performance. This can be explained considering the expression of ethylene biosynthesis and signaling genes under different N availability. A greater understanding of the regulation of N by means of ethylene modulation may help to increase NUE and directly influence crop productivity under conditions of limited N availability, leading to positive effects on the environment. Moreover, efforts should be focused on the effect of N deficiency or excess in fruit trees, where ethylene can have detrimental effects especially during postharvest.

MADS-box transcription factor AGL21 regulates lateral root development and responds to multiple external and physiological signals

Plant root system morphology is dramatically influenced by various environmental cues. The adaptation of root system architecture to environmental constraints, which mostly depends on the formation and growth of lateral roots, is an important agronomic trait. Lateral root development is regulated by the external signals coordinating closely with intrinsic signaling pathways. MADS-box transcription factors are known key regulators of the transition to flowering and flower development. However, their functions in root development are still poorly understood. Here we report that AGL21, an AGL17-clade MADS-box gene, plays a crucial role in lateral root development. AGL21 was highly expressed in root, particularly in the root central cylinder and lateral root primordia. AGL21 overexpression plants produced more and longer lateral roots while agl21 mutants showed impaired lateral root development, especially under nitrogen-deficient conditions. AGL21 was induced by many plant hormones and environmental stresses, suggesting a function of this gene in root system plasticity in response to various signals. Furthermore, AGL21 was found positively regulating auxin accumulation in lateral root primordia and lateral roots by enhancing local auxin biosynthesis, thus stimulating lateral root initiation and growth. We propose that AGL21 may be involved in various environmental and physiological signals-mediated lateral root development and growth.

Root anatomical phenes associated with water acquisition from drying soil: targets for crop improvement

Several root anatomical phenes affect water acquisition from drying soil, and may therefore have utility in breeding more drought-tolerant crops. Anatomical phenes that reduce the metabolic cost of the root cortex ('cortical burden') improve soil exploration and therefore water acquisition from drying soil. The best evidence for this is for root cortical aerenchyma; cortical cell file number and cortical senescence may also be useful in this context. Variation in the number and diameter of xylem vessels strongly affects axial water conductance. Reduced axial conductance may be useful in conserving soil water so that a crop may complete its life cycle under terminal drought. Variation in the suberization and lignification of the endodermis and exodermis affects radial water conductance, and may therefore be important in reducing water loss from mature roots into dry soil. Rhizosheaths may protect the water status of young root tissue. Root hairs and larger diameter root tips improve root penetration of hard, drying soil. Many of these phenes show substantial genotypic variation. The utility of these phenes for water acquisition has only rarely been validated, and may have strong interactions with the spatiotemporal dynamics of soil water availability, and with root architecture and other aspects of the root phenotype. This complexity calls for structural-functional plant modelling and 3D imaging methods. Root anatomical phenes represent a promising yet underexplored and untapped source of crop breeding targets.

Phenotypic plasticity of the maize root system in response to heterogeneous nitrogen availability

Mineral nutrients are distributed in a non-uniform manner in the soil. Plasticity in root responses to the availability of mineral nutrients is believed to be important for optimizing nutrient acquisition. The response of root architecture to heterogeneous nutrient availability has been documented in various plant species, and the molecular mechanisms coordinating these responses have been investigated particularly in Arabidopsis, a model dicotyledonous plant. Recently, progress has been made in describing the phenotypic plasticity of root architecture in maize, a monocotyledonous crop. This article reviews aspects of phenotypic plasticity of maize root system architecture, with special emphasis on describing (1) the development of its complex root system; (2) phenotypic responses in root system architecture to heterogeneous N availability; (3) the importance of phenotypic plasticity for N acquisition; (4) different regulation of root growth and nutrients uptake by shoot; and (5) root traits in maize breeding. This knowledge will inform breeding strategies for root traits enabling more efficient acquisition of soil resources and synchronizing crop growth demand, root resource acquisition and fertilizer application during crop growing season, thereby maximizing crop yields and nutrient-use efficiency and minimizing environmental pollution.

Hypocotyl adventitious root organogenesis differs from lateral root development

Wound-induced adventitious root (AR) formation is a requirement for plant survival upon root damage inflicted by pathogen attack, but also during the regeneration of plant stem cuttings for clonal propagation of elite plant varieties. Yet, adventitious rooting also takes place without wounding. This happens for example in etiolated Arabidopsis thaliana hypocotyls, in which AR initiate upon de-etiolation or in tomato seedlings, in which AR initiate upon flooding or high water availability. In the hypocotyl AR originate from a cell layer reminiscent to the pericycle in the primary root (PR) and the initiated AR share histological and developmental characteristics with lateral roots (LRs). In contrast to the PR however, the hypocotyl is a determinate structure with an established final number of cells. This points to differences between the induction of hypocotyl AR and LR on the PR, as the latter grows indeterminately. The induction of AR on the hypocotyl takes place in environmental conditions that differ from those that control LR formation. Hence, AR formation depends on differentially regulated gene products. Similarly to AR induction in stem cuttings, the capacity to induce hypocotyl AR is genotype-dependent and the plant growth regulator auxin is a key regulator controlling the rooting response. The hormones cytokinins, ethylene, jasmonic acid, and strigolactones in general reduce the root-inducing capacity. The involvement of this many regulators indicates that a tight control and fine-tuning of the initiation and emergence of AR exists. Recently, several genetic factors, specific to hypocotyl adventitious rooting in A. thaliana, have been uncovered. These factors reveal a dedicated signaling network that drives AR formation in the Arabidopsis hypocotyl. Here we provide an overview of the environmental and genetic factors controlling hypocotyl-born AR and we summarize how AR formation and the regulating factors of this organogenesis are distinct from LR induction.

Variation in virus symptom development and root architecture attributes at the onset of storage root initiation in 'beauregard' sweetpotato plants grown with or without nitrogen

It has been shown that virus infections, often symptomless, significantly limit sweetpotato productivity, especially in regions characterized by low input agricultural systems. In sweetpotatoes, the successful emergence and development of lateral roots (LRs), the main determinant of root architecture, determines the competency of adventitious roots to undergo storage root initiation. This study aimed to investigate the effect of some plant viruses on root architecture attributes during the onset of storage root initiation in 'Beauregard' sweetpotatoes that were grown with or without the presence of nitrogen. In two replicate experiments, virus-tested plants consistently failed to show visible symptoms at 20 days regardless of nitrogen treatment. In both experiments, the severity of symptom development among infected plants ranged from 25 to 118% when compared to the controls (virus tested plants grown in the presence of nitrogen). The presence of a complex of viruses (Sweet potato feathery mottle virus, Sweet potato virus G, Sweet potato virus C, and Sweet potato virus 2) was associated with 51% reduction in adventitious root number among plants grown without nitrogen. The effect of virus treatments on first order LR development depended on the presence or absence of nitrogen. In the presence of nitrogen, only plants infected with Sweet potato chlorotic stunt virus showed reductions in first order LR length, number, and density, which were decreased by 33%, 12%, and 11%, respectively, when compared to the controls. In the absence of nitrogen, virus tested and infected plants manifested significant reductions for all first order LR attributes. These results provide evidence that virus infection directly influences sweetpotato yield potential by reducing both the number of adventitious roots and LR development. These findings provide a framework for understanding how virus infection reduces sweetpotato yield and could lead to the development of novel strategies to mitigate virus effects on sweetpotato productivity.

Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

This work evaluates the phenotypic response of the model grass (Brachypodium distachyon (L.) P. Beauv.) to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight (R(2) > 0.92) and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response to nitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determination of genomic regions associated with superior nutrient use efficiency.

Understanding the genetic control and physiological traits associated with rhizosheath production by barley (Hordeum vulgare)

There is an urgent need for simple rapid screens of root traits that improve the acquisition of nutrients and water. Temperate cereals produce rhizosheaths of variable weight, a trait first noted on desert species sampled by Tansley over 100 yr ago. This trait is almost certainly important in tolerance to abiotic stress. Here, we screened association genetics populations of barley for rhizosheath weight and derived quantitative trait loci (QTLs) and candidate genes. We assessed whether rhizosheath weight was correlated with plant performance and phosphate uptake under combined drought and phosphorus deficiency. Rhizosheath weight was investigated in relation to root hair length, and under both laboratory and field conditions. Our data demonstrated that rhizosheath weight was correlated with phosphate uptake under dry conditions and that the differences in rhizosheath weight between genotypes were maintained in the field. Rhizosheath weight also varied significantly within barley populations, was correlated with root hair length and was associated with a genetic locus (QTL) on chromosome 2H. Putative candidate genes were identified. Rhizosheath weight is easy and rapid to measure, and is associated with relatively high heritability. The breeding of cereal genotypes for beneficial rhizosheath characteristics is achievable and could contribute to agricultural sustainability in nutrient- and water-stressed environments.

Root architecture and root and tuber crop productivity

It is becoming increasingly evident that optimization of root architecture for resource capture is vital for enabling the next green revolution. Although cereals provide half of the calories consumed by humans, root and tuber crops are the second major source of carbohydrates globally. Yet, knowledge of root architecture in root and tuber species is limited. In this opinion article, we highlight what is known about the root system in root and tuber crops, and mark new research directions towards a better understanding of the relation between root architecture and yield. We believe that unraveling the role of root architecture in root and tuber crop productivity will improve global food security, especially in regions with marginal soil fertility and low-input agricultural systems.

Feed the crop not the soil: rethinking phosphorus management in the food chain

Society relies heavily on inorganic phosphorus (P) compounds throughout its food chain. This dependency is not only very inefficient and increasingly costly but is depleting finite global reserves of rock phosphate. It has also left a legacy of P accumulation in soils, sediments and wastes that is leaking into our surface waters and contributing to widespread eutrophication. We argue for a new, more precise but more challenging paradigm in P fertilizer management that seeks to develop more sustainable food chains that maintain P availability to crops and livestock but with reduced amounts of imported mineral P and improved soil function. This new strategy requires greater public awareness of the environmental consequences of dietary choice, better understanding of soil-plant-animal P dynamics, increased recovery of both used P and unutilized legacy soil P, and new innovative technologies to improve fertilizer P recovery. In combination, they are expected to deliver significant economic, environmental, and resource-protection gains, and contribute to future global P stewardship.

Comparing simple root phenotyping methods on a core set of rice genotypes

Interest in belowground plant growth is increasing, especially in relation to arguments that shallow-rooted cultivars are efficient at exploiting soil phosphorus while deep-rooted ones will access water at depth. However, methods for assessing roots in large numbers of plants are diverse and direct comparisons of methods are rare. Three methods for measuring root growth traits were evaluated for utility in discriminating rice cultivars: soil-filled rhizotrons, hydroponics and soil-filled pots whose bottom was sealed with a non-woven fabric (a potential method for assessing root penetration ability). A set of 38 rice genotypes including the OryzaSNP set of 20 cultivars, additional parents of mapping populations and products of marker-assisted selection for root QTLs were assessed. A novel method of image analysis for assessing rooting angles from rhizotron photographs was employed. The non-woven fabric was the easiest yet least discriminatory method, while the rhizotron was highly discriminatory and allowed the most traits to be measured but required more than three times the labour of the other methods. The hydroponics was both easy and discriminatory, allowed temporal measurements, but is most likely to suffer from artefacts. Image analysis of rhizotrons compared favourably to manual methods for discriminating between cultivars. Previous observations that cultivars from the indica subpopulation have shallower rooting angles than aus or japonica cultivars were confirmed in the rhizotrons, and indica and temperate japonicas had lower maximum root lengths in rhizotrons and hydroponics. It is concluded that rhizotrons are the preferred method for root screening, particularly since root angles can be assessed.

A scanner system for high-resolution quantification of variation in root growth dynamics of Brassica rapa genotypes

The potential exists to breed for root system architectures that optimize resource acquisition. However, this requires the ability to screen root system development quantitatively, with high resolution, in as natural an environment as possible, with high throughput. This paper describes the construction of a low-cost, high-resolution root phenotyping platform, requiring no sophisticated equipment and adaptable to most laboratory and glasshouse environments, and its application to quantify environmental and temporal variation in root traits between genotypes of Brassica rapa L. Plants were supplied with a complete nutrient solution through the wick of a germination paper. Images of root systems were acquired without manual intervention, over extended periods, using multiple scanners controlled by customized software. Mixed-effects models were used to describe the sources of variation in root traits contributing to root system architecture estimated from digital images. It was calculated that between one and 43 replicates would be required to detect a significant difference (95% CI 50% difference between traits). Broad-sense heritability was highest for shoot biomass traits (>0.60), intermediate (0.25-0.60) for the length and diameter of primary roots and lateral root branching density on the primary root, and lower (<0.25) for other root traits. Models demonstrate that root traits show temporal variations of various types. The phenotyping platform described here can be used to quantify environmental and temporal variation in traits contributing to root system architecture in B. rapa and can be extended to screen the large populations required for breeding for efficient resource acquisition.

An updated model for nitrate uptake modelling in plants. II. Assessment of active root involvement in nitrate uptake based on integrated root system age: measured versus modelled outputs

Background and Aims An updated version of a mechanistic structural-functional model was developed to predict nitrogen (N) uptake throughout the growth cycle by a crop of winter oilseed rape, Brassica napus, grown under field conditions. Methods The functional component of the model derives from a revisited conceptual framework that combines the thermodynamic Flow-Force interpretation of nitrate uptake isotherms and environmental and in planta effects on nitrate influx. Estimation of the root biomass (structural component) is based upon a combination of root mapping along the soil depth profile in the field and a relationship between the specific root length and external nitrate concentration. The root biomass contributing actively to N uptake was determined by introduction of an integrated root system age that allows assignment of a root absorption capacity at a specific age of the root. Key Results Simulations were well matched to measured data of N taken up under field conditions for three levels of N fertilization. The model outputs indicated that the two topsoil layers (0-30 and 30-60 cm) contained 75-88 % of the total root length and biomass, and accounted for 90-95 % of N taken up at harvest. Conclusions This conceptual framework provides a model of nitrate uptake that is able to respond to external nitrate fluctuations at both functional and structural levels.