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Background: Genetic improvement of root system architecture is a promising approach for improved uptake of water and mineral nutrients distributed unevenly in the soil. To identify genomic regions associated with the length of different root types in rice, we quantified root system architecture in a set of 26 chromosome segment substitution lines derived from a cross between lowland indica rice, IR64, and upland tropical japonica rice, Kinandang Patong, (IK-CSSLs), using 2D & 3D root phenotyping platforms. Results: Lengths of seminal and crown roots in the IK-CSSLs grown under hydroponic conditions were measured by 2D image analysis (RootReader2D). Twelve CSSLs showed significantly longer seminal root length than the recurrent parent IR64. Of these, 8 CSSLs also exhibited longer total length of the three longest crown roots compared to IR64. Three-dimensional image analysis (RootReader3D) for these CSSLs grown in gellan gum revealed that only one CSSL, SL1003, showed significantly longer total root length than IR64. To characterize the root morphology of SL1003 under soil conditions, SL1003 was grown in Turface, a soil-like growth media, and roots were quantified using RootReader3D. SL1003 had larger total root length and increased total crown root length than did IR64, although its seminal root length was similar to that of IR64. The larger TRL in SL1003 may be due to increased crown root length. Conclusions: SL1003 carries an introgression from Kinandang Patong on the long arm of chromosome 1 in the genetic background of IR64. We conclude that this region harbors a QTL controlling crown root elongation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Low iron absorption from important staple foods may contribute to iron deficiency in developing countries. To date, few studies have examined the iron bioavailability of pulse crops as commonly prepared and consumed by humans. Objective: The objectives were to characterize the iron absorption from a test meal of intrinsically labeled (57)Fe lentils prepared as dal, to compare the bioavailability of iron from (57)Fe in dal with that observed for a reference dose of (58)Fe as ferrous sulfate, and to assess associations between iron absorption and iron status indicators. Methods: This crossover study included 19 nonpregnant women (n = 6 anemic; hemoglobin: <12.0 g/dL) who consumed 2 test meals on consecutive days in a counter-balanced order, ferrous sulfate (7 mg FeSO4 plus 1 mg (58)Fe) and 330 g dal (lentils enriched to 85.1% with (57)Fe, 8 mg native (57)Fe). Iron absorption was determined by analyzing blood samples taken 14 d after dosing with the use of magnetic sector thermal ionization mass spectrometry. Results: We found that the mean iron absorption from the dal was 2.20% ± 3.40% and was significantly lower than the 23.6% ± 13.2% observed from the same iron load given as ferrous sulfate (P < 0.001). Absorption of non-heme iron from dal and from ferrous sulfate was inversely associated with serum ferritin (SF; r = -0.50, P = 0.05 and r = -0.81, P < 0.001, respectively) and serum hepcidin (r = -0.45, P = 0.05 and r = -0.60, P = 0.007, respectively). Anemic women absorbed more iron from either source (1.20% from dal, P = 0.10; 18.3% from ferrous sulfate, P = 0.001) compared with women who were iron replete. Conclusions: Iron absorption from the dal was low overall but upregulated in anemic women. Both SF and hepcidin were inversely associated with iron absorption from both a supplemental and a food-based non-heme iron source in nonanemic and anemic women. [ABSTRACT FROM AUTHOR]

Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P defidency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mall Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition effidency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas SbO3gO06765 and SbO3gO031680 alleles increasing root surface area also increased grain yield in a low-P soft. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between ass~iation panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for SbO3gO06765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOLI genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil. [ABSTRACT FROM AUTHOR]

Al3+ and H+ toxicities predicted to occur at moderately acidic conditions (pH [water] = 5-5.5) in low-Ca soils were characterized by the combined approaches of computational modeling of electrostatic interactions of ions at the root plasma membrane (PM) surface and molecular/physiological analyses in Arabidopsis (Arabidopsis thaliana). Root growth inhibition in known hypersensitive mutants was correlated with computed {Al3+} at the PM surface ({Al3+}PM); inhibition was alleviated by increased Ca, which also reduced {A13+}PM and correlated with cellular Al responses based on expression analysis of genes that are markers for Al stress. The Al-inducible Al tolerance+ genes ALUMINUM-ACTIVATED MALATE TRANSPORTER1 and ALUMINUM SENSITIVE3 were induced by levels of {A13+ }PM too low to inhibit root growth in tolerant genotypes, indicating that protective responses are triggered when {A13+}PM was below levels that can initiate injury. Modeling of the H+ sensitivity of the SENSITIVE TO PROTON RHIZOTOXICITY1 knockout mutant identified a Ca alleviation mechanism of H+ rhizotoxicity, possibly involving stabilization of the cell wall. The phosphatidate phosphohydrolasel (pah1) pah2 double mutant showed enhanced Al susceptibility under low-P conditions, where greater levels of negatively charged phospholipids in the PM occur, which increases {Al3+}PM through increased PM surface negativity compared with wild-type plants. Finally, we found that the nonalkalinizing Ca fertilizer gypsum improved the tolerance of the sensitive genotypes in moderately acidic soils. These findings fit our modeling predictions that root toxicity to Al3+ and H+ in moderately acidic soils involves interactions between both toxic ions in relation to Ca alleviation. [ABSTRACT FROM AUTHOR]

ABSTRACT High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large-scale phenotyping studies. To demonstrate the unique capabilities and high-throughput capacity of this phenotyping platform for studying root systems, genome-wide association studies on rice ( Oryza sativa) and maize ( Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population. [ABSTRACT FROM AUTHOR]

A novel imaging and software platform was developed for the high-throughput phenotyping of three-dimensional root traits during seedling development. To demonstrate the platform's capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and imaged daily for 10 d. Rotational image sequences consisting of 40 two-dimensional images were captured using an optically corrected digital imaging system. Three-dimensional root reconstructions were generated and analyzed using a custom-designed software, RootReader3D. Using the automated and interactive capabilities of RootReader3D, five rice root types were classified and 27 phenotypic root traits were measured to characterize these two genotypes. Where possible, measurements from the three-dimensional platform were validated and were highly correlated with conventional two-dimensional measurements. When comparing gellan gum-grown plants with those grown under hydroponic and sand culture, significant differences were detected in morphological root traits (P < 0.05). This highly flexible platform provides the capacity to measure root traits with a high degree of spatial and temporal resolution and will facilitate novel investigations into the development of entire root systems or selected components of root systems. In combination with the extensive genetic resources that are now available, this platform will be a powerful resource to further explore the molecular and genetic determinants of root system architecture. [ABSTRACT FROM AUTHOR]

The genetic and physiological mechanisms of aluminum (A1) tolerance have been well studied in certain cereal crops, and A1 tolerance genes have been identified in sorghum (Sorghum bicolor) and wheat (Triticum aestivum). Rice (Oryza sativa) has been reported to be highly A1 tolerant; however, a direct comparison of rice and other cereals has not been reported, and the mechanisms of rice A1 tolerance are poorly understood. To facilitate A1 tolerance phenotyping in rice, a high-throughput imaging system and root quantification computer program was developed, permitting quantification of the entire root system, rather than just the longest root. Additionally, a novel hydroponic solution was developed and optimized for A1 tolerance screening in rice and compared with the Yoshida's rice solution commonly used for rice A1 tolerance studies. To gain a better understanding of A1 tolerance in cereals, comparisons of A1 tolerance across cereal species were conducted at four A1 concentrations using seven to nine genetically diverse genotypes of wheat, maize (Zea mays), sorghum, and rice. Rice was significantly more tolerant than maize, wheat, and sorghum at all A1 concentrations, with the mean A1 tolerance level for rice found to be 2- to 6-fold greater than that in maize, wheat, and sorghum. Physiological experiments were conducted on a genetically diverse panel of more than 20 rice genotypes spanning the range of rice A1 tolerance and compared with two maize genotypes to determine if rice utilizes the well-described A1 tolerance mechanism of root tip A1 exclusion mediated by organic acid exudation. These results clearly demonstrate that the extremely high levels of rice A1 tolerance are mediated by a novel mechanism, which is independent of root tip A1 exclusion. [ABSTRACT FROM AUTHOR]

GEOCHEM-EZ is a multi-functional chemical speciation program, designed to replace GEOCHEM-PC, which can only be used on DOS consoles. Chemical speciation programs, such as GEOCHEM and GEOCHEM-PC, have been excellent tools for scientists designing appropriate solutions for their experiments. GEOCHEM-PC is widely used in plant nutrition and soil and environmental chemistry research to perform equilibrium speciation computations, allowing the user to estimate solution ion activities and to consider simple complexes and solid phases. As helpful as GEOCHEM-PC has been to scientists, the consensus was that the program was not very user friendly, was difficult to learn and to troubleshoot, and suffered from several functional weaknesses. To enhance the usability and to address the problems found in GEOCHEM-PC, we upgraded the program with a Java graphical interface, added Help files, and improved its power and function, allowing it to run on any computer that supports Windows XP, Vista or Windows 7. [ABSTRACT FROM AUTHOR]

Malate transporters play a critical role in aluminum (Al) tolerance responses for some plant species, such as Arabidopsis (Arabidopsis thaliana). Here, we further characterize AtALMTI, an Arabidopsis aluminum-activated malate transporter, to clarify its specific role in malate release and Al stress responses. Malate excretion from the roots of accession Columbia was sharply induced by Al, which is concomitant with the induction of AtALMTI gene expression. The malate release was specific for Al among rhizotoxic stressors, namely cadmium, copper, erbium, lanthanum, sodium, and low pH, which accounts for the specific sensitivity of a null mutant to Al stress. Al-specific malate excretion can be explained by a combined regulation of AtALMTI expression and activation of AtALMT1 protein, which is specific for Al. Although low pH treatment slightly induced gene expression, other treatments did not. In addition, malate excretion in Al-activated seedlings was rapidly stopped by removing Al from the solution. Other rhizotoxic stressors were not effective in maintaining malate release. Protein kinase and phosphatase inhibitor studies indicated that reversible phosphorylation was important for the transcriptional and posttranslational regulation of AtALMTI. AtALMT1 promoter-β-glucuronidase fusion lines revealed that AtALMT1 has restricted expression within the root, such that uimecessary carbon loss is likely minimized. Lastly, a natural nonsense mutation allele of AtALMT1 was identified from the Al-hypersensitive natural accession Warschau-1. [ABSTRACT FROM AUTHOR]

Crop yields are significantly reduced by aluminum toxicity on highly acidic soils, which comprise up to 50% of the world's arable land. Candidate aluminum tolerance proteins include organic acid efflux transporters, with the organic acids forming non-toxic complexes with rhizosphere aluminum. In this study, we used positional cloning to identify the gene encoding a member of the multidrug and toxic compound extrusion (MATE) family, an aluminum-activated citrate transporter, as responsible for the major sorghum (Sorghum bicolor) aluminum tolerance locus, AltSB. Polymorphisms in regulatory regions of AltSB are likely to contribute to large allelic effects, acting to increase AltSB expression in the root apex of tolerant genotypes. Furthermore, aluminum-inducible AltSB expression is associated with induction of aluminum tolerance via enhanced root citrate exudation. These findings will allow us to identify superior AltSB haplotypes that can be incorporated via molecular breeding and biotechnology into acid soil breeding programs, thus helping to increase crop yields in developing countries where acidic soils predominate. [ABSTRACT FROM AUTHOR]

Root apical aluminum (Al) exclusion via Al-activated root citrate exudation is widely accepted as the main Al-resistance mechanism operating in maize (Zea mays) roots. Nonetheless, the correlation between Al resistance and this Al-exclusion mechanism has not been tested beyond a very small number of Al-resistant and Al-sensitive maize lines, in this study, we conducted a comparative study of the physiology of A1 resistance using six different maize genotypes that capture the range of maize A1 resistance and differ significantly in their genetic background (three Brazilian and three North American genotypes). In these maize lines, we were able to establish a clear correlation between root tip A1 exclusion (based on root A1 content) and A1 resistance. Both Al-resistant genotypes and three of the four Al-sensitive lines exhibited a significant Al-activated citrate exudation, with no evidence for A1 activation of root malate or phosphate release. There was a lack of correlation between differential A1 resistance and root citrate exudation for the six maize genotypes; in fact, one of the Al-sensitive lines, Mo17, had the largest Al-activated citrate exudation of all of the maize lines. Our results indicate that although root organic acid release may play a role in maize Al resistance, it is clearly not the only or the main resistance mechanism operating in these maize roots. A number of other potential Al-resistance mechanisms were investigated, including release of other Al-chelating ligands, Al-induced alkalinization of rhizosphere pH, changes in internal levels of Al-chelating compounds in the root, and A1 translocation to the shoot. However, we were unsuccessful in identifying additional Al-resistance mechanisms in maize. It is likely that a purely physiological approach may not be sufficient to identify these novel Al-resistance mechanisms in maize and this will require an interdisciplinary approach integrating genetic, molecular, and physiological investigations. [ABSTRACT FROM AUTHOR]

Describes the use of quantitative trait locus mapping to identify and characterize the aluminum tolerance loci in Arabidopsis. Inhibition of the root growth and water acquisition; Solubilization of aluminum; Stages for the subsequent cloning of the genes.