The Molecular Mechanisms Underlying Iron Deficiency Responses in Rice

Transcriptome Analysis Reveals the Molecular Mechanisms of Carrot Adaptation to Alternaria Leaf Blight

Carrot (Daucus carota L.) is an important vegetable crop that is rich in carotenoids and is widely cultivated throughout the world. Alternaria leaf blight (ALB), caused by infection with Alternaria dauci (A. dauci), is the most serious fungal disease in carrot production. Although several quantitative trait loci associated with ALB resistance have been identified, the genetic mechanisms underlying this resistance remain largely unelucidated. The aim of the present study was to clarify the infection mode of A. dauci and examine the molecular mechanisms underlying carrot cultivar adaptation to ALB by RNA sequencing. Microscopic observation revealed that A. dauci invades leaf tissues by entering through stomata, and resistant germplasms may significantly inhibit the infection and colonization of A. dauci. In addition, transcriptomic analyses were performed to detect the key pathways and genes associated with the differential responses between ALB-resistant (HB55) and ALB-susceptible (14088) carrot cultivars. These results suggest that the secondary metabolic process, phenylpropanoid biosynthesis, and tyrosine metabolism might play important roles in the resistance of carrots to A. dauci. Three candidate genes (LOC108208301, LOC108215577, and LOC108224339) that were specifically upregulated in the resistant carrot cultivar 'HB55' after A. dauci infection were identified as the key resistance response genes. These findings provide insights into the resistance mechanism of carrots to ALB, as well as key candidate genes and information on expression regulation for the molecular breeding of carrot disease resistance.

Sufficient manganese supply is necessary for OsNramp5 knockout rice plants to ensure normal growth and less Cd uptake

The development of crop cultivars with less Cd uptake in roots and accumulation in shoots is a most efficient and environment-friendly approach to deal with soil Cd contamination. Recently repression of Nramp5 expression or its knockout is commonly recognized to be efficient for reducing Cd accumulation in plants, but such mutant plants suffer from manganese deficiency. In this study, we assessed the efficacy of exogenous Mn addition in mitigating Cd stress in a japonica rice cultivar Xidao 1 (Wild Type, WT) and its OsNramp5 knockout mutant. Exposure to Cd stress resulted in notable low photosynthetic rate, growth inhibition, and high Cd accumulation in rice seedlings. Although the mutant plants contained much lower Cd concentration in both roots and shoots than the WT plants, their growth was significantly inhibited relative to the WT plants under the normal condition. Exogenous application of Mn (40 μM) dramatically reduces root and shoot Cd concentrations and alleviates the toxic effect of Cd stress in both rice types, with the mutant plants demonstrating lower Cd concentration and less Cd toxicity in comparison with WT plants. The alleviation of Cd toxicity by Mn addition was more effective in higher Cd level (1.0 μM) than in lower Cd level (0.1 μM). Mn increases the expression of OsNramp5 and other genes, including OsHMA2, OsHMA3, OsIRT1, and OsIRT2, which encode ion transporters related to Mn uptake and transportation, and meanwhile reduces Cd uptake and accumulation in rice seedlings. In short, the knockout of OsNramp5 results in the significant reduction of Cd uptake, but accompanies with Mn deficiency in rice plants, which can be efficiently overcome through exogenous Mn addition.

DcMYB62, a transcription factor from carrot, enhanced cadmium tolerance of Arabidopsis by inducing the accumulation of carotenoids and hydrogen sulfide

Cadmium (Cd) is a significant heavy metal contaminant within the environment, carrying a notable level of toxicity that presents a substantial hazard to both plant and human. Carrot (Daucus carota), a significant root vegetable crop globally, have evolved multiple transcriptional regulatory mechanisms to cope with Cd stress, with a crucial involvement of the myeloblastosis (MYB) transcription factor. In this study, the DcMYB62 gene encoding 288 amino acids, localized in the nucleus and demonstrated transcription activation property, was isolated from carrot (cv. 'Kuroda'). There was a positive relationship observed between the levels of DcMYB62 expression and the accumulation patterns of carotenoids in two distinct carrot cultivars. Further investigation revealed that the expression of DcMYB62 improved Cd tolerance of Arabidopsis by increasing seed germination rate, root length, and overall survival rate. The levels of carotenoids in DcMYB62 transgenic Arabidopsis surpassed those in wild type, accompanied by elevated expression levels of 15-cis-phytoene desaturase, zeta-carotene desaturase, and carotenoid isomerase. Meanwhile, the heterologous expression of DcMYB62 promoted the biosynthesis of abscisic acid (ABA) and hydrogen sulfide (H2S), which in turn suppressed the formation of hydrogen peroxide and superoxide anion, while also stimulating stomatal closure. Furthermore, the heterologous expression of DcMYB62 increased the transcription of genes associated with heavy metal resistance in Arabidopsis, notably nicotianamine synthase. Overall, this study contributes to understanding how DcMYB62 promote Cd stress resistance of plants by regulating the biosynthesis pathways of carotenoids, ABA, and H2S, which offers valuable insights into the regulatory mechanism connecting DcMYBs with Cd stress response of carrot.

An integration of genome-wide survey, homologous comparison and gene expression analysis provides a basic framework for the ZRT, IRT-like protein (ZIP) in foxtail millet

Essential mineral elements such as zinc and iron play a crucial role in maintaining crop growth and development, as well as ensuring human health. Foxtail millet is an ancient food crop rich in mineral elements and constitutes an important dietary supplement for nutrient-deficient populations. The ZIP (ZRT, IRT-like protein) transporters are primarily responsible for the absorption, transportation and accumulation of Zn, Fe and other metal ions in plants. Here, we identified 14 ZIP transporters in foxtail millet (SiZIP) and systematically characterized their phylogenetic relationships, expression characteristics, sequence variations, and responses to various abiotic stresses. As a result, SiZIPs display rich spatiotemporal expression characteristics in foxtail millet. Multiple SiZIPs demonstrated significant responses to Fe, Cd, Na, and K metal ions, as well as drought and cold stresses. Based on homologous comparisons, expression characteristics and previous studies, the functions of SiZIPs were predicted as being classified into several categories: absorption/efflux, transport/distribution and accumulation of metal ions. Simultaneously, a schematic diagram of SiZIP was drawn. In general, SiZIPs have diverse functions and extensively involve in the transport of metal ions and osmotic regulation under abiotic stresses. This work provides a fundamental framework for the transport and accumulation of mineral elements and will facilitate the quality improvement of foxtail millet.

Iron transporter1 OsIRT1 positively regulates saline-alkaline stress tolerance in Oryza sativa

Soil salinization-alkalization severely affects plant growth and crop yield worldwide, especially in the Songnen Plain of Northeast China. Saline-alkaline stress increases the pH around the plant roots, thereby limiting the absorption and transportation of nutrients and ions, such as iron (Fe). Fe is an essential micronutrient that plays important roles in many metabolic processes during plant growth and development, and it is acquired by the root cells via iron-regulated transporter1 (IRT1). However, the function of Oryza sativa IRT1 (OsIRT1) under soda saline-alkaline stress remains unknown. Therefore, in this study, we generated OsIRT1 mutant lines and OsIRT1-overexpressing lines in the background of the O. sativa Songjing2 cultivar to investigate the roles of OsIRT1 under soda saline-alkaline stress. The OsIRT1-overexpressing lines exhibited higher tolerance to saline-alkaline stress compared to the mutant lines during germination and seedling stages. Moreover, the expression of some saline-alkaline stress-related genes and Fe uptake and transport-related genes were altered. Furthermore, Fe and Zn contents were upregulated in the OsIRT1-overexpressing lines under saline-alkaline stress. Further analysis revealed that Fe and Zn supplementation increased the tolerance of O. sativa seedlings to saline-alkaline stress. Altogether, our results indicate that OsIRT1 plays a significant role in O. sativa by repairing the saline-alkaline stress-induced damage. Our findings provide novel insights into the role of OsIRT1 in O. sativa under soda saline-alkaline stress and suggest that OsIRT1 can serve as a potential target gene for the development of saline-alkaline stress-tolerant O. sativa plants.

Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis

Vascular plants have evolved intricate long-distance signaling mechanisms to cope with environmental stress, with reactive oxygen species (ROS) emerging as pivotal systemic signals in plant stress responses. However, the exact role of ROS as root-to-shoot signals in the drought response has not been determined. In this study, we reveal that compared with wild-type plants, ferric reductase defective 3 (frd3) mutants exhibit enhanced drought resistance concomitant with elevated NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) transcript levels and abscisic acid (ABA) contents in leaves as well as increased hydrogen peroxide (H2O2) levels in roots and leaves. Grafting experiments distinctly illustrate that drought resistance can be conferred by the frd3 rootstock regardless of the scion genotype, indicating that long-distance signals originating from frd3 roots promote an increase in ABA levels in leaves. Intriguingly, the drought resistance conferred by the frd3 mutant rootstock is weakened by the CAT2-overexpressing scion, suggesting that H2O2 may be involved in long-distance signaling. Moreover, the results of comparative transcriptome and proteome analyses support the drought resistance phenotype of the frd3 mutant. Taken together, our findings substantiate the notion that frd3 root-derived long-distance signals trigger ABA synthesis in leaves and enhance drought resistance, providing new evidence for root-to-shoot long-distance signaling in the drought response of plants.

OsUGE2 Regulates Plant Growth through Affecting ROS Homeostasis and Iron Level in Rice

BACKGROUND

The growth and development of rice (Oryza sativa L.) are affected by multiple factors, such as ROS homeostasis and utilization of iron. Here, we demonstrate that OsUGE2, a gene encoding a UDP-glucose 4-epimerase, controls growth and development by regulating reactive oxygen species (ROS) and iron (Fe) level in rice. Knockout of this gene resulted in impaired growth, such as dwarf phenotype, weakened root growth and pale yellow leaves. Biochemical analysis showed that loss of function of OsUGE2 significantly altered the proportion and content of UDP-Glucose (UDP-Glc) and UDP-Galactose (UDP-Gal). Cellular observation indicates that the impaired growth may result from decreased cell length. More importantly, RNA-sequencing analysis showed that knockout of OsUGE2 significantly influenced the expression of genes related to oxidoreductase process and iron ion homeostasis. Consistently, the content of ROS and Fe are significantly decreased in OsUGE2 knockout mutant. Furthermore, knockout mutants of OsUGE2 are insensitive to both Fe deficiency and hydrogen peroxide (H2O2) treatment, which further confirmed that OsUGE2 control rice growth possibly through Fe and H2O2 signal. Collectively, these results reveal a new pathway that OsUGE2 could affect growth and development via influencing ROS homeostasis and Fe level in rice.

Meta-analysis of transcriptomics studies identifies novel attributes and set of genes involved in iron homeostasis in rice

Iron (Fe) is an important micronutrient for humans as well as for plant growth and development. Rice employs multiple mechanisms to counteract the negative effects of Fe deficiency and Fe toxicity. Previously, many transcriptomics studies have identified hundreds of genes affected by Fe deficiency and/or Fe toxicity. These studies are highly valuable to identify novel genes involved in Fe homeostasis. However, in the absence of their systematic integration, they remain underutilized. A systematic meta-analysis of transcriptomics data from such ten previous studies was performed here to identify various common attributes. From this meta-analysis, it is revealed that under Fe deficiency conditions, root transcriptome is more sensitive and exhibits greater similarity across multiple studies than the shoot transcriptome. Furthermore, under Fe toxicity conditions, upregulated genes are more reliable and consistent than downregulated genes in susceptible cultivars. The integration of data from Fe deficiency and Fe toxicity conditions helped to identify key marker genes for Fe stress. As a proof-of-concept of the analysis, among the genes consistently regulated in opposite directions under Fe deficiency and toxicity conditions, two genes were selected: a proton-dependent oligopeptide transporter (POT) family protein and Vacuolar Iron Transporter (VIT)-Like (VTL) gene, and validated their expression and sub-cellular localization. Since VIT genes are known to play an important role in Fe homeostasis in plants, the entire OsVTL gene family in rice was characterized. This meta-analysis has identified many novel candidate genes that exhibit consistent expression patterns across multiple tissues, conditions, and studies. This makes them potential targets for future research aimed at developing Fe-biofortified rice varieties, as well as varieties tolerant to sub-optimal Fe levels in soil.

Research progress on iron absorption, transport, and molecular regulation strategy in plants

Iron is a trace element essential for normal plant life activities and is involved in various metabolic pathways such as chlorophyll synthesis, photosynthesis, and respiration. Although iron is highly abundant in the earth's crust, the amount that can be absorbed and utilized by plants is very low. Therefore, plants have developed a series of systems for absorption, transport, and utilization in the course of long-term evolution. This review focuses on the findings of current studies of the Fe²⁺ absorption mechanism I, Fe³⁺ chelate absorption mechanism II and plant-microbial interaction iron absorption mechanism, particularly effective measures for artificially regulating plant iron absorption and transportation to promote plant growth and development. According to the available literature, the beneficial effects of using microbial fertilizers as iron fertilizers are promising but further evidence of the interaction mechanism between microorganisms and plants is required.

Evidence That PbrSAUR72 Contributes to Iron Deficiency Tolerance in Pears by Facilitating Iron Absorption

Iron is an essential trace element for plants; however, low bioactive Fe in soil continuously places plants in an Fe-deficient environment, triggering oxidative damage. To cope with this, plants make a series of alterations to increase Fe acquisition; however, this regulatory network needs further investigation. In this study, we found notably decreased indoleacetic acid (IAA) content in chlorotic pear (Pyrus bretschneideri Rehd.) leaves caused by Fe deficiency. Furthermore, IAA treatment slightly induced regreening by increasing chlorophyll synthesis and Fe²⁺ accumulation. At that point, we identified PbrSAUR72 as a key negative effector output of auxin signaling and established its close relationship to Fe deficiency. Furthermore, the transient PbrSAUR72 overexpression could form regreening spots with increased IAA and Fe²⁺ content in chlorotic pear leaves, whereas its transient silencing does the opposite in normal pear leaves. In addition, cytoplasm-localized PbrSAUR72 exhibits root expression preferences and displays high homology to AtSAUR40/72. This promotes salt tolerance in plants, indicating a putative role for PbrSAUR72 in abiotic stress responses. Indeed, transgenic plants of Solanum lycopersicum and Arabidopsis thaliana overexpressing PbrSAUR72 displayed less sensitivity to Fe deficiency, accompanied by substantially elevated expression of Fe-induced genes, such as FER/FIT, HA, and bHLH39/100. These result in higher ferric chelate reductase and root pH acidification activities, thereby hastening Fe absorption in transgenic plants under an Fe-deficient condition. Moreover, the ectopic overexpression of PbrSAUR72 inhibited reactive oxygen species production in response to Fe deficiency. These findings contribute to a new understanding of PbrSAURs and its involvement in Fe deficiency, providing new insights for the further study of the regulatory mechanisms underlying the Fe deficiency response.

A molecular study of Italian ryegrass grown on Martian regolith simulant

In the last decade, the exploration of deep space has become the objective of the national space programs of many countries. The International Space Exploration Coordination Group has set a roadmap whose long-range strategy envisions the expansion of human presence in the solar system to progress with exploration and knowledge and to accelerate innovation. Crewed missions to Mars could be envisaged by 2040. In this scenario, finding ways to use the local resources for the provision of food, construction materials, propellants, pharmaceuticals is needed. Plants are important resources for deep space manned missions because they produce phytochemicals of pharmaceutical relevance, are sources of food and provide oxygen which is crucial in bioregenerative life support systems. Growth analysis and plant biomass yield have been previously evaluated on Martian regolith simulants; however, molecular approaches employing gene expression analysis and proteomics are still missing. The present work aims at filling this gap by providing molecular data on a representative member of the Poaceae, Lolium multiflorum Lam., grown on potting soil and a Martian regolith simulant (MMS-1). The molecular data were complemented with optical microscopy of root/leaf tissues and physico-chemical analyses. The results show that the plants grew for 2 weeks on regolith simulants. The leaves were bent downwards and chlorotic, the roots developed a lacunar aerenchyma and small brownish deposits containing Fe were observed. Gene expression analysis and proteomics revealed changes in transcripts related to the phenylpropanoid pathway, stress response, primary metabolism and proteins involved in translation and DNA methylation. Additionally, the growth of plants slightly but significantly modified the pH of the regolith simulants. The results here presented constitute a useful resource to get a comprehensive understanding of the major factors impacting the growth of plants on MMS-1.

The bHLH Transcription Factor OsbHLH057 Regulates Iron Homeostasis in Rice

Many basic Helix-Loop-Helix (bHLH) transcription factors precisely regulate the expression of Fe uptake and translocation genes to control iron (Fe) homeostasis, as both Fe deficiency and toxicity impair plant growth and development. In rice, three clade IVc bHLH transcription factors have been characterised as positively regulating Fe-deficiency response genes. However, the function of OsbHLH057, another clade IVc bHLH transcription factor, in regulating Fe homeostasis is unknown. Here, we report that OsbHLH057 is involved in regulating Fe homeostasis in rice. OsbHLH057 was highly expressed in the leaf blades and lowly expressed in the roots; it was mainly expressed in the stele and highly expressed in the lateral roots. In addition, OsbHLH057 was slightly induced by Fe deficiency in the shoots on the first day but was not affected by Fe availability in the roots. OsbHLH057 localised in the nucleus exhibited transcriptional activation activity. Under Fe-sufficient conditions, OsbHLH057 knockout or overexpression lines increased or decreased the shoot Fe concentration and the expression of several Fe homeostasis-related genes, respectively. Under Fe-deficient conditions, plants with an OsbHLH057 mutation showed susceptibility to Fe deficiency and accumulated lower Fe concentrations in the shoot compared with the wild type. Unexpectedly, the OsbHLH057-overexpressing lines had reduced tolerance to Fe deficiency. These results indicate that OsbHLH057 plays a positive role in regulating Fe homeostasis, at least under Fe-sufficient conditions.

Mechanistic assessment of tolerance to iron deficiency mediated by Trichoderma harzianum in soybean roots

AIMS

Iron (Fe) deficiency in soil is a continuing problem for soybean (Glycine max L.) production, partly as a result of continuing climate change. This study elucidates how Trichoderma harzianum strain T22 (TH) mitigates growth retardation associated with Fe-deficiency in a highly sensitive soybean cultivar.

METHODS AND RESULTS

Soil TH supplementation led to mycelial colonization and the presence of UAOX1 gene in roots that caused substantial improvement in chlorophyll score, photosynthetic efficiency and morphological parameters, indicating a positive influence on soybean health. Although rhizosphere acidification was found to be a common feature of Fe-deficient soybean, the upregulation of Fe-reductase activity (GmFRO2) and total phenol secretion were two of the mechanisms that substantially increased the Fe availability by TH. Heat-killed TH applied to soil caused no improvement in photosynthetic attributes and Fe-reductase activity, confirming the active role of TH in mitigating Fe-deficiency. Consistent increases in tissue Fe content and increased Fe-transporter (GmIRT1, GmNRAMP2a, GmNRAMP2b and GmNRAMP7) mRNA levels in roots following TH supplementation were observed only under Fe-deprivation. Root cell death, electrolyte leakage, superoxide (O2 •- ) and hydrogen peroxide (H2 O2 ) substantially declined due to TH in Fe-deprived plants. Further, the elevation of citrate and malate concentration along with the expression of citrate synthase (GmCs) and malate synthase (GmMs) caused by TH suggest improved chelation of Fe in Fe-deficient plants. Results also suggest that TH has a role in triggering antioxidant defence by increasing the activity of glutathione reductase (GR) along with elevated S-metabolites (glutathione and methionine) to stabilize redox status under Fe-deficiency.

CONCLUSIONS

TH increases the availability and mobilization of Fe by inducing Fe-uptake pathways, which appears to help provide resistance to oxidative stress associated with Fe-shortage in soybean.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings indicate that while Fe deficiency does not affect the rate or degree of TH hyphal association in soybean roots, the beneficial effects of TH alone may be Fe deficiency-dependent.

Phosphite treatment can improve root biomass and nutrition use efficiency in wheat

Phosphite represents a reduced form of phosphate that belongs to a class of crop growth-promoting chemicals termed biostimulants. Previous research has shown that phosphite application can enhance root growth, but its underlying mechanism, especially during environmental stresses, remains elusive. To uncover this, we undertook a series of morphological and physiological analyses under nutrient, water and heat stresses following a foliar application in wheat. Non-invasive 3D imaging of root system architecture directly in soil using X-ray Computed Tomography revealed that phosphite treatment improves root architectural traits and increased root biomass. Biochemical and physiological assays identified that phosphite treatment significantly increases Nitrate Reductase (NR) activity, leaf photosynthesis and stomatal conductance, suggesting improved Nitrogen and Carbon assimilation, respectively. These differences were more pronounced under heat or drought treatment (photosynthesis and photosystem II stability) and nutrient deficiency (root traits and NR). Overall our results suggest that phosphite treatment improves the ability of plants to tolerate abiotic stresses through improved Nitrogen and Carbon assimilation, combined with improved root growth which may improve biomass and yield.

Proteomic and Genomic Studies of Micronutrient Deficiency and Toxicity in Plants

Micronutrients are essential for plants. Their growth, productivity and reproduction are directly influenced by the supply of micronutrients. Currently, there are eight trace elements considered to be essential for higher plants: Fe, Zn, Mn, Cu, Ni, B, Mo, and Cl. Possibly, other essential elements could be discovered because of recent advances in nutrient solution culture techniques and in the commercial availability of highly sensitive analytical instrumentation for elemental analysis. Much remains to be learned about the physiology of micronutrient absorption, translocation and deposition in plants, and about the functions they perform in plant growth and development. With the recent advancements in the proteomic and molecular biology tools, researchers have attempted to explore and address some of these questions. In this review, we summarize the current knowledge of micronutrients in plants and the proteomic/genomic approaches used to study plant nutrient deficiency and toxicity.

Effect of different concentrations of foliar iron fertilizer on chlorophyll fluorescence characteristics of iron-deficient rice seedlings under saline sodic conditions

The effectiveness of iron is reduced in saline conditions, which can easily lead to iron deficiency and inhibit photosynthesis in rice. In this study, 4-week-old Fe-deficient rice seedlings were treated under saline sodic stress (50 mM) to different concentrations (0, 0.2%, 0.4%, 0.8%, 1.6%, and 3.2%) of foliar iron fertilizer (FeEDDHA). Differences in prompting fluorescence and the MR₈₂₀ signal of rice leaves after 7 days of treatment were probed using the JIP-test. The results show that the performances of the two rice varieties were in general agreement. Under iron deficiency and soda salinity stress conditions, rice growth was inhibited, and the pigment content, specific energy flux, quantum yield, performance of the active PSII reaction center (PI_ABS) and the oxidation (V_ox) and reduction rates (V_red) of PSI were reduced. These indicators first increase and then decrease with increasing iron fertiliser concentrations. The best results were obtained with the Fe3 treatment (0.8%). Fluorescence parameters such as the relative variable fluorescence (W_K and V_J) and the quantum yield of energy dissipation (φ_Do) showed opposite trends. This suggests that iron deficiency/excess and soda saline stress disrupt the electron and energy transport in the photosystem. Appropriate iron fertilization concentration can repair the photosynthetic electron transport chain, improve electron transport efficiency and promote balanced energy distribution. Therefore, we suggest that moderate amounts of Fe are beneficial for improving the electron and energy transport properties of the photosystem, while spraying high concentrations of Fe fertilizer has a negative effect on improving salt tolerance in rice.

An insight into the act of iron to impede arsenic toxicity in paddy agro-system

Surplus research on the widespread arsenic (As) revealed its disturbing role in obstructing the metabolic function of plants. Also, the predilection of As towards rice has been an interesting topic. Contrary to As, iron (Fe) is an essential micronutrient for all life forms. Past findings propound about the enhanced As-resistance in rice plants during Fe supplementation. Thus, considering the severity of As contamination and resulting exposure through rice crops, as well as the studied cross-talks between As and Fe, we found this topic of relevance. Keeping these in view, we bring this review discussing the presence of As-Fe in the paddy environment, the criticality of Fe plaque in As sequestration, and the effectiveness of various Fe forms to overcome As toxicity in rice. This type of interactive analysis for As and Fe is also crucial in the context of the involvement of Fe in cellular redox activities such as oxidative stress. Also, this piece of work highlights Fe biofortification approaches for better rice varieties with optimum intrinsic Fe and limited As. Though elaborated by others, we lastly present the acquisition and transport mechanisms of both As and Fe in rice tissues. Altogether we suggest that Fe supply and Fe plaque might be a prospective agronomical tool against As poisoning and for phytostabilization, respectively.

Genome-Wide Association Analysis Reveals the Genetic Basis of Iron-Deficiency Stress Tolerance in Maize

Iron (Fe) is an essential trace element for almost all organisms and is often the major limiting nutrient for normal growth. Fe deficiency is a worldwide agricultural problem, which affects crop productivity and product quality. Understanding the Fe-deficiency response in plants is necessary for improving both plant health and the human diet. In this study, Fe-efficient (Ye478) and Fe-inefficient maize inbred lines (Wu312) were used to identify the genotypic difference in response to low Fe stress during different developmental stages and to further determine the optimal Fe-deficient Fe(II) supply level which leads to the largest phenotypic difference between Ye478 and Wu312. Then, genome-wide association analysis was performed to further identify candidate genes associated with the molecular mechanisms under different Fe nutritional statuses. Three candidate genes involved in Fe homeostasis of strategy II plants (strategy II genes) were identified, including ZmDMAS1, ZmNAAT1, and ZmYSL11. Furthermore, candidate genes ZmNAAT1, ZmDMAS1, and ZmYSL11 were induced in Fe-deficient roots and shoots, and the expression of ZmNAAT1 and ZmDMAS1 responded to Fe deficiency more in shoots than in roots. Beyond that, several genes that may participate in Fe homeostasis of strategy I plants (strategy I genes) were identified, which were either encoding Fe transporters (ZmIRT1 and ZmZIP4), or acting as essential ethylene signal transducers (ZmEBF1). Interestingly, ZmIRT1, ZmZIP4, and ZmEBF1 were significantly upregulated under low Fe stress, suggesting that these genes may be involved in Fe-deficiency tolerance in maize which is considered as strategy II plant. This study demonstrates the use of natural variation in the association population to identify important genes associated with Fe-deficiency tolerance and may further provide insights for understanding the molecular mechanism underlying the tolerance to Fe-deficiency stress in maize.

A Glucuronic Acid-Producing Endophyte Pseudomonas sp. MCS15 Reduces Cadmium Uptake in Rice by Inhibition of Ethylene Biosynthesis

Dynamic regulation of phytohormone levels is pivotal for plant adaptation to harmful conditions. It is increasingly evidenced that endophytic bacteria can regulate plant hormone levels to help their hosts counteract adverse effects imposed by abiotic and biotic stresses, but the mechanisms underlying the endophyte-induced stress resistance of plants remain largely elusive. In this study, a glucuronic acid-producing endophyte Pseudomonas sp. MCS15 alleviated cadmium (Cd) toxicity in rice plants. Inoculation with MCS15 significantly inhibited the expression of ethylene biosynthetic genes including OsACO3, OsACO4, OsACO5, OsACS2, and OsACS5 and thus reduced the content of ethylene in rice roots. In addition, the expression of iron uptake-related genes including OsIRT1, OsIRT2, OsNAS1, OsNAS2 and OsYSL15 was significantly downregulated in the MCS15-inoculated roots under Cd stress. Similarly, glucuronic acid treatment also remarkably inhibited root uptake of Cd and reduced the production of ethylene. However, treatment with 1-aminocyclopropyl carboxylic acid (ACC), a precursor of ethylene, almost abolished the MCS15 or glucuronic acid-induced inhibition of Cd accumulation in rice plants. Conversely, treatment with aminoethoxyvinyl glycine (AVG), an inhibitor of ethylene biosynthesis, markedly reduced the Cd accumulation in plants. Taken together, our results revealed that the endophytic bacteria MCS15-secreted glucuronic acid inhibited the biosynthesis of ethylene and thus weakened iron uptake-related systems in rice roots, which contributed to preventing the Cd accumulation.

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.

Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress

Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Mapping of the Quantitative Trait Loci and Candidate Genes Associated With Iron Efficiency in Maize

Iron (Fe) is a mineral micronutrient for plants, and Fe deficiency is a major abiotic stress in crop production because of its low solubility under aerobic and alkaline conditions. In this study, 18 maize inbred lines were used to preliminarily illustrate the physiological mechanism underlying Fe deficiency tolerance. Then biparental linkage analysis was performed to identify the quantitative trait loci (QTLs) and candidate genes associated with Fe deficiency tolerance using the recombinant inbred line (RIL) population derived from the most Fe-efficient (Ye478) and Fe-inefficient (Wu312) inbred lines. A total of 24 QTLs was identified under different Fe nutritional status in the Ye478 × Wu312 RIL population, explaining 6.1-26.6% of phenotypic variation, and ten candidate genes were identified. Plants have evolved two distinct mechanisms to solubilize and transport Fe to acclimate to Fe deficiency, including reduction-based strategy (strategy I) and chelation-based strategy (strategy II), and maize uses strategy II. However, not only genes involved in Fe homeostasis verified in strategy II plants (strategy II genes), which included ZmYS1, ZmYS3, and ZmTOM2, but also several genes associated with Fe homeostasis in strategy I plants (strategy I genes) were identified, including ZmFIT, ZmPYE, ZmILR3, ZmBTS, and ZmEIN2. Furthermore, strategy II gene ZmYS1 and strategy I gene ZmBTS were significantly upregulated in the Fe-deficient roots and shoots of maize inbred lines, and responded to Fe deficiency more in shoots than in roots. Under Fe deficiency, greater upregulations of ZmYS1 and ZmBTS were observed in Fe-efficient parent Ye478, not in Fe-inefficient parent Wu312. Beyond that, ZmEIN2 and ZmILR3, were found to be Fe deficiency-inducible in the shoots. These findings indicate that these candidate genes may be associated with Fe deficiency tolerance in maize. This study demonstrates the use of natural variation to identify important Fe deficiency-regulated genes and provides further insights for understanding the response to Fe deficiency stress in maize.

Genome-Wide Identification of Wheat ZIP Gene Family and Functional Characterization of the TaZIP13-B in Plants

The ZIP (Zn-regulated, iron-regulated transporter-like protein) transporter plays an important role in regulating the uptake, transport, and accumulation of microelements in plants. Although some studies have identified ZIP genes in wheat, the significance of this family is not well understood, particularly its involvement under Fe and Zn stresses. In this study, we comprehensively characterized the wheat ZIP family at the genomic level and performed functional verification of three TaZIP genes by yeast complementary analysis and of TaZIP13-B by transgenic Arabidopsis. Totally, 58 TaZIP genes were identified based on the genome-wide search against the latest wheat reference (IWGSC_V1.1). They were then classified into three groups, based on phylogenetic analysis, and the members within the same group shared the similar exon-intron structures and conserved motif compositions. Expression pattern analysis revealed that the most of TaZIP genes were highly expressed in the roots, and nine TaZIP genes displayed high expression at grain filling stage. When exposed to ZnSO₄ and FeCl₃ solutions, the TaZIP genes showed differential expression patterns. Additionally, six ZIP genes responded to zinc-iron deficiency. A total of 57 miRNA-TaZIP interactions were constructed based on the target relationship, and three miRNAs were downregulated when exposed to the ZnSO₄ and FeCl₃ stresses. Yeast complementation analysis proved that TaZIP14-B, TaZIP13-B, and TaIRT2-A could transport Zn and Fe. Finally, overexpression of TaZIP13-B in Arabidopsis showed that the transgenic plants displayed better tolerance to Fe/Zn stresses and could enrich more metallic elements in their seeds than wild-type Arabidopsis. This study systematically analyzed the genomic organization, gene structure, expression profiles, regulatory network, and the biological function of the ZIP family in wheat, providing better understanding of the regulatory roles of TaZIPs and contributing to improve nutrient quality in wheat crops.

Iron Deficiency Leads to Chlorosis Through Impacting Chlorophyll Synthesis and Nitrogen Metabolism in Areca catechu L

Deficiency of certain elements can cause leaf chlorosis in Areca catechu L. trees, which causes considerable production loss. The linkage between nutrient deficiency and chlorosis phenomenon and physiological defect in A. catechu remains unclear. Here, we found that low iron supply is a determinant for chlorosis of A. catechu seedling, and excessive iron supply resulted in dark green leaves. We also observed morphological characters of A. catechu seedlings under different iron levels and compared their fresh weight, chlorophyll contents, chloroplast structures and photosynthetic activities. Results showed that iron deficiency directly caused chloroplast degeneration and reduced chlorophyll synthesis in chlorosis leaves, while excessive iron treatment can increase chlorophyll contents, chloroplasts sizes, and inflated starch granules. However, both excessive and deficient of iron decreases fresh weight and photosynthetic rate in A. catechu seedlings. Therefore, we applied transcriptomic and metabolomic approaches to understand the effect of different iron supply to A. catechu seedlings. The genes involved in nitrogen assimilation pathway, such as NR (nitrate reductase) and GOGAT (glutamate synthase), were significantly down-regulated under both iron deficiency and excessive iron. Moreover, the accumulation of organic acids and flavonoids indicated a potential way for A. catechu to endure iron deficiency. On the other hand, the up-regulation of POD-related genes was assumed to be a defense strategy against the excessive iron toxicity. Our data demonstrated that A. catechu is an iron-sensitive species, therefore the precise control of iron level is believed to be the key point for A. catechu cultivation.

Transcriptional integration of plant responses to iron availability

Iron is one of the most important micronutrients for plant growth and development. It functions as the enzyme cofactor or component of electron transport chains in various vital metabolic processes, including photosynthesis, respiration, and amino acid biosynthesis. To maintain iron homeostasis, and therefore prevent any deficiency or excess that could be detrimental, plants have evolved complex transcriptional regulatory networks to tightly control iron uptake, translocation, assimilation, and storage. These regulatory networks are composed of various transcription factors; among them, members of the basic helix-loop-helix (bHLH) family play an essential role. Here, we first review recent advances in understanding the roles of bHLH transcription factors involved in the regulatory cascade controlling iron homeostasis in the model plant Arabidopsis, and extend this understanding to rice and other plant species. The importance of other classes of transcription factors will also be discussed. Second, we elaborate on the post-translational mechanisms involved in the regulation of these regulatory networks. Finally, we provide some perspectives on future research that should be conducted in order to precisely understand how plants control the homeostasis of this micronutrient.

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.

Identifying transcripts associated with efficient transport and accumulation of Fe and Zn in hexaploid wheat (T. aestivum L.)

Wheat (T. aestivum L.) is the second most important staple food crop consumed in the form of various end-use products across the world. However, it contains lower concentrations of Fe and Zn leading to micronutrient deficiency in human beings where wheat is the sole diet. Therefore, increasing grain Fe/Zn content in wheat has become priority in wheat breeding programmes across the world. Understanding the molecular mechanism of Fe/Zn transport and accumulation in grains is required to expedite the breeding process. For this purpose, whole seedling transcriptome analysis was conducted in four wheat genotypes (CRP 1660, Sonora 64, Vinata, : high, and DBW17: low) differing in grain Fe/Zn content under controlled and Fe/Zn deficient conditions. Twenty eight key transcripts involved in phytosiderophore biosynthesis, Fe/Zn uptake and transport were identified. Expression analysis of 12 of the transcripts using qPCR was conducted in seedling stage and flag leaf which exhibited greater differential accumulation in CRP 1660 followed by Vinata, Sonora 64 and DBW 17 in both flag leaf and seedling. However, there was significantly higher differential accumulation of the transcripts in flag leaf as compared to seedling. In CRP 1660, transcripts pertaining to phytosiderophore biosynthesis like DMAS1-B, NRAMP2 and NAAT2-D showed greater accumulation. Additionally, corresponding miRNAs were also identified for these 28 transcripts. The findings will help in better understanding of molecular basis of Fe/Zn transport and accumulation in grain and subsequent utilization in breeding to improve Fe/Zn content in wheat grain.