Transporters involved in mineral nutrient uptake in rice

Targeting OsNIP3;1 via CRISPR/Cas9: A strategy for minimizing arsenic accumulation and boosting rice resilience

Arsenic (As) contamination in rice poses a significant threat to human health due to its toxicity and widespread consumption. Identifying and manipulating key genes governing As accumulation in rice is crucial for reducing this threat. The large NIP gene family of aquaporins in rice presents a promising target due to functional redundancy, potentially allowing for gene manipulation without compromising plant growth. This study aimed to utilize genome editing to generate knock-out (KO) lines of genes of NIP family (OsLsi1, OsNIP3;1) and an anion transporter family (OsLsi2), in order to assess their impact on As accumulation and stress tolerance in rice. KO lines were created using CRISPR/Cas9 technology, and the As accumulation patterns, physiological performance, and grain yield were compared against wild-type (WT) under As-treated conditions. KO lines exhibited significantly reduced As accumulation in grain compared to WT. Notably, Osnip3;1 KO line displayed reduced As in xylem sap (71-74%) and grain (32-46%) upon treatment. Additionally, these lines demonstrated improved silicon (23%) uptake, photosynthetic pigment concentrations (Chl a: 77%; Chl b: 79%, Total Chl: 79% & Carotenoid: 49%) overall physiological and agronomical performance under As stress compared to WT. This study successfully utilized genome editing for the first time to identify OsNIP3;1 as a potential target for manipulating As accumulation in rice without compromising grain yield or plant vigor.

Understanding phloem's role in long-distance transport and accumulation of arsenic (As) in rice: toward low-As-accumulating grain development

MAIN CONCLUSION

This review highlights the roles of phloem in the long-distance transport and accumulation of As in rice plants, facilitating the formulation of new strategies to reduce the grain As content. Rice is a staple diet for a significant proportion of the global population. As toxicity is a major issue affecting the rice productivity and quality worldwide. Phloem tissues of rice plants play vital roles in As speciation, long-distance transport, and unloading, thereby controlling the As accumulation in rice grains. Phloem transport accounts for a significant proportion of As transport to grains, ranging from 54 to 100% depending on the species [inorganic arsenate (As(V)), arsenite (As(III)), or organic dimethylarsinic acid (DMA(V)]. However, the specific mechanism of As transport through phloem leading to its accumulation in grains remains unknown. Therefore, understanding the molecular mechanism of phloem-mediated As transport is necessary to determine the roles of phloem in long-distance As transport and subsequently reduce the grain As content via biotechnological interventions. This review discusses the roles of phloem tissues in the long-distance transport and accumulation of As in rice grains. This review also highlights the biotechnological approaches using critical genetic factors involved in nodal accumulation, vacuolar sequestration, and cellular efflux of As in phloem- or phloem-associated tissues. Furthermore, the limitations of existing transgenic techniques are outlined to facilitate the formulation of novel strategies for the development of rice with reduced grain As content.

Polylactic acid microplastics have stronger positive effects on the qualitative traits of rice (Oryza sativa L.) than polyethylene microplastics: Evidence from a simulated field experiment

Soil pollution by microplastics (MPs) from different types of agricultural films has received substantial attention due to its potential effects on crop quality. To date, the effects of different types of MPs on rice grain quality and their underlying molecular mechanisms have not been clarified. In this study, we examined the effects of polyethylene MPs (PE-MPs) and biodegradable polylactic acid MPs (PLA-MPs) on rice grain quality at the environmental level (0.5 %) and evaluated the molecular mechanism through transcriptome analysis. PE- and PLA-MPs increased the number of rice grains per plant by 19.83 % and 24.66 %, respectively, and decreased the rice empty-shell rate by 55.89 % and 26.53 %, respectively. However, PLA-MPs increased the 1000-seed weight by 11.37 %, whereas PE-MPs had no obvious impact in this respect. Furthermore, MP exposure, especially that of PE-MPs, affected the content of mineral elements, fatty acids, and amino acids of rice grains by disturbing the expression of genes related to these functions and metabolism. Our findings provide insights into the response of rice grains to the stress caused by different MPs.

Masson pine pollen aqueous extract ameliorates cadmium-induced kidney damage in rats

Introduction: Cadmium (Cd) is a hazardous environmental pollutant present in soil, water, and food. Accumulation of Cd in organisms can cause systematic injury and damage to the kidney. The Masson pine pollen aqueous extract (MPPAE) has attracted increasing attention due to its antioxidant activity and ability to enhance immunity. Methods: In this study, we investigated the potential of MPPAE to protect against Cd-induced kidney damage in rats and the underlying mechanism. The transcriptome and metabolome of rats with Cd-induced kidney damage, following treatment with MPPAE, were explored. Results: The concentrations of superoxide dismutase (SOD) and malondialdehyde (MDA) were both significantly altered after treatment with MPPAE. Furthermore, sequencing and analysis of the transcriptome and metabolome of rats with Cd-induced kidney damage, following treatment with MPPAE, revealed differential expression of numerous genes and metabolites compared with the untreated control rats. These differentially expressed genes (DEGs) included detoxification-related genes such as cytochrome P450 and the transporter. The differentially expressed metabolites (DEMs) included 4-hydroxybenzoic acid, L-ascorbate, and ciliatine. Conjoint transcriptome and metabolome analysis showed that several DEGs were correlated with DEMs. Conclusion: These preliminary findings indicate the potential of MPPAE for the treatment of toxic metal poisoning.

Risk assessment of toxic and hazardous metals in paddy agroecosystem by biochar-for bio-membrane applications

Toxic and carcinogenic metal (loid)s, such arsenic (As) and cadmium (Cd), found in contaminated paddy soils pose a serious danger to environmental sustainability. Their geochemical activities are complex, making it difficult to manage their contamination. Rice grown in Cd and As-polluted soils ends up in people's bellies, where it can cause cancer, anemia, and the deadly itai sickness. Solving this issue calls for research into eco-friendly and cost-effective remediation technology to lower rice's As and Cd levels. This research delves deeply into the origins of As and Cd in paddy soils, as well as their mobility, bioavailability, and uptake mechanisms by rice plants. It also examines the current methods and reactors used to lower As and Cd contamination in rice. Iron-modified biochar (Fe-BC) is a promising technology for reducing As and Cd toxicity in rice, improving soil health, and boosting rice's nutritional value. Biochar's physiochemical characteristics are enhanced by the addition of iron, making it a potent adsorbent for As and Cd ions. In conclusion, Fe-BC's biomembrane properties make them an attractive option for remediating As- and Cd-contaminated paddy soils. More efficient mitigation measures, including the use of biomembrane technology, can be developed when sustainable agriculture practices are combined with these technologies.

Comparative Transcriptome Analysis Reveals the Effect of miR156a Overexpression on Mineral Nutrient Homeostasis in Nicotiana tabacum

Mineral nutrition plays an important role in crop growth, yield and quality. MiR156 is a regulatory hub for growth and development. To date, the understanding of miR156-mediated mineral homeostasis is limited. In this study, we overexpressed Nta-miR156a in the tobacco cultivar TN90 and analyzed the effects of miR156 on mineral element homeostasis in tobacco by comparative transcriptome analysis. The results showed that the overexpression of miR156a caused significant morphological changes in transgenic tobacco. Chlorophyll and three anti-resistance markers, proline, total phenolics, and total flavonoids, were altered due to increased miR156 expression levels. Interestingly, the distribution of Cu, Mn, Zn, and Fe in different tissues of transgenic tobacco was disordered compared with that of the wild type. Comparative transcriptome analysis showed that the overexpression of miR156 resulted in 2656 significantly differentially expressed genes. The expression levels of several metal-transport-related genes, such as NtABC, NtZIP, NtHMA, and NtCAX, were significantly increased or decreased in transgenic tobacco. These results suggest that miR156 plays an essential role in regulating mineral homeostasis. Our study provides a new perspective for the further study of mineral nutrient homeostasis in plants.

Molecular membrane separation: plants inspire new technologies

Plants draw up their surrounding soil solution to gain water and nutrients required for growth, development and reproduction. Obtaining adequate water and nutrients involves taking up both desired and undesired elements from the soil solution and separating resources from waste. Desirable and undesirable elements in the soil solution can share similar chemical properties, such as size and charge. Plants use membrane separation mechanisms to distinguish between different molecules that have similar chemical properties. Membrane separation enables distribution or retention of resources and efflux or compartmentation of waste. Plants use specialised membrane separation mechanisms to adapt to challenging soil solution compositions and distinguish between resources and waste. Coordination and regulation of these mechanisms between different tissues, cell types and subcellular membranes supports plant nutrition, environmental stress tolerance and energy management. This review considers membrane separation mechanisms in plants that contribute to specialised separation processes and highlights mechanisms of interest for engineering plants with enhanced performance in challenging conditions and for inspiring the development of novel industrial membrane separation technologies. Knowledge gained from studying plant membrane separation mechanisms can be applied to developing precision separation technologies. Separation technologies are needed for harvesting resources from industrial wastes and transitioning to a circular green economy.

Plant Plasma Membrane Proton Pump: One Protein with Multiple Functions

In plants, the plasma membrane proton pump (PM H⁺-ATPase) regulates numerous transport-dependent processes such as growth, development, basic physiology, and adaptation to environmental conditions. This review explores the multifunctionality of this enzyme in plant cells. The abundance of several PM H⁺-ATPase isogenes and their pivotal role in energizing transport in plants have been connected to the phenomena of pleiotropy. The multifunctionality of PM H⁺-ATPase is a focal point of numerous studies unraveling the molecular mechanisms of plant adaptation to adverse environmental conditions. Furthermore, PM H⁺-ATPase is a key element in plant defense mechanisms against pathogen attack; however, it also functions as a target for pathogens that enable plant tissue invasion. Here, we provide an extensive review of the PM H⁺-ATPase as a multitasking protein in plants. We focus on the results of recent studies concerning PM H⁺-ATPase and its role in plant growth, physiology, and pathogenesis.

Physiological and Molecular Mechanisms of Plant Responses to Copper Stress

Copper (Cu) is an essential micronutrient for humans, animals, and plants, and it participates in various morphological, physiological, and biochemical processes. Cu is a cofactor for a variety of enzymes, and it plays an important role in photosynthesis, respiration, the antioxidant system, and signal transduction. Many studies have demonstrated the adverse effects of excess Cu on crop germination, growth, photosynthesis, and antioxidant activity. This review summarizes the biological functions of Cu, the toxicity of excess Cu to plant growth and development, the roles of Cu transport proteins and chaperone proteins, and the transport process of Cu in plants, as well as the mechanisms of detoxification and tolerance of Cu in plants. Future research directions are proposed, which provide guidelines for related research.

Mitigating the accumulation of arsenic and cadmium in rice grain: A quantitative review of the role of water management

Arsenic exposure through rice consumption is a growing concern. Compared to Continuous Flooding (CF), irrigation practices that dry the soil at least once during the growing season [referred to here as Alternate Wetting and Drying (AWD)] can decrease As accumulation in grain; however, this can simultaneously increase grain Cd to potentially unsafe levels. We modelled grain As and Cd from field studies comparing AWD and CF to identify optimal AWD practices to minimize the accumulation of As and Cd in grain. The severity of soil drying during AWD drying event(s), quantified as soil water potential (SWP), was the main factor leading to a reduction in grain total As and inorganic As, compared to CF. However, lower SWP levels were necessary to decrease grain inorganic As, compared to total As. Therefore, if the goal is to decrease grain inorganic As, the soil needs to be dried further than it would for decreasing total As alone. The main factor driving grain Cd accumulation was when AWD was practiced during the season. Higher grain Cd levels were observed when AWD occurred during the early reproductive stage. Further, higher Cd levels were observed when AWD spanned multiple rice growth stages, compared to one stage. If Cd levels are concerning, the minimum trade-off between total As and Cd accumulation in rice grain occurred when AWD was implemented at a SWP of -47 kPa during one stage other than the early reproductive. While these results are not meant to be comprehensive of all the interactions affecting the As and Cd dynamics in rice systems, they can be used as a first guide for implementing AWD practices with the goal of minimizing the accumulation of As and Cd in rice grain.

Natural Molecular Mechanisms of Plant Hyperaccumulation and Hypertolerance towards Heavy Metals

The main mechanism of plant tolerance is the avoidance of metal uptake, whereas the main mechanism of hyperaccumulation is the uptake and neutralization of metals through specific plant processes. These include the formation of symbioses with rhizosphere microorganisms, the secretion of substances into the soil and metal immobilization, cell wall modification, changes in the expression of genes encoding heavy metal transporters, heavy metal ion chelation, and sequestration, and regenerative heat-shock protein production. The aim of this work was to review the natural plant mechanisms that contribute towards increased heavy metal accumulation and tolerance, as well as a review of the hyperaccumulator phytoremediation capacity. Phytoremediation is a strategy for purifying heavy-metal-contaminated soils using higher plants species as hyperaccumulators.

Drought specifically downregulates mineral nutrition: Plant ionomic content and associated gene expression

One of the main limiting factors of plant yield is drought, and while the physiological responses to this environmental stress have been broadly described, research addressing its impact on mineral nutrition is scarce. Brassica napus and Triticum aestivum were subjected to moderate or severe water deficit, and their responses to drought were assessed by functional ionomic analysis, and derived calculation of the net uptake of 20 nutrients. While the uptake of most mineral nutrients decreased, Fe, Zn, Mn, and Mo uptake were impacted earlier and at a larger scale than most physiological parameters assessed (growth, ABA concentration, gas exchanges and photosynthetic activity). Additionally, in B. napus, the patterns of 183 differentially expressed genes in leaves related to the ionome (known ionomic genes, KIGs) or assumed to be involved in transport of a given nutrient were analyzed. This revealed three patterns of gene expression under drought consisting of up (transport of Cl and Co), down (transport of N, P, B, Mo, and Ni), or mixed levels (transport of S, Mg, K, Zn, Fe, Cu, or Mn) of regulation. The three patterns of gene regulations are discussed in relation to specific gene functions, changes of leaf ionomic composition and with consideration of the crosstalks that have been established between elements. It is suggested that the observed reduction in Fe uptake occurred via a specific response to drought, leading indirectly to reduced uptake of Zn and Mn, and these may be taken up by common transporters encoded by genes that were downregulated.

Three OsMYB36 members redundantly regulate Casparian strip formation at the root endodermis

Plants have evolved a lignin-based Casparian strip (CS) in roots that restricts passive diffusion of mineral elements from the soil to the stele. However, the molecular mechanisms underlying CS formation in rice (Oryza sativa), which contains a CS at both the exodermis and endodermis, are poorly understood. Here, we demonstrate that CS formation at the rice endodermis is redundantly regulated by three MYELOBLASTOSIS (MYB) transcription factors, OsMYB36a, OsMYB36b, and OsMYB36c, that are highly expressed in root tips. Knockout of all three genes resulted in a complete absence of CS at the endodermis and retarded plant growth in hydroponic conditions and in soil. Compared with the wild-type, the triple mutants showed higher calcium (Ca) levels and lower Mn, Fe, Zn, Cu, and Cd levels in shoots. High Ca supply further inhibited mutant growth and increased Ca levels in shoots. Transcriptome analysis identified 1,093 downstream genes regulated by OsMYB36a/b/c, including the key CS formation gene OsCASP1 and other genes that function in CS formation at the endodermis. Three OsMYB36s regulate OsCASP1 and OsESB1 expression by directly binding to MYB-binding motifs in their promoters. Our findings thus provide important insights into the mechanism of CS formation at the endodermis and the selective uptake of mineral elements in roots.

Cell-Type-Dependent but CME-Independent Polar Localization of Silicon Transporters in Rice

Silicon (Si) is an important nutrient required for sustainable and high production of rice and its uptake is mediated by a pair of influx (OsLsi1)-efflux (OsLsi2) transporters showing polar localization. However, the mechanisms underlying their polarity are unknown. Here, we revealed that the polarity of the Si transporters depends on cell types. The polar localization of both OsLsi1 and OsLsi2 was not altered by Si supply, but their protein abundance was reduced. Double immunostaining showed that localization of OsLsi1 and OsLsi2 was separated at the edge of the lateral polar domain by Casparian strips in the endodermis, whereas they were slightly overlapped at the transversal side of the exodermis. When OsLsi1 was ectopically expressed in the shoots, it showed polar localization at the xylem parenchyma cells of the basal node and leaf sheath, but not at the phloem companion cells. Ectopic expression of non-polar Si transporters, barley HvLsi2 and maize ZmLsi2 in rice, resulted in their polar localization at the proximal side. The polar localization of OsLsi1 and OsLsi2 was not altered by inhibition of clathrin-mediated endocytosis (CME) by dominant-negative induction of dynamin-related protein1A and knockout of mu subunit of adaptor protein 2 complex, although the knockout mutants of OsAP2M gene showed dwarf phenotype. These results indicate that CME is not required for the polar localization of Si transporters. Taken together, our results indicate that CME-independent machinery controls the polar localization of Si transporters in exodermis, endodermis of root cells and xylem parenchyma cells.

Sorghum Ionomics Reveals the Functional SbHMA3a Allele that Limits Excess Cadmium Accumulation in Grains

Understanding uptake and redistribution of essential minerals or sequestering of toxic elements is important for optimized crop production. Although the mechanisms controlling mineral transport have been elucidated in rice and other species, little is understood in sorghum-an important C4 cereal crop. Here, we assessed the genetic factors that govern grain ionome profiles in sorghum using recombinant inbred lines (RILs) derived from a cross between BTx623 and NOG (Takakibi). Pairwise correlation and clustering analysis of 22 elements, measured in sorghum grains harvested under greenhouse conditions, indicated that the parental lines, as well as the RILs, show different ionomes. In particular, BTx623 accumulated significantly higher levels of cadmium (Cd) than NOG, because of differential root-to-shoot translocation factors between the two lines. Quantitative trait locus (QTL) analysis revealed a prominent QTL for grain Cd concentration on chromosome 2. Detailed analysis identified SbHMA3a, encoding a P1B-type ATPase heavy metal transporter, as responsible for low Cd accumulation in grains; the NOG allele encoded a functional HMA3 transporter (SbHMA3a-NOG) whose Cd-transporting activity was confirmed by heterologous expression in yeast. BTx623 possessed a truncated, loss-of-function SbHMA3a allele. The functionality of SbHMA3a in NOG was confirmed by Cd concentrations of F2 grains derived from the reciprocal cross, in which the NOG allele behaved in a dominant manner. We concluded that SbHMA3a-NOG is a Cd transporter that sequesters excess Cd in root tissues, as shown in other HMA3s. Our findings will facilitate the isolation of breeding cultivars with low Cd in grains or in exploiting high-Cd cultivars for phytoremediation.

Joint approaches to reduce cadmium exposure risk from rice consumption

In-situ soil cadmium (Cd) immobilization helps to reduce Cd accumulation in rice grain, while its effects on bioaccessibility of Cd in rice during digestion and the associated health risk from rice consumption remain unclear. Here, we combined in-situ soil Cd immobilization and bioaccessibility-corrected health risk assessment (HRA) to minimize both the risk and uncertainty of Cd exposure from rice consumption. Wollastonite with or without four different phosphates (P) were applied to immobilize soil Cd at paddy fields, and their influences on Cd, essential elements, and amino acids in rice grain were analyzed. Moreover, a bioaccessibility-corrected HRA was conducted to accurately reflect the Cd exposure risk from ingesting these rices. The results showed the co-application of wollastonite and four different P reduced Cd concentrations in rice grain equally, while their impacts on bioaccessibility of Cd in rice during simulated human digestion were inconsistent (53-71%). The HRA based on bioaccessibility of Cd in rice revealed that Cd exposure risk from rice consumption was lowest with the application of wollastonite, followed by the co-application of wollastonite and sodium hexametaphosphate. This work highlights the value of bioaccessibility-corrected HRA for screening the optimal Cd immobilization strategy to achieve safer rice consumption.

OsAT1, an anion transporter, negatively regulates grain size and yield in rice

Improving the grain yield of rice is a central goal of basic and applied scientific research. Here, we identified an anion transporter, OsAT1, localized in the endoplasmic reticulum and Golgi. OsAT1 is highly expressed in flag, stem, and sheath as monitored using qRT-PCR and pOsAT1::GUS. Thousand-grain weight, grain weight per plant, and content of starch were significantly increased in OsAT1 knock-down mutants (OsAT1-Ri) but significantly decreased in OsAT1 overexpressed lines (OsAT1-OE). In addition, the grain weight per plant increased by 6.17% to 6.78% in OsAT1-RNAi lines, whereas it decreased by 45.93% to 46.76% in OsAT1-OE lines, compared to wild-type. Moreover, the copper content was noticeably reduced in flag leaf of OsAT1-Ri lines and increased in OsAT1-OE lines. RNA-sequencing analysis of OsAT1-OE lines revealed that the genes related to starch biosynthesis and metabolism pathway were enriched in the down-regulated category. Thus, our results suggest that knock-down of OsAT1 in rice possibly reduces copper accumulation and improves the accumulation of storage starch, hence, increasing the grain size and weight. OsAT1 may be a useful gene to consider for cereal breeding programs.

Insights to improve the plant nutrient transport by CRISPR/Cas system

We need to improve food production to feed the ever growing world population especially in a changing climate. Nutrient deficiency in soils is one of the primary bottlenecks affecting the crop production both in developed and developing countries. Farmers are forced to apply synthetic fertilizers to improve the crop production to meet the demand. Understanding the mechanism of nutrient transport is helpful to improve the nutrient-use efficiency of crops and promote the sustainable agriculture. Many transporters involved in the acquisition, export and redistribution of nutrients in plants are characterized. In these studies, heterologous systems like yeast and Xenopus were most frequently used to study the transport function of plant nutrient transporters. CRIPSR/Cas system introduced recently has taken central stage for efficient genome editing in diverse organisms including plants. In this review, we discuss the key nutrient transporters involved in the acquisition and redistribution of nutrients from soil. We draw insights on the possible application CRISPR/Cas system for improving the nutrient transport in plants by engineering key residues of nutrient transporters, transcriptional regulation of nutrient transport signals, engineering motifs in promoters and transcription factors. CRISPR-based engineering of plant nutrient transport not only helps to study the process in native plants with conserved regulatory system but also aid to develop non-transgenic crops with better nutrient use-efficiency. This will reduce the application of synthetic fertilizers and promote the sustainable agriculture strengthening the food and nutrient security.

A pericycle-localized silicon transporter for efficient xylem loading in rice

Rice is able to accumulate high concentrations of silicon (Si) in the shoots, and this ability is required for the mitigation of abiotic and biotic stresses. Although transporters for Si uptake have been identified, a transporter for the xylem loading of Si has not been found. We functionally characterized a Si transporter, OsLsi3, in terms of tissue-specific localization, knockout line phenotype and mathematic simulation. OsLsi3 was shown to be an efflux Si transporter. OsLsi3 was mainly expressed in the mature root region, and its expression was downregulated by Si. Immunostaining with a specific antibody showed that OsLsi3 was localized to the pericycle in the roots, without polarity. However, when it was expressed under the control of the OsLsi2 promoter, OsLsi3 became polarly localized to the proximal side of both the exodermis and endodermis. Knockout of this gene resulted in decreased Si uptake and concentration in the xylem sap under low Si supply, but not under high Si supply. Mathematical modeling showed that localization of OsLsi3 to the pericycle accounts for c. 30% of the total Si loading to the xylem under low Si concentrations. In summary, OsLsi3 was involved in the xylem loading of Si in rice roots, which is required for the efficient root-to-shoot translocation of Si.

Zinc transport in rice: how to balance optimal plant requirements and human nutrition

Zinc (Zn) is an essential micronutrient for both plants and animals, while its deficiency in crops and humans is a global problem that affects both crop productivity and human health. Since plants and humans differ in their Zn requirements, it is crucial to balance plant nutrition and human nutrition for Zn. In this review, we focus on the transport system of Zn from soil to grain in rice (Oryza sativa), which is a major dietary source of Zn for people subsiding on rice-based diets. We describe transporters belonging to the different families that are involved in the uptake, vacuolar sequestration, root-to-shoot translocation, and distribution of Zn, and discuss their mechanisms of regulation. We give examples for enhancing Zn accumulation and bioavailability in rice grains through the manipulation of genes that are highly expressed in the nodes, where Zn is deposited at high concentrations. Finally, we provide our perspectives on breeding rice cultivars with both increased tolerance to Zn-deficiency stress and high Zn density in the grains.

Boron uptake in rice is regulated post-translationally via a clathrin-independent pathway

Uptake of boron (B) in rice (Oryza sativa) is mediated by the Low silicon rice 1 (OsLsi1) channel, belonging to the NOD26-like intrinsic protein III subgroup, and the efflux transporter B transporter 1 (OsBOR1). However, it is unknown how these transporters cooperate for B uptake and how they are regulated in response to B fluctuations. Here, we examined the response of these two transporters to environmental B changes at the transcriptional and posttranslational level. OsBOR1 showed polar localization at the proximal side of both the exodermis and endodermis of mature root region, forming an efficient uptake system with OsLsi1 polarly localized at the distal side of the same cell layers. Expression of OsBOR1 and OsLsi1 was unaffected by B deficiency and excess. However, although OsLsi1 protein did not respond to high B at the protein level, OsBOR1 was degraded in response to high B within hours, which was accompanied with a significant decrease of total B uptake. The high B-induced degradation of OsBOR1 was inhibited in the presence of MG-132, a proteasome inhibitor, without disturbance of the polar localization. In contrast, neither the high B-induced degradation of OsBOR1 nor its polarity was affected by induced expression of dominant-negative mutated dynamin-related protein 1A (OsDRP1AK47A) or knockout of the mu subunit (AP2M) of adaptor protein-2 complex, suggesting that clathrin-mediated endocytosis is not involved in OsBOR1 degradation and polar localization. These results indicate that, in contrast to Arabidopsis thaliana, rice has a distinct regulatory mechanism for B uptake through clathrin-independent degradation of OsBOR1 in response to high B.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

NILs of Cold Tolerant Japonica Cultivar Exhibited New QTLs for Mineral Elements in Rice

Chilling stress at booting stage can cause floret deterioration and sterility by limiting the supply of food chain and the accumulation of essential mineral elements resulting in reduction of yield and grain quality attributes in rice. Genomic selection of chilling tolerant rice with reference to the accumulation of mineral elements will have great potential to cope with malnutrition and food security in times of climate change. Therefore, a study was conducted to explore the genomic determinants of cold tolerance and mineral elements content in near-isogenic lines (NILs) of japonica rice subjected to chilling stress at flowering stage. Detailed morphological analysis followed by quantitative analysis of 17 mineral elements revealed that the content of phosphorus (P, 3,253 mg/kg) and potassium (K, 2,485 mg/kg) were highest while strontium (Sr, 0.26 mg/kg) and boron (B, 0.34 mg/kg) were lowest among the mineral elements. The correlation analysis revealed extremely positive correlation of phosphorus (P) and copper (Cu) with most of the cold tolerance traits. Among all the effective ear and the second leaf length correlation was significant with half of the mineral elements. As a result of comparative analysis, some QTLs (qBRCC-1, qBRCIC-2, qBRZC-6, qBRCHC-6, qBRMC-6, qBRCIC-6a, qBRCIC-6b, qBRCHC-6, and qBRMC-6) identified for calcium (Ca), zinc (Zn), chromium (Cr) and magnesium (Mg) on chromosome number 1, 2, and 6 while, a novel QTL (qBCPC-1) was identified on chromosome number 1 for P element only. These findings provided bases for the identification of candidate genes involved in mineral accumulation and cold tolerance in rice at booting stage.

Metalloid transporters and their regulation in plants

Transport of metalloids including B, Si, and As is mediated by a combination of channels and efflux transporters in plants, which are strictly regulated in response to environmental changes.

Three polarly localized ammonium transporter 1 members are cooperatively responsible for ammonium uptake in rice under low ammonium condition

Ammonium is a preferential nitrogen form for rice (Oryza sativa) grown in paddy field, but the molecular mechanisms for ammonium uptake have not been well understood. We functionally characterized three members belonging to ammonium transporter 1 (AMT1) and investigated their contributions to ammonium uptake. Spatial expression analysis showed that the upregulated expression of OsAMT1;1 and OsAMT1;2 and downregulated expression of OsAMT1;3 by ammonium were higher in the root mature region than in the root tips. All OsAMT1 members were polarly localized at the distal side of exodermis in the mature region of crown roots and lateral roots. Upon exposure to ammonium, localization of OsAMT1;1 and OsAMT1;2 was also observed in the endoplasmic reticulum, but their abundance in the plasma membrane was not changed. Single knockout of either gene did not affect ammonium uptake, but knockout of all three genes resulted in 95% reduction of ammonium uptake. However, the nitrogen uptake did not differ between the wild-type rice and triple mutants at high ammonium and nitrate supply. Our results indicate that three OsAMT1 members are cooperatively required for uptake of low ammonium in rice roots and that they undergo a distinct regulatory mechanism in response to ammonium.

A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica

This study presents a comprehensive study of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diverse panel of indica accessions, each genotyped with 5.2 million markers. GWAS was performed for twelve elements including B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn and four agronomic traits including days to 50% flowering, grain yield, plant height and thousand grain weight. GWAS identified 128 loci associated with the grain elements and 57 associated with the agronomic traits. There were sixteen co-localization regions containing QTL for two or more traits. Fourteen grain element quantitative trait loci were stable across growing environments, which can be strong candidates to be used in marker-assisted selection to improve the concentrations of nutritive elements in rice grain. Potential candidate genes were revealed including OsNAS3 linked to the locus that controls the variation of Zn and Co concentrations. The effects of starch synthesis and grain filling on multiple grain elements were elucidated through the likely involvement of OsSUS1 and OsGSSB1 genes. Overall, our study provides crucial insights into the genetic basis of ionomic variations in rice and will facilitate improvement in breeding for trace mineral content.

Cell wall modification induced by an arbuscular mycorrhizal fungus enhanced cadmium fixation in rice root

The chemistry of root cell wall of rice could be changed by inoculation of arbuscular mycorrhizal fungi (AMF). Hydroponic experiments were conducted to investigate the roles of such changes on cadmium (Cd) uptake and distribution in rice. Results showed that inoculation of AM fungus Rhizophagus intraradices (RI) significantly enhanced (p < 0.05) shoot biomass, plant height and root length of rice, and decreased Cd concentration in shoot and root under Cd stress. Moreover, Cd in root was mainly found in pectin and hemicellulose 1 (HC1) components of root cell wall. Inoculation of RI increased the levels of pectin, HC1 and lignin content, accompanied by the increments of L-phenylalanine ammonia-lyase (PAL) and pectin methylesterase (PME) activities. Results of Fourier transform infrared spectroscopy further showed that more hydroxyl and carboxyl groups in root cell wall were observed in mycorrhizal treatment, compared with control. This study demonstrates that cell wall components could be the locations for Cd fixation, which reduced Cd transportation from root to shoot. Inoculation of AMF may remodel root cell wall biosynthesis and affect the characteristics of Cd fixation. The entering and fixing mechanisms should be further studied.

External and Internal Reshaping of Plant Thermomorphogenesis

Plants dynamically adapt to changing temperatures to ensure propagation and reproductive success, among which morphogenic responses to warm temperatures have been extensively studied in recent years. As readily inferred from the cyclic co-oscillations of environmental cues in nature, plant thermomorphogenesis is coordinately reshaped by various external conditions. Accumulating evidence supports that internal and developmental cues also contribute to harmonizing thermomorphogenic responses. The external and internal reshaping of thermomorphogenesis is facilitated by versatile temperature sensing and interorgan communication processes, circadian and photoperiodic gating of thermomorphogenic behaviors, and their metabolic coordination. Here, we discuss recent advances in plant thermal responses with focus on the diel and seasonal reshaping of thermomorphogenesis and briefly explore its application to developing climate-smart crops.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

Ionomic variation in leaves of 819 plant species growing in the botanical garden of Hokkaido University, Japan

Ionomics is the measurement of total metal, metalloid, and nonmetal accumulation in living organisms. Plant ionomics has been applied to various types of research in the last decade. It has been reported that the ionome of a plant is strongly affected by its evolution and by environmental factors. In this study, we analyzed the concentration of 23 elements in leaves of 819 plant species (175 families) growing in the Botanic Garden of Hokkaido University, Japan. Relative variation estimated by the coefficient of variation in foliar concentrations of essential elements among various plant species tended to be low, whereas nickel concentration showed exceptionally large relative variation. By contrast, the relative variation in nonessential elements was high, particularly in sodium, aluminum, and arsenic. The higher relative variations in these element concentrations can be explained by the occurrence of plants that are hyperaccumulators for these elements. Differences in life forms such as herbaceous/woody species, deciduous/evergreen woody species and annual/perennial herbaceous species affected the concentration of several elements in the leaves. These differences were considered to be due to the combined factors including differences in lifespan, growth rate, and cell wall thickness of the leaves. Results of principal component analyses (based on concentration data of essential and nonessential elements in leaf samples) indicated phylogenetic influences on plant ionomes at the family level in Polypodiales, Pinales, Poales, and Ericales. Furthermore, when analyzing correlations among concentrations of all elements in each order and comparing among different orders, the results also suggested that Polypodiales, Pinales, and Poales each had a specific ion homeostasis network.

Specificity and Plasticity of the Functional Ionome of Brassica napus and Triticum aestivum Exposed to Micronutrient or Beneficial Nutrient Deprivation and Predictive Sensitivity of the Ionomic Signatures

The specific variation in the functional ionome was studied in Brassica napus and Triticum aestivum plants subjected to micronutrient or beneficial mineral nutrient deprivation. Effects of these deprivations were compared to those of macronutrient deprivation. In order to identify early events, plants were harvested after 22 days, i.e., before any significant reduction in growth relative to control plants. Root uptake, tissue concentrations and relative root nutrient contents were analyzed revealing numerous interactions with respect to the 20 elements quantified. The assessment of the functional ionome under individual mineral nutrient deficiency allows the identification of a large number of interactions between elements, although it is not totally exhaustive, and gives access to specific ionomic signatures that discriminate among deficiencies in N, P, S, K, Ca, Mn, Fe, Zn, Na, Si, and Se in both species, plus Mg, Cl, Cu, and Mo in wheat. Ionome modifications and components of ionomic signatures are discussed in relation to well-known mechanisms that may explain crosstalks between mineral nutrients, such as between Na and K, V, Se, Mo and S or Fe, Zn and Cu. More surprisingly, when deprived of beneficial nutrients such as Na, Si, Co, or Se, the plant ionome was strongly modified while these beneficial nutrients contributed greatly to the leaf ionomic signature of most mineral deficiencies.

Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism

Background

Silicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data.

Methods

We established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L⁻¹ Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis.

Results

Si concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors.

Conclusion

Pepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper.

OsNRAMP1 transporter contributes to cadmium and manganese uptake in rice

Rice is a major dietary source of the toxic metal, cadmium (Cd). Previous studies reported that the rice transporter, OsNRAMP1, (Natural resistance-associated macrophage protein 1) could transport iron (Fe), Cd and arsenic (As) in heterologous yeast assays. However, the in planta function of OsNRAMP1 remains unknown. Here, we showed that OsNRAMP1 was able to transport Cd and manganese (Mn) when expressed in yeast, but did not transport Fe or As. OsNRAMP1 was mainly expressed in roots and leaves and encoded a plasma membrane-localized protein. OsNRAMP1 expression was induced by Cd treatment and Fe deficiency. Immunostaining showed that OsNRAMP1 was localized in all root cells, except the central vasculature, and in leaf mesophyll cells. The knockout of OsNRAMP1 resulted in significant decreases in root uptake of Cd and Mn and their accumulation in rice shoots and grains, and increased sensitivity to Mn deficiency. The knockout of OsNRAMP1 had smaller effects on Cd and Mn uptake than knockout of OsNRAMP5, while knockout of both genes resulted in large decreases in the uptake of the two metals. Taken together, OsNRAMP1 contributes significantly to the uptake of Mn and Cd in rice, and the functions of OsNRAMP1 and OsNRAMP5 are similar but not redundant.

Overexpression of the manganese/cadmium transporter OsNRAMP5 reduces cadmium accumulation in rice grain

Rice is a major dietary source of the toxic metal cadmium (Cd), and reducing its accumulation in the grain is therefore important for food safety. We selected two cultivars with contrasting Cd accumulation and generated transgenic lines overexpressing OsNRAMP5, which encodes a major influx transporter for manganese (Mn) and Cd. We used two different promoters to control the expression, namely OsActin1 and maize Ubiquitin. Overexpression of OsNRAMP5 increased Cd and Mn uptake into the roots, but markedly decreased Cd accumulation in the shoots, whilst having a relatively small effect on Mn accumulation in the shoots. The overexpressed OsNRAMP5 protein was localized to the plasma membrane of all cell types in the root tips and lateral root primordia without polarity. Synchrotron X-ray fluorescence mapping showed that the overexpression lines accumulated more Cd in the root tips and lateral root primordia compared with the wild-type. When grown in three Cd-contaminated paddy soils, overexpression of OsNRAMP5 decreased concentration of Cd in the grain by 49-94% compared with the wild type. OsNRAMP5-overexpression plants had decreased Cd translocation from roots to shoots as a result of disruption of its radial transport into the stele for xylem loading, demonstrating the effect of transporter localization and polarity on ion homeostasis.

Genetic Manipulation for Improved Nutritional Quality in Rice

Food with higher nutritional value is always desired for human health. Rice is the prime staple food in more than thirty developing countries, providing at least 20% of dietary protein, 3% of dietary fat and other essential nutrients. Several factors influence the nutrient content of rice which includes agricultural practices, post-harvest processing, cultivar type as well as manipulations followed by selection through breeding and genetic means. In addition to mutation breeding, genetic engineering approach also contributed significantly for the generation of nutrition added varieties of rice in the last decade or so. In the present review, we summarize the research update on improving the nutritional characteristics of rice by using genetic engineering and mutation breeding approach. We also compare the conventional breeding techniques of rice with modern molecular breeding techniques toward the generation of nutritionally improved rice variety as compared to other cereals in areas of micronutrients and availability of essential nutrients such as folate and iron. In addition to biofortification, our focus will be on the efforts to generate low phytate in seeds, increase in essential fatty acids or addition of vitamins (as in golden rice) all leading to the achievements in rice nutrition science. The superiority of biotechnology over conventional breeding being already established, it is essential to ascertain that there are no serious negative agronomic consequences for consumers with any difference in grain size or color or texture, when a nutritionally improved variety of rice is generated through genetic engineering technology.

Plant Nutrition for Human Nutrition: Hints from Rice Research and Future Perspectives

Both plants and humans require mineral elements for their healthy growth and development. Mineral elements in the soil are taken up by the plant roots and transported to the edible parts for human consumption through various different transporters. An ideal future crop for human health should be rich in essential mineral elements but with less toxic elements in the edible parts. However, due to the great difference in the numbers and amounts of mineral elements required between plants and humans, it is a challenge to balance plant growth and nutrient requirement for humans. In this article, we mainly focus on the transport system of mineral elements from soil to grain in rice, a staple food for half of the world's population, and discuss recent progress on the underlying genetic and physiological mechanisms. Examples are given for silicon, zinc, and iron essential/beneficial for both plants and humans, selenium and iodine only essential for humans, and toxic cadmium and arsenic for all organisms. Manipulation of some transporters for these elements, especially those localized in the node for allocation of mineral elements to the grain, has been successful in generating rice with higher density and bioavailability of essential elements but with less accumulation of toxic elements. We provide our perspectives toward breeding future crops for human health.

Silicon Regulates Source to Sink Metabolic Homeostasis and Promotes Growth of Rice Plants Under Sulfur Deficiency

Being an essential macroelement, sulfur (S) is pivotal for plant growth and development, and acute deficiency in this element leads to yield penalty. Since the last decade, strong evidence has reported the regulatory function of silicon (Si) in mitigating plant nutrient deficiency due to its significant diverse benefits on plant growth. However, the role of Si application in alleviating the negative impact of S deficiency is still obscure. In the present study, an attempt was undertaken to decipher the role of Si application on the metabolism of rice plants under S deficiency. The results showed a distinct transcriptomic and metabolic regulation in rice plants treated with Si under both short and long-term S deficiencies. The expression of Si transporters OsLsi1 and OsLsi2 was reduced under long-term deficiency, and the decrease was more pronounced when Si was provided. The expression of OsLsi6, which is involved in xylem loading of Si to shoots, was decreased under short-term S stress and remained unchanged in response to long-term stress. Moreover, the expression of S transporters OsSULTR tended to decrease by Si supply under short-term S deficiency but not under prolonged S stress. Si supply also reduced the level of almost all the metabolites in shoots of S-deficient plants, while it increased their level in the roots. The levels of stress-responsive hormones ABA, SA, and JA-lle were also decreased in shoots by Si application. Overall, our finding reveals the regulatory role of Si in modulating the metabolic homeostasis under S-deficient condition.

Effects of external Mn2+ activities on OsNRAMP5 expression level and Cd accumulation in indica rice

Manganese (Mn) transporter OsNRAMP5 was widely reported to regulate cadmium (Cd) uptake in rice. However, the relationship between OsNRAMP5 expression level and Cd accumulation, impacts of external ion activities on OsNRAMP5 expression level and Cd accumulation are still unclear. Investigations of the relationship between OsNRAMP5 expression level and Cd accumulation in three indica rice genotypes were conducted under various external Mn²⁺ activities ranging from Mn deficiency to toxicity in EGTA-buffered nutrient solution. Results in this work indicated that OsNRAMP5 expression level in roots significantly up-regulated at Mn phytotoxicity compared to that at Mn deficiency, which may stimulate by the increasing uptake of Mn. Our work also demonstrated that root Cd concentration of all the tested rice decreased notably when external Mn²⁺ activity reached the level of toxicity. This may explain by the increasing competition between the excess Mn²⁺ and Cd²⁺ as well as the disorder of element absorption caused by root damage at Mn toxicity. Our work also revealed that the relationship between OsNRAMP5 expression level in roots and Cd accumulation in roots was insignificant for all the tested genotypes. Besides, OsNRAMP5 expression level in roots seemed more related to root Mn accumulation. The fact that function of OsNRAMP5 mainly focuses on Mn uptake, together with the fact that many transporter genes involved in Cd uptake might result in the insignificant correlation between OsNRAMP5 expression level and Cd accumulation in roots. At last, multi-level regulating and processing of the process from gene expression to protein translation might account for the inconsistent relationship between root OsNRAMP5 expression level and Cd accumulation in roots.

Potential Implications of Interactions between Fe and S on Cereal Fe Biofortification

Iron (Fe) and sulfur (S) are two essential elements for plants, whose interrelation is indispensable for numerous physiological processes. In particular, Fe homeostasis in cereal species is profoundly connected to S nutrition because phytosiderophores, which are the metal chelators required for Fe uptake and translocation in cereals, are derived from a S-containing amino acid, methionine. To date, various biotechnological cereal Fe biofortification strategies involving modulation of genes underlying Fe homeostasis have been reported. Meanwhile, the resultant Fe-biofortified crops have been minimally characterized from the perspective of interaction between Fe and S, in spite of the significance of the crosstalk between the two elements in cereals. Here, we intend to highlight the relevance of Fe and S interrelation in cereal Fe homeostasis and illustrate the potential implications it has to offer for future cereal Fe biofortification studies.

Plastic transport systems of rice for mineral elements in response to diverse soil environmental changes

Climate change will increase frequency of drought and flooding, which threaten global crop productivity and food security. Rice (Oryza sativa) is unique in that it is able to grow in both flooded and upland conditions, which have large differences in the concentrations and chemical forms of mineral elements available to plants. To comprehensively understand the mechanisms of rice for coping with different water status, we performed ionomics and transcriptomics analysis of the roots, nodes and leaves of rice grown in flooded and upland conditions. Focusing the analysis on genes encoding proteins involved in transport functions for mineral elements, it was found that, although rice plants maintained similar levels of each element in the shoots for optimal growth, different transporters for mineral elements were utilised for nitrogen, iron, copper and zinc to deal with different soil water conditions. For example, under flooded conditions, rice roots take up nitrogen using transporters for both ammonium (OsAMT1/2) and nitrate (OsNPF2.4, OsNRT1.1A and OsNRT2.3), whereas under upland conditions, nitrogen uptake is mediated by different nitrate transporters (OsNRT1.1B and OsNRT1.5A). This study shows that rice possesses plastic transport systems for mineral elements in response to different water conditions (upland and flooding).

Altered Root Structure Affects Both Expression and Cellular Localization of Transporters for Mineral Element Uptake in Rice

One of the most important roles of plant roots is to take up mineral elements for their growth. Although several genes involved in root growth have been identified, the association between root structure and mineral element uptake is less investigated. In this study, we isolated a rice mutant (dice1, defective in cell elongation 1) with short-root phenotype. This mutant was characterized by partial defect in the formation of root outer cell layers. Mapping of the responsible gene revealed that the short-root phenotype in the mutant was caused by a single-nucleotide substitution of a gene encoding a membrane-anchored endo-1,4-beta-glucanase (OsGlu3). The growth of both the roots and shoots was partially recovered with increasing strength of nutrient solution and glucose in the mutant. The mutant showed a decreased uptake (normalized by root dry weight) for Mg, Mn, Fe, Cu, Zn, Cd, As and Ge but increased uptake for K and Ca. The expression level of some transporter genes including OsLsi1 and OsLsi2 for Si uptake and OsNramp5 for Mn uptake was significantly decreased in the mutant compared with the wild-type (WT) rice. Furthermore, the cellular localization of OsLsi1 was altered; OsLsi1 localized at the root exodermis of the WT rice was changed to be localized to other cell layers of the mutant roots. However, this localization became normal in the presence of exogenous glucose in the mutant. Our results indicate that a normal root structure is required for maintaining the expression and localization of transporters involved in the mineral element uptake.

Characterization of the Soybean GmIREG Family Genes and the Function of GmIREG3 in Conferring Tolerance to Aluminum Stress

The IREG (IRON REGULATED/ferroportin) family of genes plays vital roles in regulating the homeostasis of iron and conferring metal stress. This study aims to identify soybean IREG family genes and characterize the function of GmIREG3 in conferring tolerance to aluminum stress. Bioinformatics and expression analyses were conducted to identify six soybean IREG family genes. One GmIREG, whose expression was significantly enhanced by aluminum stress, GmIREG3, was studied in more detail to determine its possible role in conferring tolerance to such stress. In total, six potential IREG-encoding genes with the domain of Ferroportin1 (PF06963) were characterized in the soybean genome. Analysis of the GmIREG3 root tissue expression patterns, subcellular localizations, and root relative elongation and aluminum content of transgenic Arabidopsis overexpressing GmIREG3 demonstrated that GmIREG3 is a tonoplast localization protein that increases transgenic Arabidopsis aluminum resistance but does not alter tolerance to Co and Ni. The systematic analysis of the GmIREG gene family reported herein provides valuable information for further studies on the biological roles of GmIREGs in conferring tolerance to metal stress. GmIREG3 contributes to aluminum resistance and plays a role similar to that of FeIREG3. The functions of other GmIREG genes need to be further clarified in terms of whether they confer tolerance to metal stress or other biological functions.

Cytokinin-dependent regulatory module underlies the maintenance of zinc nutrition in rice

Zinc (Zn) deficiency is a critical problem in human nutrition. Rice is the main source of calories for nearly half the world's population but has the shortcoming, from a nutritional perspective, of being low in Zn and other essential nutrients. Here we performed analyses with cytokinin-related mutants and transgenic lines to provide unequivocal evidence that cytokinins have a key role in controlling Zn status in plants. Transporters responsible for Zn uptake and chelators for the internal transport of Zn were strictly controlled by cytokinins. Moreover, cytokinin metabolism was regulated in a highly dynamic way in response to Zn status, which allows rice to adapt to heterogeneous Zn availability. Subsequently, fine-tuning of cytokinin metabolism by root-specific expression of a cytokinin degradation enzyme was able to improve both Zn nutrient and yield traits. Importantly, X-ray fluorescence imaging revealed that the increased Zn was broadly distributed from the aleurone layer to the inner endosperm. These findings show that metabolic control of cytokinin could provide the key to breeding Zn-enriched rice.

Bioimaging of multiple elements by high-resolution LA-ICP-MS reveals altered distribution of mineral elements in the nodes of rice mutants

Inter-vascular transfer in rice (Oryza sativa) nodes is required for delivering mineral elements to developing tissues, which is mediated by various transporters in the nodes. However, the effect of these transporters on distribution of mineral elements in the nodes at a cellular level is still unknown. Here, we established a protocol for bioimaging of multiple elements at a cellular level in rice node by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), and compared the mineral distribution profile between wild-type (WT) rice and mutants. Both relative comparison of mineral distribution normalized by endogenous ¹³ C and quantitative analysis using spiked standards combined with soft ablation gave valid results. Overall, macro-nutrients such as K and Mg were accumulated more in the phloem region, while micro-nutrients such as Fe and Zn were highly accumulated at the inter-vascular tissues of the node. In mutants of nodal Zn transporter OsHMA2, Zn localization pattern in the node tissues did not differ from that of WT; however, Zn accumulation in the inter-vascular tissues was lower in uppermost node I but higher in the third upper node III compared with the WT. In contrast, Si deposition in the mutants of three nodal Si transporters Lsi2, Lsi3 and Lsi6 showed different patterns, which are consistent with the localization of these transporters. This improved LA-ICP-MS analysis combined with functional characterization of transporters will provide further insight into mineral element distribution mechanisms in rice and other plant species.

Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq

BACKGROUND

Cadmium (Cd) is a widespread toxic heavy metal pollutant in agricultural soil, and Cd accumulation in rice grains is a major intake source of Cd for Asian populations that adversely affect human health. However, the molecular mechanism underlying Cd uptake, translocation and accumulation has not been fully understood in rice plants.

RESULTS

In this study, a mutant displaying extremely low Cd accumulation (lcd1) in rice plant and grain was generated by EMS mutagenesis from indica rice cultivar 9311 seeds. The candidate SNPs associated with low Cd accumulation phenotype in the lcd1 mutant were identified by MutMap and the transcriptome changes between lcd1 and WT under Cd exposure were analyzed by RNA-seq. The lcd1 mutant had lower Cd uptake and accumulation in rice root and shoot, as well as less growth inhibition compared with WT in the presence of 5 μM Cd. Genetic analysis showed that lcd1 was a single locus recessive mutation. The SNP responsible for low Cd accumulation in the lcd1 mutant located at position 8,887,787 on chromosome 7, corresponding to the seventh exon of OsNRAMP5. This SNP led to a Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 in the lcd1 mutant. A total of 1208 genes were differentially expressed between lcd1 and WT roots under Cd exposure, and DEGs were enriched in transmembrane transport process GO term. Increased OsHMA3 expression probably adds to the effect of OsNRAMP5 mutation to account for the significant decreases in Cd accumulation in rice plant and grain of the lcd1 mutant.

CONCLUSIONS

An extremely low Cd mutant lcd1 was isolated and identified using MutMap and RNA-seq. A Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 is likely responsible for low Cd accumulation in the lcd1 mutant. This work provides more insight into the mechanism of Cd uptake and accumulation in rice, and will be helpful for developing low Cd accumulation rice by marker-assisted breeding.

A Missing Link in Radial Ion Transport: Ion Transporters in the Endodermis

In higher plants, roots have important functions, such as the acquisition of water and ions, as well as transportation into the aerial parts of the plant via the xylem vessels. Radial ion transport in the root is strongly regulated in the endodermis, which is characterized by the presence of the Casparian strip (CS) and suberin lamellae. Although tremendous progress has been made with regard to the ion transporters and endodermal cells, little is known about the relationship between the ion transporters in the endodermis and ion homeostasis in aboveground tissues. This review summarizes the current knowledge about the location of the ion transporters (or channels) in the endodermis. We mainly discuss the effects of mutants related to the CS and/or suberin formation on the role of endodermal ion transporters in ion homeostasis. We also wish to emphasize the critical role of endodermal ion transporters in the regulation of radial ion transport in the root.

Molecular processes in iron and zinc homeostasis and their modulation for biofortification in rice

More than a billion people suffer from iron or zinc deficiencies globally. Rice (Oryza sativa L.) iron and zinc biofortification; i.e., intrinsic iron and zinc enrichment of rice grains, is considered the most effective way to tackle these deficiencies. However, rice iron biofortification, by means of conventional breeding, proves difficult due to lack of sufficient genetic variation. Meanwhile, genetic engineering has led to a significant increase in the iron concentration along with zinc concentration in rice grains. The design of impactful genetic engineering biofortification strategies relies upon vast scientific knowledge of precise functions of different genes involved in iron and zinc uptake, translocation and storage. In this review, we present an overview of molecular processes controlling iron and zinc homeostasis in rice. Further, the genetic engineering approaches adopted so far to increase the iron and zinc concentrations in polished rice grains are discussed in detail, highlighting the limitations and/or success of individual strategies. Recent insight suggests that a few genetic engineering strategies are commonly utilized for elevating iron and zinc concentrations in different genetic backgrounds, and thus, it is of great importance to accumulate scientific evidence for diverse genetic engineering strategies to expand the pool of options for biofortifying farmer-preferred cultivars.

Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.

OsMTP11, a trans-Golgi network localized transporter, is involved in manganese tolerance in rice

Metal tolerance proteins (MTPs) belong to the cation diffusion facilitator family (CDF) and have been implicated in metal transport and homeostasis in different plant species. Here we report on the rice gene OsMTP11 that encodes a putative CDF transporter that is homologous to members of the Mn-CDF cluster. The expression of OsMTP11 was found to enhance Mn tolerance in the Mn-sensitive yeast mutant pmr1. Knockdown of OsMTP11 resulted in growth inhibition in the presence of high concentrations of Mn, and also led to increased accumulation of Mn in the shoots and roots. The overexpression of OsMTP11 was found to enhance Mn tolerance in rice, and under supplementation with a toxic level of Mn, decreased Mn concentration was observed in the shoots and roots. Subcellular localization in rice protoplasts and tobacco epidermal cells revealed that OsMTP11 localizes to the trans-Golgi network (TGN), and a significant relocalization to the plasma membrane can be triggered by high extracellular Mn in tobacco epidermal cells. These findings suggest that OsMTP11 is a TGN-localized Mn transporter that is required for Mn homeostasis and contributes towards Mn tolerance in rice.

Decreasing arsenic accumulation in rice by overexpressing OsNIP1;1 and OsNIP3;3 through disrupting arsenite radial transport in roots

Rice is a major dietary source of the toxic metalloid arsenic. Reducing arsenic accumulation in rice grain is important for food safety. We generated transgenic rice overexpressing two aquaporin genes, OsNIP1;1 and OsNIP3;3, under the control of a maize ubiquitin promoter or the rice OsLsi1 promoter, and tested the effect on arsenite uptake and translocation. OsNIP1;1 and OsNIP3;3 were highly permeable to arsenite in Xenopus oocyte assays. Both transporters were localized at the plasma membrane. Knockout of either gene had little effect on arsenite uptake or translocation. Overexpression of OsNIP1;1 or OsNIP3;3 in rice did not affect arsenite uptake but decreased root-to-shoot translocation of arsenite and shoot arsenic concentration markedly. The overexpressed OsNIP1;1 and OsNIP3;3 proteins were localized in all root cells without polarity. Expression of OsNIP1;1 driven by the OsLsi1 promoter produced similar effects. When grown in two arsenic-contaminated paddy soils, overexpressing lines contained significantly lower arsenic concentration in rice grain than the wild-type without compromising plant growth or the accumulation of essential nutrients. Overexpression of OsNIP1;1 or OsNIP3;3 provides a route for arsenite to leak out of the stele, thus restricting arsenite loading into the xylem. This strategy is effective in reducing arsenic accumulation in rice grain.