How Does Rice Defend Against Excess Iron?: Physiological and Molecular Mechanisms

Ferritin From Striped Stem Borer (Chilo suppressalis) Oral Secretion Acts as an Effector Helping to Maintain Iron Homoeostasis and Impair Defenses in Rice

The striped stem borer (Chilo suppressalis, SSB) is a highly destructive insect pest in rice (Oryza sativa). SSB oral secretions (OSs) can induce plant defense responses in rice. However, the specific effectors in SSB OSs that mediate these interactions with rice remain poorly understood. In this study, hallmarks of ferroptosis-like plant defense response, such as the reprogramming of ferroptosis-related genes, reduced glutathione levels, accumulation of ferric ion, and enhanced lipid peroxidation by reactive oxygen species (ROS), were detected in rice subjected to SSB infestation and SSB OSs treatment. Furthermore, we identified and characterized a protein from SSB OSs, the ferritin CsFer1, which plays a critical role in the regulation of plant iron homoeostasis. CsFer1 was shown to possess Fe2+ binding capacity and ferroxidase activity. Through recombinant CsFer1 protein treatment, overexpression of CsFer1 in rice and SSB larvae with silencing CsFer1 feeding in rice, we found that CsFer1 helped maintain iron homoeostasis under SSB infestation, suppressing H2O2 and JA accumulation, ultimately compromising rice resistance to herbivorous pests. Moreover, such a phenomenon about the regulation of iron homoeostasis and suppression of insect resistance was observed in the CsFer1 overexpressed tobacco. Collectively, these findings suggest that CsFer1 functions as an effector involved in the regulation of iron homoeostasis- and lipid peroxidation-related plant defense during plant-insect interaction.

Formation of Apoplastic Barriers to Radial O₂ Loss in Rice Roots: Effects of Low-O₂ and High-Fe Conditions, and the Roles of Suberin, Glycerol Esters, and Iron Plaques

Lack of O2 and high concentrations of iron (Fe) are common in flooded soils where Rice (Oryza sativa L.) is cultivated. We tested the hypothesis that growing in stagnant or high Fe conditions might induce the formation of apoplastic barriers in roots with different properties and chemical compositions. We measured radial O2 loss (ROL) from intact roots, the chemical composition of roots and the formation of root iron plaques in Fe-sensitive and Fe-tolerant rice genotypes grown in aerated, deoxygenated stagnant solutions or in aerated solutions containing high concentrations of Fe. Roots of plants grown in stagnant conditions developed tight barriers to ROL, while those grown in high Fe conditions developed only partial barriers. Chemical analysis of enzymatically isolated sclerenchyma/exodermal root cells indicated that roots grown in stagnant conditions showed increased amounts of suberin and glycerol esters. In contrast, roots in high Fe conditions showed an increase in suberization along with formation of iron plaques covering the roots. In high Fe conditions, exodermal suberization and the formation of partial ROL barriers were not influenced by the genotype's tolerance to Fe. The amount of O2 diffused from roots is influenced by the various layers that impede O2 diffusion. Specifically, increased amounts of glycerol esters in the suberized exodermis provide the greater resistance to ROL.

The Role of Organic Materials in Shaping the Content of Trace Elements in Iron-Contaminated Soil

Iron contamination negatively affects how plants grow and develop, and it has an analogous influence on the health of other organisms. The use of different types of organic soil amendments can be a strategy to reduce the effects of excess iron stress and limit its assimilation by plants. The aim of this experiment was to investigate the possibility of using organic material in the form of humic acids (HAs) to reduce the influence of iron contamination on the content of trace elements (TEs) in the soil. The content of iron in the soil increased linearly (by 14%) as more iron was added. The addition of humic acids to the soil also promoted an increase in soil Fe content (by 12%) in comparison to the series without HAs. The highest dose of iron resulted in a decrease in Cd (by 49%), Pb (by 29%), Cr (by 13%), and Zn (by 10%) and an increase in Mn (by 6%), Cu (by 16%), and Co (by 33%) in the soil in comparison to the object without Fe. However, the first dose of iron increased the lead content, and the first and second dose of Fe also increased the Zn content in the soil. The nickel content in the soil also increased to 500 mg Fe kg-1 of soil. Thereafter, a decline was observed in the nickel content. The addition of organic material had a different influence on the content of individual TEs in the iron-contaminated soils. The most evident constraining impact of HAs pertained to the level of Cd (reducing it by 14%) and Zn in the soil (only for two of its doses). The content of other TEs in the soil after the addition of organic material was found to be higher than in the series without HAs. This was especially evident for elements such as cobalt (Co) and lead (Pb).

OsSPL9 promotes Cu uptake and translocation in rice grown in high-Fe red soil

Most rice varieties are able to grow in red high-Fe soil, but the underlying mechanism remains elusive. Through forward genetic screening, we identified a red soil-sensitive-1 (rss1) mutant that exhibited severely retarded growth when grown in red soil but showed no evident phenotype in cinnamon soil. Under the red soil/high-Fe conditions, rss1 exhibited increased Fe but decreased copper (Cu) concentrations in both roots and shoots, and the rss1 phenotype was partially rescued by Cu supplement. RSS1 encodes an OsSPL9 transcription factor that is expressed in pericycle cells and parenchyma cells surrounding xylem in roots. Under high-Fe conditions, OsSPL9 activated expression of Cu transporters, including OsYSL16, OsCOPT1, and OsCOPT5 by binding to their promoters, and OsYSL16 overexpression partially rescued rss1 defects. We thus propose that OsSPL9 overcomes high-Fe imposed Cu deficiency by activating the expressions of Cu transporter genes, allowing rice to adapt to red soil.

Arabidopsis MEB3 functions as a vacuolar metal transporter to regulate iron accumulation in roots

Iron is an essential nutrient for plant photosynthesis and development, but excess iron leads to stress. After absorption from the soil, plants store iron in roots and distribute it to shoots via long-distance transport. The vacuole is involved in iron storage and the maintenance of cellular iron homeostasis, and vacuolar iron transporter (VIT) family proteins have been identified as plant vacuolar iron transporters. However, the contribution of vacuolar iron transporters to overall iron homeostasis in plants is not fully understood. Here, we show that MEMBRANE PROTEIN OF ER BODY 3 (MEB3), a VIT family member, functions as a vacuolar metal transporter for iron distribution in Arabidopsis thaliana. Heterologous expression of Arabidopsis MEB3 in yeast vacuolar iron or zinc transporter mutants restored the iron- and zinc-resistance phenotypes of the respective mutants, indicating that MEB3 regulates iron and zinc transport. In Arabidopsis, MEB3 was expressed in almost all tissues, albeit to higher levels in roots and seedlings, and MEB3 protein localized to the tonoplast. Iron but not zinc levels were reduced in meb3 knockout mutant roots, suggesting that the knockout reduced iron storage capacity in roots. At high iron concentration, meb3 mutants accumulated more iron in shoots and less iron in roots than the wild type, indicating impairment of proper iron distribution in meb3 mutants. These findings demonstrate that MEB3 is a vacuolar transporter involved in the homeostasis of iron and other metals in plants.

Morpho-Physiological Adaptations of Rice Cultivars Under Heavy Metal Stress: A Systematic Review and Meta-Analysis

Soil contamination, including in rice fields, arises from a variety of natural processes and anthropogenic activities, leading to an accumulation of heavy metals. While extensive research has addressed the bioaccumulation of heavy metals in rice, only limited systematic reviews have examined their specific impact on the morpho-physiological traits of rice plants. This review aims to provide a comprehensive synthesis of current studies detailing the rice cultivars, types of heavy metals investigated, study designs, sampling locations, and experimental sites while systematically analyzing the morphological and physiological responses of rice cultivars to heavy metal stress. Studies show that morphological traits generally exhibit a decline under heavy metal exposure. Physiologically, rice cultivars tend to show decreased total chlorophyll and carotenoid levels, along with increased levels of malondialdehyde (MDA), hydrogen peroxide (H₂O₂), and antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), and proline. These findings suggest that plant genotype, type of heavy metal, and intensity of stress significantly modulate the morphological and physiological responses of rice, highlighting critical areas for further research in heavy metal stress tolerance in rice cultivars.

Excess iron accumulation affects maize endosperm development by inhibiting starch synthesis and inducing DNA damage

Iron (Fe) storage in cereal seeds is the principal source of dietary Fe for humans. In maize (Zea mays), the accumulation of Fe in seeds is known to be negatively correlated with crop yield. Hence, it is essential to understand the underlying mechanism, which is crucial for developing and breeding maize cultivars with high yields and high Fe concentrations in the kernels. Here, through the successful application of in vitro kernel culture, we demonstrated that excess Fe supply in the medium caused the kernel to become collapsed and lighter in color, consistent with those found in yellow strip like 2 (ysl2, a small kernel mutant), implicated a crucial role of Fe concentration in kernel development. Indeed, over-accumulation of Fe in endosperm inhibited the abundance and activity of ADP-glucose pyrophosphorylase (AGPase) and the kernel development defect was alleviated by overexpression of Briittle 2 (Bt2, encoding a small subunit of AGPase) in ysl2 mutant. Imaging and quantitative analyses of reactive oxygen species (ROS) and cell death showed that Fe stress-induced ROS burst and severe DNA damage in endosperm cells. In addition, we have successfully identified candidate genes that are associated with iron homeostasis within the kernel, as well as upstream transcription factors that regulate ZmYSL2 by yeast one-hybrid screening. Collectively, our study will provide insights into the molecular mechanism of Fe accumulation-regulated seed development and promote the future efficient application of Fe element in corn improvement.

You can't always get as much iron as you want: how rice plants deal with excess of an essential nutrient

Iron (Fe) is an essential nutrient for almost all organisms. However, free Fe within cells can lead to damage to macromolecules and oxidative stress, making Fe concentrations tightly controlled. In plants, Fe deficiency is a common problem, especially in well-aerated, calcareous soils. Rice (Oryza sativa L.) is commonly cultivated in waterlogged soils, which are hypoxic and can cause Fe reduction from Fe3+ to Fe2+, especially in low pH acidic soils, leading to high Fe availability and accumulation. Therefore, Fe excess decreases rice growth and productivity. Despite the widespread occurrence of Fe excess toxicity, we still know little about the genetic basis of how rice plants respond to Fe overload and what genes are involved in variation when comparing genotypes with different tolerance levels. Here, we review the current knowledge about physiological and molecular data on Fe excess in rice, providing a comprehensive summary of the field.

Physiological and molecular mechanisms of plant-root responses to iron toxicity

The chemical form and physiological activity of iron (Fe) in soil are dependent on soil pH and redox potential (Eh), and Fe levels in soils are frequently elevated to the point of causing Fe toxicity in plants, with inhibition of normal physiological activities and of growth and development. In this review, we describe how iron toxicity triggers important physiological changes, including nitric-oxide (NO)-mediated potassium (K+) efflux at the tips of roots and accumulation of reactive oxygen species (ROS) and reactive nitrogen (RNS) in roots, resulting in physiological stress. We focus on the root system, as the first point of contact with Fe in soil, and describe the key processes engaged in Fe transport, distribution, binding, and other mechanisms that are drawn upon to defend against high-Fe stress. We describe the root-system regulation of key physiological processes and of morphological development through signaling substances such as ethylene, auxin, reactive oxygen species, and nitric oxide, and discuss gene-expression responses under high Fe. We especially focus on studies on the physiological and molecular mechanisms in rice and Arabidopsis under high Fe, hoping to provide a valuable theoretical basis for improving the ability of crop roots to adapt to soil Fe toxicity.

Exogenous γ-aminobutyric acid and Bacillus pumilus reduce arsenic uptake and toxicity in rice

In this study, the addition of γ-aminobutyric acid (GABA), Bacillus pumilus, or both, was found to enhance rice growth and yield while significantly decreasing arsenic (As) accumulation in Oryza sativa rice tissues. GABA emerged as a regulator of iron (Fe) homeostasis, acting as a signaling modulator that influenced phytosiderophore secretions in the plant. Meanwhile, B. pumilus directly increased Fe levels through siderophore production, promoting the development of Fe-rich rice plants. Subsequently, Fe competed with As uptake at the root surface, leading to decreased As levels and translocation to the grains. Furthermore, the addition of GABA and B. pumilus optimized rice indole-3 acetic acid (IAA) contents, thereby adjusting cell metabolite balance under As stress. This adjustment results in low malondialdehyde (MDA) contents in the leaves and roots during the early and late vegetative phases, effectively reducing oxidative stress. When added to As-contaminated soil, GABA and B. pumilus effectively maintained endogenous GABA levels and exhibited low ROS generation, similar to normal soil. Concurrently, GABA and B. pumilus significantly downregulated the activity of OsLsi1, OsLsi2, and OsABCC1 in roots, reducing As uptake through roots, shoots, and grains, respectively. These findings suggest that GABA and B. pumilus additions impede As translocation through grains, ultimately enhancing rice productivity under As stress.

Biofertilizers from wastewater treatment as a potential source of mineral nutrients for growth of amaranth plants

Exploring alternative fertilizers is crucial in agriculture due to the cost and environmental impact of inorganic options. This study investigated the potential of sewage-derived biofertilizers on the growth and physiology of Amaranthus cruentus plants. Various treatments were compared, including control treatments with inorganic fertilizer and treatments with biofertilizers composed of microalgae, biosolids and reclaimed water. The following traits were investigated: photosynthetic pigments, gas exchange, growth, and leaf nutrient concentrations. The results showed that the concentrations of N, P, Cu, Fe Zn and Na nutrients, in the dry microalgae and biosolids, were quite high for the needs of the plants. The wet microalgae presented high concentration of Cu, Fe and Zn nutrients while reclaimed water contained high concentration of N, K, Ca and S. Na and Zn nutrients increased in the leaf of plants treated with dry microalgae and biosolid, respectively. At the beginning of the flowering phase, total chlorophyll and carotenoids contents were lower for plants grown with wet microalgae while for plants grown with higher doses of biosolid or reclaimed water total chlorophyll was increased, and carotenoids were not affected. Lower photosynthetic pigments under wet microalgae resulted in lower photosynthetic rates. On the other hand, amendments with dry microalgae and biosolid increased photosynthetic rates with the biosolid being the most effective. Higher applications of biosolid, wet and dry microalgae produced a considerable increase in shoot biomass of amaranth, with the dry microalgae being the most effective. Additionally, reclaimed water obtained after tertiary treatment of sewage with microalgae and biosolids applied alone showed promising effects on plant growth. Overall, these findings suggest that organic fertilizers derived from sewage treatment have the potential to enhance plant growth and contribute to sustainable agricultural practices.

Plant Iron Research in African Countries: Current "Hot Spots", Approaches, and Potentialities

Plant iron (Fe) nutrition and metabolism is a fascinating and challenging research topic; understanding the role of Fe in the life cycle of plants requires knowledge of Fe chemistry and biochemistry and their impact during development. Plant Fe nutritional status is dependent on several factors, including the surrounding biotic and abiotic environments, and influences crop yield and the nutritional quality of edible parts. The relevance of plant Fe research will further increase globally, particularly for Africa, which is expected to reach 2.5 billion people by 2050. The aim of this review is to provide an updated picture of plant Fe research conducted in African countries to favor its dissemination within the scientific community. Three main research hotspots have emerged, and all of them are related to the production of plants of superior quality, i.e., development of Fe-dense crops, development of varieties resilient to Fe toxicity, and alleviation of Fe deficiency, by means of Fe nanoparticles for sustainable agriculture. An intensification of research collaborations between the African research groups and plant Fe groups worldwide would be beneficial for the progression of the identified research topics.

Iron (Fe) toxicity, uptake, translocation, and physio-morphological responses in Catharanthus roseus

Iron (Fe) toxicity in plant species depends on the availability of Fe in the soil, uptake ability by the root system, and translocation rate to other parts of the plant. The aim of this study was to assess Fe uptake by root tissues of Catharanthus roseus, translocation rate to leaf tissues, and the impairment of plant physio-morphological characteristics. Fe uptake by the roots (~ 700 µg g-1 DW) of C. roseus was observed during the early exposure period (1 week), and translocation factor from root to shoot was fluctuated as an independent strategy. A high level of Fe content in the root tissues significantly inhibited root length and root dry weight. Under acidic pH condition, an enrichment of Fe in the shoots (~ 400 µg g-1 DW) led to increase in leaf temperature (> 2.5 °C compared to control) and crop stress index (> 0.6), resulting in stomatal closure, subsequently decreasing CO2 assimilation rate and H2O transpiration rate. An increment of CSI in Fe-stressed plants was negatively related to stomatal conductance, indicating stomatal closure with an increase in Fe in the leaf tissues. High Fe levels in the leaf tissues directly induced toxic symptoms including leaf bronzing, leaf spotting, leaf necrosis, leaf chlorosis, and leaf senescence in C. roseus plants. In summary, C. roseus was identified as a good candidate plant for Fe phytoextraction, depending on Fe bioaccumulation, therefore 50 mM Fe treatment was designated as an excess Fe to cause the growth inhibition, especially in the prolonged Fe incubation periods.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01379-5.

Magnesium supply alleviates iron toxicity-induced leaf bronzing in rice through exclusion and tissue-tolerance mechanisms

Introduction

Iron (Fe) toxicity is a widespread nutritional disorder in lowland rice causing growth retardation and leaf symptoms referred to as leaf bronzing. It is partly caused by an imbalance of nutrients other than Fe and supply of these is known to mitigate the toxicity. But the physiological and molecular mechanisms involved are unknown.

Methods

We investigated the effect of magnesium (Mg) on Fe toxicity tolerance in a field study in the Central Highlands of Madagascar and in hydroponic experiments with excess Fe (300 mg Fe L-1). An RNA-seq analysis was conducted in a hydroponic experiment to elucidate possible mechanisms underlying Mg effects.

Results and discussion

Addition of Mg consistently decreased leaf bronzing under both field and hydroponic conditions, whereas potassium (K) addition caused minor effects. Plants treated with Mg tended to have smaller shoot Fe concentrations in the field, suggesting enhanced exclusion at the whole-plant level. However, analysis of multiple genotypes showed that Fe toxicity symptoms were also mitigated without a concomitant decrease of Fe concentration, suggesting that increased Mg supply confers tolerance at the tissue level. The hydroponic experiments also suggested that Mg mitigated leaf bronzing without significantly decreasing Fe concentration or oxidative stress as assessed by the content of malondialdehyde, a biomarker for oxidative stress. An RNA-seq analysis revealed that Mg induced more changes in leaves than roots. Subsequent cis-element analysis suggested that NAC transcription factor binding sites were enriched in genes induced by Fe toxicity in leaves. Addition of Mg caused non-significant enrichment of the same binding sites, suggesting that NAC family proteins may mediate the effect of Mg. This study provides clues for mitigating Fe toxicity-induced leaf bronzing in rice.

MsNRAMP2 Enhances Tolerance to Iron Excess Stress in Nicotiana tabacum and MsMYB Binds to Its Promoter

Iron(Fe) is a trace metal element necessary for plant growth, but excess iron is harmful to plants. Natural resistance-associated macrophage proteins (NRAMPs) are important for divalent metal transport in plants. In this study, we isolated the MsNRAMP2 (MN_547960) gene from alfalfa, the perennial legume forage. The expression of MsNRAMP2 is specifically induced by iron excess. Overexpression of MsNRAMP2 conferred transgenic tobacco tolerance to iron excess, while it conferred yeast sensitivity to excess iron. Together with the MsNRAMP2 gene, MsMYB (MN_547959) expression is induced by excess iron. Y1H indicated that the MsMYB protein could bind to the "CTGTTG" cis element of the MsNRAMP2 promoter. The results indicated that MsNRAMP2 has a function in iron transport and its expression might be regulated by MsMYB. The excess iron tolerance ability enhancement of MsNRAMP2 may be involved in iron transport, sequestration, or redistribution.

Growth Developmental Defects of Mitochondrial Iron Transporter 1 and 2 Mutants in Arabidopsis in Iron Sufficient Conditions

Iron is the most abundant micronutrient in plant mitochondria, and it has a crucial role in biochemical reactions involving electron transfer. It has been described in Oryza sativa that Mitochondrial Iron Transporter (MIT) is an essential gene and that knockdown mutant rice plants have a decreased amount of iron in their mitochondria, strongly suggesting that OsMIT is involved in mitochondrial iron uptake. In Arabidopsis thaliana, two genes encode MIT homologues. In this study, we analyzed different AtMIT1 and AtMIT2 mutant alleles, and no phenotypic defects were observed in individual mutant plants grown in normal conditions, confirming that neither AtMIT1 nor AtMIT2 are individually essential. When we generated crosses between the Atmit1 and Atmit2 alleles, we were able to isolate homozygous double mutant plants. Interestingly, homozygous double mutant plants were obtained only when mutant alleles of Atmit2 with the T-DNA insertion in the intron region were used for crossings, and in these cases, a correctly spliced AtMIT2 mRNA was generated, although at a low level. Atmit1 Atmit2 double homozygous mutant plants, knockout for AtMIT1 and knockdown for AtMIT2, were grown and characterized in iron-sufficient conditions. Pleiotropic developmental defects were observed, including abnormal seeds, an increased number of cotyledons, a slow growth rate, pinoid stems, defects in flower structures, and reduced seed set. A RNA-Seq study was performed, and we could identify more than 760 genes differentially expressed in Atmit1 Atmit2. Our results show that Atmit1 Atmit2 double homozygous mutant plants misregulate genes involved in iron transport, coumarin metabolism, hormone metabolism, root development, and stress-related response. The phenotypes observed, such as pinoid stems and fused cotyledons, in Atmit1 Atmit2 double homozygous mutant plants may suggest defects in auxin homeostasis. Unexpectedly, we observed a possible phenomenon of T-DNA suppression in the next generation of Atmit1 Atmit2 double homozygous mutant plants, correlating with increased splicing of the AtMIT2 intron containing the T-DNA and the suppression of the phenotypes observed in the first generation of the double mutant plants. In these plants with a suppressed phenotype, no differences were observed in the oxygen consumption rate of isolated mitochondria; however, the molecular analysis of gene expression markers, AOX1a, UPOX, and MSM1, for mitochondrial and oxidative stress showed that these plants express a degree of mitochondrial perturbation. Finally, we could establish by a targeted proteomic analysis that a protein level of 30% of MIT2, in the absence of MIT1, is enough for normal plant growth under iron-sufficient conditions.

Diproline-induced resistance to parasitic nematodes in the same and subsequent rice generations: Roles of iron, nitric oxide and ethylene

Induced resistance (IR) is a plant phenotype characterized by lower susceptibility to biotic challenges upon elicitation by so-called IR stimuli. Earlier, we identified diproline (cyclo(l-Pro-l-Pro)) as IR stimulus that protects rice (Oryza sativa) against the root-knot nematode Meloidogyne graminicola (Mg). In the current study, detailed transcriptome analyses at different time points, and under uninfected and nematode-infected conditions revealed that this rice IR phenotype is correlated with induction of genes related to iron (Fe), ethylene (ET) and reactive oxygen species (ROS)/reactive nitrogen species (RNS) metabolism. An infection experiment under Fe limiting conditions confirmed that diproline-IR is only effective under optimal Fe supply. Although total root Fe levels were not affected in diproline-treated plants, phytosiderophore secretion was found to be induced by this treatment. Experiments on mutant and transgenic rice lines impaired in ET or ROS/RNS metabolism confirmed that these metabolites are involved in diproline-IR. Finally, we provide evidence for transgenerational inheritance of diproline-IR (diproline-TIR), as two successive generations of diproline-treated ancestors exhibited an IR phenotype while themselves never being exposed to diproline. Transcriptome analyses on the offspring plants revealed extensive overlap between the pathways underpinning diproline-IR and diproline-TIR. Although diproline induces significant systemic changes in global DNA methylation levels early after treatment, such changes in DNA methylation were not detected in the descendants of these plants. To our knowledge, this is the first report of TIR in rice and the first transcriptional assessment of TIR in monocots.

An Environmentally Friendly Compact Microfluidic Hydrodynamic Sequential Injection System Using Curcuma putii Maknoi & Jenjitt. Extract as a Natural Reagent for Colorimetric Determination of Total Iron in Water Samples

The miniaturization of analytical systems and the utilization of nontoxic natural extract from plants play significant roles for green analytical chemistry methodology. In this work, the microfluidic hydrodynamic sequential injection (HSI) with the LED-phototransistor colorimetric detection system has been proposed to create an ecofriendly and low-cost miniaturized analytical system for online determination of iron in water samples using Curcuma putii Maknoi & Jenjitt. extracts as high stability and good selectivity of a natural reagent. The proposed method was designed for online solution mixing and colorimetric detection on a microfluidic platform. The Curcuma putii Maknoi & Jenjitt. extracts and standard/samples were sequentially aspirated to fill the channel before entering the built-in flow cell. The intensity of iron-Curcuma putii Maknoi & Jenjitt. extract complex was monitored under the optimum conditions of flow rate, sample volume, mixing zone length, and aspiration sequences, by altering the gain control of the colorimetric detector to achieve good sensitivity. The results demonstrated a good performance of the green analytical systems. A linear calibration graph in the range of 0.5-6.0 mg L^-1 was obtained with a limit of detection at an adequate level of 0.11 mg L^-1 for water samples with a sample throughput of 30 h^-1. The precise and accurate measurement results were achieved with relative standard deviations in the range of 1.61-1.72%, and percent recoveries were found in the range of 90.6-113.4. The proposed method offers cost-effective, easy operation over an appropriate analysis time (2 min/injection) with good sensitivity and is environmentally friendly with low consumption of solutions and the use of high stability and good selectivity of nontoxic reagents. The achieved method was demonstrated to be a good choice for routine analysis.

Iron Availability and Homeostasis in Plants: A Review of Responses, Adaptive Mechanisms, and Signaling

Iron is an essential element for all living organisms, playing a major role in plant biochemistry as a redox catalyst based on iron redox properties. Iron is the fourth most abundant element of the Earth's crust, but its uptake by plants is complex because it is often in insoluble forms that are not easily accessible for plants to use. The physical and chemical speciation of iron, as well as rhizosphere activity, are key factors controlling the bioavailability of Fe. Iron can be under reduced (Fe²⁺) or oxidized (Fe³⁺) ionic forms, adsorbed onto mineral surfaces, forming complexes with organic molecules, precipitated to form poorly crystalline hydroxides to highly crystalline iron oxides, or included in crystalline Fe-rich mineral phases. Plants must thus adapt to a complex and changing iron environment, and their response is finely regulated by multiple signaling pathways initiated by a diversity of stimulus perceptions. Higher plants possess two separate strategies to uptake iron from rhizosphere soil: the chelation strategy and the reduction strategy in grass and non-grass plants, respectively. Molecular actors involved in iron uptake and mobilization through the plant have been characterized for both strategies. All these processes that contribute to iron homeostasis in plants are highly regulated in response to iron availability by downstream signaling responses, some of which are characteristic signaling signatures of iron dynamics, while others are shared with other environmental stimuli. Recent research has thus revealed key transcription factors, cis-acting elements, post-translational regulators, and other molecular mechanisms controlling these genes or their encoded proteins in response to iron availability. In addition, the most recent research is increasingly highlighting the crosstalk between iron homeostasis and nutrient response regulation. These regulatory processes help to avoid plant iron concentrations building up to potential cell functioning disruptions that could adversely affect plant fitness. Indeed, when iron is in excess in the plant, it can lead to the production and accumulation of dangerous reactive oxygen species and free radicals (H₂O₂, HO^•, O₂^•-, HO^•₂) that can cause considerable damages to most cellular components. To cope with iron oxidative stress, plants have developed defense systems involving the complementary action of antioxidant enzymes and molecular antioxidants, safe iron-storage mechanisms, and appropriate morphological adaptations.

Endophytic yeast protect plants against metal toxicity by inhibiting plant metal uptake through an ethylene-dependent mechanism

Toxic metal pollution requires significant adjustments in plant metabolism. Here, we show that the plant microbiota plays an important role in this process. The endophytic Sporobolomyces ruberrimus isolated from a serpentine population of Arabidopsis arenosa protected plants against excess metals. Coculture with its native host and Arabidopsis thaliana inhibited Fe and Ni uptake. It had no effect on host Zn and Cd uptake. Fe uptake inhibition was confirmed in wheat and rape. Our investigations show that, for the metal inhibitory effect, the interference of microorganisms in plant ethylene homeostasis is necessary. Application of an ethylene synthesis inhibitor, as well as loss-of-function mutations in canonical ethylene signalling genes, prevented metal uptake inhibition by the fungus. Coculture with S. ruberrimus significantly changed the expression of Fe homeostasis genes: IRT1, OPT3, OPT6, bHLH38 and bHLH39 in wild-type (WT) A. thaliana. The expression pattern of these genes in WT plants and in the ethylene signalling defective mutants significantly differed and coincided with the plant accumulation phenotype. Most notably, down-regulation of the expression of IRT1 solely in WT was necessary for the inhibition of metal uptake in plants. This study shows that microorganisms optimize plant Fe and Ni uptake by fine-tuning plant metal homeostasis.

The oxidative damage of the Lagerstroemia indica chlorosis mutant gl1 involves in ferroptosis

Photooxidation is the major physiological performance of the Lagerstroemia indica chlorosis mutant gl1 under field conditions. The mechanisms of the progressive symptoms of oxidative damage from the lower older leaves to the upper mature leaves are complicated and still unclear. The aim of this work was to investigate the physiological mechanisms of oxidative stress from the perspective of the photosynthetic metabolites. The phytosynthetic metabolites of gl1 mutant changed significantly compared to wild type (WT) L. indica, such as by increasing phenolics, decreasing soluble sugar, protein and ascorbate, and redistributing antioxidant enzyme activities. The co-accumulation of phenolics and guaiacol-POD in gl1 mutant promote the removal of H₂O₂, as well the increase of phenoxyl radicals levels. Furthermore, the ion balance was significantly disturbed and Fe accumulated the most among these fluctuating nutrients in the leaves of gl1 mutant. The accumulated Fe was found neither in the chloroplasts nor in the cell wall of the leaves and became unshielded Fe, which favors the Fenton/Haber-Weiss reaction and stabilizes the phenoxyl radicals in metal complexation. The results suggested that the increase of phenolics and Fe accumulation were obviously involved in oxidative damage of gl1 mutant.

Iron Induces Resistance Against the Rice Blast Fungus Magnaporthe oryzae Through Potentiation of Immune Responses

Iron is an essential nutrient required for plant growth and development. The availability of iron might also influence disease resistance in plants. However, the molecular mechanisms involved in the plant response to iron availability and immunity have been investigated separately from each other. In this work, we found that exposure of rice plants to high iron enhances resistance to infection by the fungal pathogen Magnaporthe oryzae, the causal agent of blast disease. RNA-Seq analysis revealed that blast resistance in iron-treated rice plants was associated with superinduction of defense-related genes during pathogen infection, including Pathogenesis-Related genes. The expression level of genes involved in the biosynthesis of phytoalexins, both diterpene phytoalexins and the flavonoid phytoalexin sakuranetin, was also higher in iron-treated plants compared with control plants, which correlated well with increased levels of phytoalexins in these plants during M. oryzae infection. Upon pathogen infection, lipid peroxidation was also higher in iron-treated plants compared with non-treated plants. We also show that M. oryzae infection modulates the expression of genes that play a pivotal role in the maintenance of iron homeostasis. Histochemical analysis of M. oryzae-infected leaves revealed colocalization of iron and reactive oxygen species in cells located in the vicinity of fungal penetration sites (e.g. appressoria) in rice plants that have been exposed to iron. Together these findings support that ferroptosis plays a role in the response of iron-treated rice plants to infection by virulent M. oryzae. Understanding interconnected regulations between iron signaling and immune signaling in rice holds great potential for developing novel strategies to improve blast resistance in rice.

Rice iron storage protein ferritin 2 (OsFER2) positively regulates ferroptotic cell death and defense responses against Magnaporthe oryzae

Ferritin is a ubiquitous iron storage protein that regulates iron homeostasis and oxidative stress in plants. Iron plays an important role in ferroptotic cell death response of rice (Oryza sativa) to Magnaporthe oryzae infection. Here, we report that rice ferritin 2, OsFER2, is required for iron- and reactive oxygen species (ROS)-dependent ferroptotic cell death and defense response against the avirulent M. oryzae INA168. The full-length ferritin OsFER2 and its transit peptide were localized to the chloroplast, the most Fe-rich organelle for photosynthesis. This suggests that the transit peptide acts as a signal peptide for the rice ferritin OsFER2 to move into chloroplasts. OsFER2 expression is involved in rice resistance to M. oryzae infection. OsFER2 knock-out in wild-type rice HY did not induce ROS and ferric ion (Fe³⁺) accumulation, lipid peroxidation and hypersensitive response (HR) cell death, and also downregulated the defense-related genes OsPAL1, OsPR1-b, OsRbohB, OsNADP-ME2-3, OsMEK2 and OsMPK1, and vacuolar membrane transporter OsVIT2 expression. OsFER2 complementation in ΔOsfer2 knock-out mutants restored ROS and iron accumulation and HR cell death phenotypes during infection. The iron chelator deferoxamine, the lipid-ROS scavenger ferrostatin-1, the actin microfilament polymerization inhibitor cytochalasin E and the redox inhibitor diphenyleneiodonium suppressed ROS and iron accumulation and HR cell death in rice leaf sheaths. However, the small-molecule inducer erastin did not trigger iron-dependent ROS accumulation and HR cell death induction in ΔOsfer2 mutants. These combined results suggest that OsFER2 expression positively regulates iron- and ROS-dependent ferroptotic cell death and defense response in rice-M. oryzae interactions.

Genetic Approaches for Iron and Zinc Biofortification and Arsenic Decrease in Oryza sativa L. Grains

Rice is the staple diet to half of the world's population, being a major source of carbohydrates, vitamins, and some essential elements. However, rice naturally contains low amounts of essential minerals such as iron (Fe) and zinc (Zn), which are drastically decreased after milling. Thus, populations that consume mostly rice may have micronutrient deficiency, which is associated with different diseases. On the other hand, rice irrigated by flooding has a high ability to accumulate arsenic (As) in the grain. Therefore, when rice is grown in areas with contaminated soil or irrigation water, it represents a risk factor for consumers, since As is associated with cancer and other diseases. Different strategies have been used to mitigate micronutrient deficiencies such as Fe and Zn and to prevent As from entering the food chain. Each strategy has its positive and its negative sides. The development of genetically biofortified rice plants with Fe and Zn and with low As accumulation is one of the most promising strategies, since it does not represent an additional cost for farmers, and gives benefits to consumers as well. Considering the importance of genetic improvement (traditional or molecular) to decrease the impact of micronutrient deficiencies such as Fe and Zn and contamination with As, this review aimed to summarize the major efforts, advances, and challenges for genetic biofortification of Fe and Zn and decrease in As content in rice grains.

The ferroxidases are critical for Fe(II) oxidation in xylem to ensure a healthy Fe allocation in Arabidopsis thaliana

The long-distance transport of iron (Fe) in the xylem is critical for maintaining systemic Fe homeostasis in plants. The loading form of Fe(II) into the xylem and the long-distance translocation form of Fe(III)-citrate have been identified, but how Fe(II) is oxidized to Fe(III) in the xylem remains unknown. Here, we showed that the cell wall-resided ferroxidases LPR1 and LPR2 (LPRs) were both specifically expressed in the vascular tissues of Arabidopsis thaliana, while disruption of both of them increased Fe(II) in the xylem sap and caused excessive Fe deposition in the xylem vessel wall under Fe-sufficient conditions. As a result, a large amount of Fe accumulated in both roots and shoots, hindering plant growth. Moreover, under low-Fe conditions, LPRs were preferentially induced in old leaves, but the loss of LPRs increased Fe deposition in the vasculature of older leaves and impeded Fe allocation to younger leaves. Therefore, disruption of both LPRs resulted in severer chlorosis in young leaves under Fe-deficient conditions. Taken together, the oxidation of Fe(II) to Fe(III) by LPRs in the cell wall of vasculature plays an important role in xylem Fe allocation, ensuring healthy Fe homeostasis for normal plant growth.

Physiological and proteomic dissection of the rice roots in response to iron deficiency and excess

Iron (Fe) disorder is a pivotal factor that limits rice yields in many parts of the world. Extensive research has been devoted to studying how rice molecularly copes with the stresses of Fe deficiency or excess. However, a comprehensive dissection of the whole Fe-responsive atlas at the protein level is still lacking. Here, different concentrations of Fe (0, 40, 350, and 500 μM) were supplied to rice to demonstrate its response differences to Fe deficiency and excess via physiological and proteomic analysis. Results showed that compared with the normal condition, the seedling growth and contents of Fe and manganese were significantly disturbed under either Fe stress. Proteomic analysis revealed that differentially accumulated proteins under Fe deficiency and Fe excess were commonly enriched in localization, carbon metabolism, biosynthesis of amino acids, and antioxidant system. Notably, proteins with abundance retuned by Fe starvation were individually associated with phenylpropanoid biosynthesis, cysteine and methionine metabolism, while ribosome- and endocytosis-related proteins were specifically enriched in treatment of Fe overdose of 500 μM. Moreover, several novel proteins which may play potential roles in rice Fe homeostasis were predicted. These findings expand the understanding of rice Fe nutrition mechanisms, and provide efficient guidance for genetic breeding work. SIGNIFICANCE: Both iron (Fe) deficiency and excess significantly inhibited the growth of rice seedlings. Fe deficiency and excess disturbed processes of localization and cellular oxidant detoxification, metabolisms of carbohydrates and amino acids in different ways. The Fe-deficiency and Fe-excess-responsive proteins identified by the proteome were somewhat different from the reported transcriptional profiles, providing complementary information to the transcriptomic data.

Expression levels of genes involved in metal homeostasis, physiological adaptation, and growth characteristics of rice (Oryza sativa L.) genotypes under Fe and/or Al toxicity

Acid sulphate soil contains high amounts of iron (Fe) and aluminum (Al), and their contamination has been reported as major problems, especially in rainfed and irrigated lowland paddy fields. Rice is sensitive to Fe and Al grown in acid soil (pH < 5.5), leading to growth inhibition and grain yield loss. The objective of this study was to evaluate Fe and/or Al uptake, translocation, physiological adaptation, metal toxicity, and growth inhibition in rice genotypes grown in acid soil. Fe and Al in the root tissues of all rice genotypes were enriched depending on the exogenous application of either Fe or Al in the soil solution, leading to root growth inhibition, especially in the KDML105 genotype. Expression level of OsYSL1 in KDML105 was increased in relation to metal uptake into root tissues, whereas OsVIT2 was downregulated, leading to Fe (50.3 mg g^-1 DW or 13.1 folds over the control) and Al (4.8 mg g^-1 DW or 2.2 folds over the control) translocation to leaf tissues. Consequently, leaf greenness (SPAD), net photosynthetic rate (P_n), stomatal conductance (g_s), and transpiration rate (E) in the leaf tissues of genotype KDML105 under Fe + Al toxicity significantly declined by 28.4%, 35.3%, 55.6%, and 51.6% over the control, respectively. In Azucena (AZU; Fe/Al tolerant), there was a rapid uptake of Fe and Al by OsYSL1 expression in the root tissues, but a limited secretion into vacuole organelles by OsVIT2, leading to a maintenance of low level of toxicity driven by an enhanced accumulation of glutathione together with downregulation of OsGR expression level. In addition, Fe and Al restrictions in the root tissues of genotype RD35 were evident; therefore, crop stress index (CSI) of Fe + Al-treated plants was the maximum, leading to an inhibition of g_s (53.6% over the control) and E (49.0% over the control). Consequently, free proline, total phenolic compounds, and ascorbic acid in the leaf tissues of rice under Fe + Al toxicity significantly increased by 3.2, 1.2, and 1.5 folds over the control, respectively, indicating their functions in non-enzymatic antioxidant defense. Moreover, physiological parameters including leaf temperature (T_leaf) increment, high level of CSI (>0.6), SPAD reduction, photon yield of PSII (Φ_PSII) diminution, P_n, g_s, and E inhibition in rice genotype IR64 (Fe/Al-sensitive) under Fe + Al treatment were clearly demonstrated as good indicators of metal-induced toxicity. Our results on Fe- and/or Al-tolerant screening to find out the candidate genotypes will contribute to present screening and breeding efforts, which in turn help increase rice production in the Fe/Al-contaminated acid soil under lowland conditions.

Zinc regulation of iron uptake and translocation in rice (Oryza sativa L.): Implication from stable iron isotopes and transporter genes

Iron (Fe) is an essential nutrient for living organisms and Fe deficiency is a worldwide problem for the health of both rice and humans. Zinc (Zn) contamination in agricultural soils is frequently observed. Here, we studied Fe isotope compositions and transcript levels of Fe transporter genes in rice growing in nutrient solutions having a range of Zn concentrations. Our results show Zn stress reduces Fe uptake by rice and drives its δ⁵⁶Fe value to that of the nutrient solution. These observations can be explained by the weakened Fe(II) uptake through Strategy I but enhanced Fe(III) uptake through Strategy II due to the competition between Zn and Fe(II) combining with OsIRT1 (Fe(II) transporter) in root, which is supported by the downregulated expression of OsIRT1 and upregulated expression of OsYSL15 (Fe(III) transporter). Using a mass balance box model, we also show excess Zn reduces Fe(II) translocation in phloem and its remobilization from senescent leaf, indicating a competition of binding sites on nicotianamine between Zn and Fe(II). This study provides direct evidence that how Zn regulates Fe uptake and translocation in rice and is of practical significance to design strategies to treat Fe deficiency in rice grown in Zn-contaminated soils.

Plant iron nutrition: the long road from soil to seeds

Iron (Fe) is an essential plant micronutrient since many cellular processes including photosynthesis, respiration, and the scavenging of reactive oxygen species depend on adequate Fe levels; however, non-complexed Fe ions can be dangerous for cells, as they can act as pro-oxidants. Hence, plants possess a complex homeostatic control system for safely taking up Fe from the soil and transporting it to its various cellular destinations, and for its subcellular compartmentalization. At the end of the plant's life cycle, maturing seeds are loaded with the required amount of Fe needed for germination and early seedling establishment. In this review, we discuss recent findings on how the microbiota in the rhizosphere influence and interact with the strategies adopted by plants to take up iron from the soil. We also focus on the process of seed-loading with Fe, and for crop species we also consider its associated metabolism in wild relatives. These two aspects of plant Fe nutrition may provide promising avenues for a better comprehension of the long pathway of Fe from soil to seeds.

Below-ground plant-soil interactions affecting adaptations of rice to iron toxicity

Iron toxicity is a major constraint to rice production, particularly in highly weathered soils of inland valleys in sub-Saharan Africa where the rice growing area is rapidly expanding. There is a wide variation in tolerance of iron toxicity in the rice germplasm. However, the introgression of tolerance traits into high-yielding germplasm has been slow owing to the complexity of the tolerance mechanisms and large genotype-by-environment effects. We review current understanding of tolerance mechanisms, particularly those involving below-ground plant-soil interactions. Until now these have been less studied than above-ground mechanisms. We cover processes in the rhizosphere linked to exclusion of toxic ferrous iron by oxidation, and resulting effects on the mobility of nutrient ions. We also cover the molecular physiology of below-ground processes controlling iron retention in roots and root-shoot transport, and also plant iron sensing. We conclude that future breeding programmes should be based on well-characterized molecular markers for iron toxicity tolerance traits. To successfully identify such markers, the complex tolerance response should be broken down into its components based on understanding of tolerance mechanisms, and tailored screening methods should be developed for individual mechanisms.

Transcriptomic Analysis Revealed Reactive Oxygen Species Scavenging Mechanisms Associated With Ferrous Iron Toxicity in Aromatic Keteki Joha Rice

Lowland acidic soils with water-logged regions are often affected by ferrous iron (Fe²⁺) toxicity, a major yield-limiting factor of rice production. Under severe Fe²⁺ toxicity, reactive oxygen species (ROS) are crucial, although molecular mechanisms and associated ROS homeostasis genes are still unknown. In this study, a comparative RNA-Seq based transcriptome analysis was conducted to understand the Fe²⁺ toxicity tolerance mechanism in aromatic Keteki Joha. About 69 Fe homeostasis related genes and their homologs were identified, where most of the genes were downregulated. Under severe Fe²⁺ toxicity, the biosynthesis of amino acids, RNA degradation, and glutathione metabolism were induced, whereas phenylpropanoid biosynthesis, photosynthesis, and fatty acid elongation were inhibited. The mitochondrial iron transporter (OsMIT), vacuolar iron transporter 2 (OsVIT2), ferritin (OsFER), vacuolar mugineic acid transporter (OsVMT), phenolic efflux zero1 (OsPEZ1), root meander curling (OsRMC), and nicotianamine synthase (OsNAS3) were upregulated in different tissues, suggesting the importance of Fe retention and sequestration for detoxification. However, several antioxidants, ROS scavenging genes and abiotic stress-responsive transcription factors indicate ROS homeostasis as one of the most important defense mechanisms under severe Fe²⁺ toxicity. Catalase (CAT), glutathione (GSH), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) were upregulated. Moreover, abiotic stress-responsive transcription factors, no apical meristem (NAC), myeloblastosis (MYB), auxin response factor (ARF), basic helix-loop-helix (bZIP), WRKY, and C2H2-zinc finger protein (C2H2-ZFP) were also upregulated. Accordingly, ROS homeostasis has been proposed as an essential defense mechanism under such conditions. Thus, the current study may enrich the understanding of Fe-homeostasis in rice.

Using an improved Si-rich husk ash to decrease inorganic arsenic in rice grain

Paddy rice is efficient at arsenite accumulation by sharing the uptake and transport pathway for silicic acid. To limit As entry into rice by increasing soil Si availability, rice husk with concentrated Si deposition was subject to an ethanol-aided open combustion in this work to promote Si release from organic matrix. Compared to original husk, the content of amorphous silica was almost tripled in the resultant ash (Si-ash) with an apparent elimination of hydrocarbon groups. Following its incorporation into soil, 3.4-fold higher Si dissolution was maintained in rice rhizosphere compared to control, which was accompanied by 15.9-40.5% decrease in porewater As from tillering to harvest. Correspondingly, As sequestration in soil solid phase and root plaque increased by 8.0% and 26.9% with Si-ash, which could result from promoted FeAs co-precipitation by the liming effect of Si-ash and was linked to a notable decline in As transport through node I. Consequently, inorganic As (iAs) in white rice decreased from 0.36 mg kg^-1 in control to 0.17 mg kg^-1 with Si-ash, which is 15% lower than Chinese food safety standard. Results from this study highlight the advantage of Si-ash in securing rice production by mitigating iAs accumulation in white rice with fortified Si nutrition.

Transcriptome Analysis Revealed the Molecular Response Mechanism of Non-heading Chinese Cabbage to Iron Deficiency Stress

Iron is a trace metal that is found in animals, plants, and the human body. Human iron absorption is hampered by plant iron shortage, which leads to anemia. Leafy vegetables are one of the most direct and efficient sources of iron for humans. Despite the fact that ferrotrophic disorder is common in calcareous soil, however, non-heading Chinese cabbage performs a series of reactions in response to iron deficiency stress that help to preserve iron homeostasis in vivo. In this study, we discovered that iron deficiency stress caused leaf yellowing and impeded plant development in both iron-deficient and control treatments by viewing or measuring phenotypic, chlorophyll content, and Fe²⁺ content in both iron-deficient and control treatments. We found a total of 9213 differentially expressed genes (DEGs) in non-heading Chinese cabbage by comparing root and leaf transcriptome data with iron deficiency and control treatments. For instance, 1927 DEGs co-expressed in root and leaf, including 897 up-regulated and 1030 down-regulated genes, respectively. We selected some key antioxidant genes, hormone signal transduction, iron absorption and transport, chlorophyll metabolism, and transcription factors involved in the regulation of iron deficiency stress utilizing GO enrichment, KEGG enrichment, multiple types of functional annotation, and Weighted Gene Co-expression Network Analysis (WGCNA). This study identifies prospective genes for maintaining iron homeostasis under iron-deficient stress, offering a theoretical foundation for further research into the molecular mechanisms of greater adaptation to iron-deficient stress, and perhaps guiding the development of iron-tolerant varieties.

Challenges and opportunities to regulate mineral transport in rice

Iron (Fe) is an essential mineral for plants, and its deficiency as well as toxicity severely affects plant growth and development. Although Fe is ubiquitous in mineral soils, its acquisition by plants is difficult to regulate particularly in acidic and alkaline soils. Under alkaline conditions, where lime is abundant, Fe and other mineral elements are sparingly soluble. In contrast, under low pH conditions, especially in paddy fields, Fe toxicity could occur. Fe uptake is complicated and could be integrated with copper (Cu), manganese (Mn), zinc (Zn), and cadmium (Cd) uptake. Plants have developed sophisticated mechanisms to regulate the Fe uptake from soil and its transport to root and above-ground parts. Here, we review recent developments in understanding metal transport and discuss strategies to effectively regulate metal transport in plants with a particular focus on rice.

Elucidation of Novel cis-Regulatory Elements and Promoter Structures Involved in Iron Excess Response Mechanisms in Rice Using a Bioinformatics Approach

Iron (Fe) excess is a major constraint on crop production in flooded acidic soils, particularly in rice cultivation. Under Fe excess, plants activate a complex mechanism and network regulating Fe exclusion by roots and isolation in various tissues. In rice, the transcription factors and cis-regulatory elements (CREs) that regulate Fe excess response mechanisms remain largely elusive. We previously reported comprehensive microarray analyses of several rice tissues in response to various levels of Fe excess stress. In this study, we further explored novel CREs and promoter structures in rice using bioinformatics approaches with this microarray data. We first performed network analyses to predict Fe excess-related CREs through the categorization of the gene expression patterns of Fe excess-responsive transcriptional regulons, and found four major expression clusters: Fe storage type, Fe chelator type, Fe uptake type, and WRKY and other co-expression type. Next, we explored CREs within these four clusters of gene expression types using a machine-learning method called microarray-associated motif analyzer (MAMA), which we previously established. Through a comprehensive bioinformatics approach, we identified a total of 560 CRE candidates extracted by MAMA analyses and 42 important conserved sequences of CREs directly related to the Fe excess response in various rice tissues. We explored several novel cis-elements as candidate Fe excess CREs including GCWGCWGC, CGACACGC, and Myb binding-like motifs. Based on the presence or absence of candidate CREs using MAMA and known PLACE CREs, we found that the Boruta-XGBoost model explained expression patterns with high accuracy of about 83%. Enriched sequences of both novel MAMA CREs and known PLACE CREs led to high accuracy expression patterns. We also found new roles of known CREs in the Fe excess response, including the DCEp2 motif, IDEF1-, Zinc Finger-, WRKY-, Myb-, AP2/ERF-, MADS- box-, bZIP and bHLH- binding sequence-containing motifs among Fe excess-responsive genes. In addition, we built a molecular model and promoter structures regulating Fe excess-responsive genes based on new finding CREs. Together, our findings about Fe excess-related CREs and conserved sequences will provide a comprehensive resource for discovery of genes and transcription factors involved in Fe excess-responsive pathways, clarification of the Fe excess response mechanism in rice, and future application of the promoter sequences to produce genotypes tolerant of Fe excess.

Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron

Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity (FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study (GWAS) was performed using genotyping by sequencing and six phenotypic data (leaf bronzing score (LBS), chlorophyll content, shoot height, root length, shoot biomass, and root dry weight) under both normal and FT conditions. LBS showed a high negative correlation with the ratio of chlorophyll content and shoot biomass, indicating the FT-tolerant accessions can regulate cellular homeostasis when encountering stress. Sixteen significant single nucleotide polymorphisms (SNPs) were identified by association mapping. Validation of candidate SNP using other FT-tolerant accessions revealed that SNP:2_21262165 might be associated with tolerance to FT; therefore, it could be used for SNP marker development. Among the candidate genes controlling FT tolerance, RAR1 encodes an innate immune responsive protein that links to cellular redox homeostasis via interacting with abiotic stress-responsive Hsp90. Future research may apply the knowledge obtained from this study in the molecular breeding program to develop FT-tolerant rice varieties.

γ-Aminobutyric Acid Suppresses Iron Transportation from Roots to Shoots in Rice Seedlings by Inducing Aerenchyma Formation

γ-Aminobutyric acid (GABA) is a widely distributed non-protein amino acid mediated the regulation of nitrate uptake and Al³⁺ tolerance in plants. However, there are few reports about the involvement of GABA in the regulation of iron (Fe) acquisition and translocation. Here, we show that GABA regulates Fe homeostasis in rice seedlings. Exogenous GABA decreased the chlorophyll concentration in leaves, with or without Fe supply. Over-expression of glutamate decarboxylase (GAD) gene, coding a crucial enzyme of GABA production, elevated endogenous GABA content and caused more leaf chlorosis than wild type (Nipponbare). GABA inhibited Fe transportation from roots to shoots and GABA application elevated the expression levels of Fe deficiency (FD)-related genes under conditions of Fe-sufficiency (FS), suggesting that GABA is a regulator of Fe translocation. Using Perls’ blue staining, we found that more ferric iron (Fe³⁺) was deposited in the epidermal cells of roots treated with GABA compared with control roots. Anatomic section analysis showed that GABA treatment induced more aerenchyma formation compared with the control. Aerenchyma facilitated the oxidization of soluble ferrous iron (Fe²⁺) into insoluble Fe³⁺, resulted in Fe precipitation in the epidermis, and inhibited the transportation of Fe from roots to shoots.