Rapid characterization of plant mutants with an altered ion-profile: a case study using Lotus japonicus

Beneficial or detrimental? How nickel application alters the ionome of soybean plants

The use of nickel (Ni) in agriculture may represent one of the most significant cases of plant hormesis ever reported, as plants exhibit both positive and negative responses depending on the level of exposure to this element. For a more comprehensive understanding of this effect, the next step is to conduct studies on the dynamics of pre-existing chemical elements in the system (ionomic profile), especially when introducing Ni as a novel nutrient for the plants. This micronutrient is of particular interest to the fertilization of leguminous plants, such as the soybean, due to its additional effects on the biological nitrogen fixation process. This study thus evaluated the influence of five doses of Ni (0.0, 0.5, 1.0, 3.0, and 9.0 mg of Ni kg-1) on the ionomic profile of soybean genotypes using modern quantification techniques. The results revealed that the addition of Ni reduced the concentration of cationic micronutrients manganese (Mn), iron (Fe), zinc (Zn), and copper (Cu), while it increased the concentration of macronutrients nitrogen (N) and magnesium (Mg). The application of Ni also resulted in a reduction of the potentially toxic element aluminum (Al). Correlations were also observed for these elements, indicating that Ni could be a controlling agent in elemental absorption and translocation. The ionome of the leaf tissues exhibited the most significant alterations, followed by the grains, nodules, and roots. Exogenous agronomic doses of Ni proved beneficial for the growth and production of soybean plants, although a genotypic effect was observed. The treatment with 9.0 mg of Ni kg-1, resulted in a new ionomic profile related to toxicity, demonstrating suboptimal plant development. Thus, the application of Ni in appropriate doses had a significant impact on the ionomic profile of soybeans, improving plant development and implying resistance to potentially toxic elements such as Al.

Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes

The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.

Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.

Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.)

KEY MESSAGE

Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.

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.

Glucose modulates copper induced changes in photosynthesis, ion uptake, antioxidants and proline in Cucumis sativus plants

Glucose is recognized as signaling molecule that regulates growth and development of plants under various environmental cues, but their effect in regulation of copper induced toxicity in plants is not yet investigated. This study revealed the effect of exogenously sourced glucose on Cucumber plants exposed to increasing concentration of copper. Glucose mediated response on growth performance, photosynthetic efficiency, antioxidant enzymes, oxidative stress markers, ion uptake were analyzed in the presence and absence of copper. Glucose alone and in combination with lower concentration of copper improved the growth, photosynthetic performance, and antioxidant capacity of cucumber plants. However, higher concentrations of copper alone showed oxidative damage through increased electrolyte leakage, H₂O₂ accumulation, lipid peroxidation and reduced uptake of macronutrients. Application of glucose to copper-stressed plants enhanced activities of Rubisco, antioxidant enzymes, proline accumulation and maintained copper level in aerial parts of plants. These enhanced activities of antioxidant enzymes, proline accumulation, uptake of NPK and maintained equilibrium of copper in plants, leading to detoxification of copper stress in cucumber plants. This study provides an understanding that exogenous application of glucose can be employed as vital biochemical approach in alleviating copper-induced toxicity and could be utilized as phytoremediation technique for removal of excess transition metal from polluted soil.

Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective

For several decades, researchers are working toward improving the "major" crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing "integrating omics" for gaining a better understanding of crops' response to abiotic and biotic stresses.

The guard cell ionome: Understanding the role of ions in guard cell functions

The ionome is critical for plant growth, productivity, defense, and it eventually affects human food quantity and quality. Located on the leaf surface, stomatal guard cells are critical gatekeepers for water, gas, and pathogens. Insights form ionomics (metallomics) is imperative as we enter an omics-driven systems biology era where an understanding of guard cell function and physiology is advanced through efforts in genomics, transcriptomics, proteomics, and metabolomics. While the roles of major cations (K, Ca) and anions (Cl) are well known in guard cell function, the related physiology, movement and regulation of trace elements, metal ions, and heavy metals are poorly understood. The majority of the information on the role of trace elements in guard cells emanates from classical feeding experiments, field or in vitro fortification, micropropagation, and microscopy studies, while novel insights are available from limited metal ion transporter and ion channel studies. Given the rejuvenated and recent interest in the constantly changing ionome in plant mineral balance and eventually in human nutrition and health, we looked into the far from established guard cell ionome in lieu of the modern omics era of high throughput research endeavors. Newer technologies and tools i.e., high resolution mass spectrometry, advanced imaging, and phenomics are now available to delve into the guard cell ionomes. In this review, research efforts on guard cell ionomes were collated and categorized, and we highlight the underlying role of the largely unknown ionome in guard cell function towards a systems physiology understanding of plant health and productivity.

Multivariate Analysis of the Cotton Seed Ionome Reveals a Shared Genetic Architecture

To mitigate the effects of heat and drought stress, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in a hot, arid environment. The elemental concentrations (ionome) of seed samples from the population were profiled in addition to those of soil samples taken from throughout the field site to better model environmental variation. The elements profiled in seeds exhibited moderate to high heritabilities, as well as strong phenotypic and genotypic correlations between elements that were not altered by the imposed irrigation regimes. Quantitative trait loci (QTL) mapping results from a Bayesian classification method identified multiple genomic regions where QTL for individual elements colocalized, suggesting that genetic control of the ionome is highly interrelated. To more fully explore this genetic architecture, multivariate QTL mapping was implemented among groups of biochemically related elements. This analysis revealed both additional and pleiotropic QTL responsible for coordinated control of phenotypic variation for elemental accumulation. Machine learning algorithms that utilized only ionomic data predicted the irrigation regime under which genotypes were evaluated with very high accuracy. Taken together, these results demonstrate the extent to which the seed ionome is genetically interrelated and predictive of plant physiological responses to adverse environmental conditions.

Variations in nutrient and trace element composition of rice in an organic rice-frog coculture system

Introducing frogs into paddy fields can control pests and diseases, and organic farming can improve soil fertility and rice growth. The aim of this 2-year field study was compare the yield and elemental composition of rice between an organic farming system including frogs (ORF) and a conventional rice culture system (CR). The grain yields were almost the same in the ORF system and the CR system. The ORF significantly increased the contents of phosphorus (P), ion (Fe), zinc (Zn), molybdenum (Mo) and selenium (Se) in rice grain at one or both years. However, the ORF system decreased the calcium (Ca) content in grice grains, and increased the concentration of cadmium, which is potentially toxic. A principal components analysis showed the main impacts of ORF agro-ecosystem on the rice grain ionome was to increase the concentration of P and trace metal(loid)s. The results showed that the ORF system is an ecologically, friendly strategy to avoid excessive use of chemical fertilizers, herbicides and pesticides without decreasing yields, and to improve the nutritional status of rice by increasing the micronutrient contents. The potential risks of increasing Cd contents in rice grain should be addressed if this cultivation pattern is used in the long term.

LjMOT1, a high-affinity molybdate transporter from Lotus japonicus, is essential for molybdate uptake, but not for the delivery to nodules

Molybdenum (Mo) is an essential nutrient for plants, and is required for nitrogenase activity of legumes. However, the pathways of Mo uptake from soils and then delivery to the nodules have not been characterized in legumes. In this study, we characterized a high-affinity Mo transporter (LjMOT1) from Lotus japonicus. Mo concentrations in an ethyl methanesulfonate-mutagenized line (ljmot1) decreased by 70-95% compared with wild-type (WT). By comparing the DNA sequences of four AtMOT1 homologs between mutant and WT lines, one point mutation was found in LjMOT1, which altered Trp²⁹² to a stop codon; no mutation was found in the other homologous genes. The phenotype of Mo concentrations in F₂ progeny from ljmot1 and WT crosses were associated with genotypes of LjMOT1. Introduction of endogenous LjMOT1 to ljmot1 restored Mo accumulation to approximately 60-70% of the WT. Yeast expressing LjMOT1 exhibited high Mo uptake activity, and the K_m was 182 nm. LjMOT1 was expressed mainly in roots, and its expression was not affected by Mo supply or rhizobium inoculation. Although Mo accumulation in the nodules of ljmot1 was significantly lower than that of WT, it was still high enough for normal nodulation and nitrogenase activity, even for cotyledons-removed ljmot1 plants grown under low Mo conditions, in this case the plant growth was significantly inhibited by Mo deficiency. Our results suggest that LjMOT1 is an essential Mo transporter in L. japonicus for Mo uptake from the soil and growth, but is not for Mo delivery to the nodules.

Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit

BACKGROUND

Mineral nutrient uptake and utilisation by plants are controlled by many traits relating to root morphology, ion transport, sequestration and translocation. The aims of this study were to determine the phenotypic diversity in root morphology and leaf and seed mineral composition of a polyploid crop species, Brassica napus L., and how these traits relate to crop habit. Traits were quantified in a diversity panel of up to 387 genotypes: 163 winter, 127 spring, and seven semiwinter oilseed rape (OSR) habits, 35 swede, 15 winter fodder, and 40 exotic/unspecified habits. Root traits of 14 d old seedlings were measured in a 'pouch and wick' system (n = ~24 replicates per genotype). The mineral composition of 3-6 rosette-stage leaves, and mature seeds, was determined on compost-grown plants from a designed experiment (n = 5) by inductively coupled plasma-mass spectrometry (ICP-MS).

RESULTS

Seed size explained a large proportion of the variation in root length. Winter OSR and fodder habits had longer primary and lateral roots than spring OSR habits, with generally lower mineral concentrations. A comparison of the ratios of elements in leaf and seed parts revealed differences in translocation processes between crop habits, including those likely to be associated with crop-selection for OSR seeds with lower sulphur-containing glucosinolates. Combining root, leaf and seed traits in a discriminant analysis provided the most accurate characterisation of crop habit, illustrating the interdependence of plant tissues.

CONCLUSIONS

High-throughput morphological and composition phenotyping reveals complex interrelationships between mineral acquisition and accumulation linked to genetic control within and between crop types (habits) in B. napus. Despite its recent genetic ancestry (<10 ky), root morphology, and leaf and seed composition traits could potentially be used in crop improvement, if suitable markers can be identified and if these correspond with suitable agronomy and quality traits.

Analysis of Ionomic Profiles of Canine Hairs Exposed to Lipopolysaccharide (LPS)-Induced Stress

The purpose of this study was to provide a new insight on the response of canines to stress exposure; the ionomic profiles of canine hair (2.8 ± 0.3 years, 15.17 ± 2.1 kg) (n = 10) was determined before and after lipopolysaccharide (LPS) injections. LPS was intramuscularly injected to induce inflammatory stress responses which were confirmed by observing increases in the level of serum cortisol, aldosterone, and inflammatory cytokines such as IL-6, IL-1β, and TNF-α. The hair contents of 17 elements were obtained by applying analytical procedures using the inductively coupled plasma mass spectrometry (ICP-MS). The following elements: sodium(Na) and potassium(K) among macro-elements, iron(Fe) and manganese(Mn) among micro-elements, and aluminum(Al), nickel(Ni), and lead(Pb) for toxic elements, showed significant increased levels with the immunological stress. The degree of increase in toxic elements was remarkable with the stress exposure. A forty-five-fold increase seen in Al accumulation with the stress exposure was noteworthy. Although mercury(Hg) and cadmium(Cd) showed decreased levels with the stress exposure, the degree was negligible compared to the level of increase. Correlation pattern between the elements was changed with the immunological stress. Toxic elements became more correlated with macro- or micro-elements than with toxic elements themselves after the stress exposure. Principal component analysis (PCA) showed that LPS challenge shifted the overall hair mineral profiles to a consistent direction changing Al and K up, even in animals with different hair mineral profiles before LPS treatment. In conclusion, the multivariate data processing and study of element distribution patterns provided new information about the ionomic response of the canine hairs to immunological stress, i.e., the ionomic profiles of canine hairs is strongly affected by the stress induced by LPS injections.

Plant Ionomics: From Elemental Profiling to Environmental Adaptation

Ionomics is a high-throughput elemental profiling approach to study the molecular mechanistic basis underlying mineral nutrient and trace element composition (also known as the ionome) of living organisms. Since the concept of ionomics was first introduced more than 10 years ago, significant progress has been made in the identification of genes and gene networks that control the ionome. In this update, we summarize the progress made in using the ionomics approach over the last decade, including the identification of genes by forward genetics and the study of natural ionomic variation. We further discuss the potential application of ionomics to the investigation of the ecological functions of ionomic alleles in adaptation to the environment.

Application of ionomics to plant and soil in fields under long-term fertilizer trials

Ionomics is the study of elemental accumulation in living organisms using high-throughput elemental profiling. In the present study, we examined the ionomic responses to nutrient deficiency in maize grown in the field in long-term fertilizer trials. Furthermore, the available elements in the field soils were analyzed to investigate their changes under long-term fertilizer treatment and the ionomic relationships between plant and soil. Maize was cultivated in a field with the following five long-term fertilizer treatments: complete fertilization, fertilization without nitrogen, without phosphorus, without potassium, and no fertilization. Concentrations of 22 elements in leaves at an early flowering stage and in soils after harvest were determined. The fertilizer treatments changed the availabilities of many elements in soils. For example, available cesium was decreased by 39 % and increased by 126 % by fertilizations without nitrogen and potassium, respectively. Effects of treatments on the ionome in leaves were evaluated using the translocation ratio (the concentration in leaves relative to the available concentration in soils) for each element. Nitrogen deficiency specifically increased the uptake ability of molybdenum, which might induce the enhancement of nitrogen assimilation and/or endophytic nitrogen fixation in plant. Potassium deficiency drastically enhanced the uptake ability of various cationic elements. These elements might act as alternatives to K in osmoregulation and counterion of organic/inorganic anions. Two major groups of elements were detected by multivariate analyses of plant ionome. Elements in the same group may be linked more or less in uptake and/or translocation systems. No significant correlation between plant and soil was found in concentrations of many elements, even though various soil extraction methods were applied, implying that the interactions between the target and other elements in soil must be considered when analyzing mineral dynamics between plant and soil.

Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits?

It has been more than 10 years since the concept of the ionome, all of the mineral nutrients in a cell tissue or organism, was introduced. In the intervening years, ionomics, high throughput elemental profiling, has been used to analyse over 400,000 samples from at least 10 different organisms. There are now multiple published examples where an ionomics approach has been used to find genes of novel function, find lines or environments that produce foods with altered nutritional profiles, or define gene by environmental effects on elemental accumulation. In almost all of these studies, the ionome has been treated as a collection of independent elements, with the analysis repeated on each measured element. However, many elements share chemical properties, are known to interact with each other, or have been shown to have similar interactions with biological molecules. Accordingly, there is strong evidence from ionomic studies that the elements of the ionome do not behave independently and that combinations of elements should be treated as the phenotypes of interest. In this review, I will consider the evidence that we have for the interdependence of the ionome, some of its causes, methods for incorporating this interdependence into analyses and the benefits, drawbacks, and challenges of taking these approaches.

Genetics- and genomics-based interventions for nutritional enhancement of grain legume crops: status and outlook

Meeting the food demands and ensuring nutritional security of the ever increasing global population in the face of degrading natural resource base and impending climate change is the biggest challenge of the twenty first century. The consequences of mineral/micronutrient deficiencies or the hidden hunger in the developing world are indeed alarming and need urgent attention. In addressing the problems associated with mineral/micronutrient deficiency, grain legumes as an integral component of the farming systems in the developing world have to play a crucial role. For resource-poor populations, a strategy based on selecting and/or developing grain legume cultivars with grains denser in micronutrients, by biofortification, seems the most appropriate and attractive approach to address the problem. This is evident from the on-going global research efforts on biofortification to provide nutrient-dense grains for use by the poorest of the poor in the developing countries. Towards this end, rapidly growing genomics technologies hold promise to hasten the progress of breeding nutritious legume crops. In conjunction with the myriad of expansions in genomics, advances in other 'omics' technologies particularly plant ionomics or ionome profiling open up novel opportunities to comprehensively examine the elemental composition and mineral networks of an organism in a rapid and cost-effective manner. These emerging technologies would effectively guide the scientific community to enrich the edible parts of grain legumes with bio-available minerals and enhancers/promoters. We believe that the application of these new-generation tools in turn would provide crop-based solutions to hidden hunger worldwide for achieving global nutritional security.

Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions

The concentrations of mineral nutrients in seeds are critical to both the life cycle of plants as well as human nutrition. These concentrations are strongly influenced by soil conditions, as shown here by quantifying the concentration of 14 elements in seeds from Arabidopsis thaliana plants grown under four different soil conditions: standard, or modified with NaCl, heavy metals, or alkali. Each of the modified soils resulted in a unique change to the seed ionome (the mineral nutrient content of the seeds). To help identify the genetic networks regulating the seed ionome, changes in elemental concentrations were evaluated using mutants corresponding to 760 genes as well as 10 naturally occurring accessions. The frequency of ionomic phenotypes supports an estimate that as much as 11% of the A. thaliana genome encodes proteins of functional relevance to ion homeostasis in seeds. A subset of mutants were analyzed with two independent alleles, providing five examples of genes important for regulation of the seed ionome: SOS2, ABH1, CCC, At3g14280 and CNGC2. In a comparison of nine different accessions to a Col-0 reference, eight accessions were observed to have reproducible differences in elemental concentrations, seven of which were dependent on specific soil conditions. These results indicate that the A. thaliana seed ionome is distinct from the vegetative ionome, and that elemental analysis is a sensitive approach to identify genes controlling ion homeostasis, including those that regulate gene expression, phospho-regulation, and ion transport.

Ionomic profiling of Nicotiana langsdorffii wild-type and mutant genotypes exposed to abiotic stresses

To provide a new insight into the response of plants to abiotic stresses, the ionomic profiles of Nicotiana langsdorffii specimens have been determined before and after exposure to toxic metals (chromium) or drought conditions. The plants were genetically transformed with the rat glucocorticoid receptor (GR) or the gene for Agrobacterium rhizogenes rolC, because these modifications are known to produce an imbalance in phytohormone equilibria and a significant change in the defence response of the plant. Elemental profiles were obtained by developing and applying analytical procedures based on inductively coupled plasma atomic emission and mass spectrometry (ICP-AES/MS). In particular, the removal of isobaric interferences affecting the determination of Cr and V by ICP-MS was accomplished by use of a dynamic reaction cell, after optimization of the relevant conditions. The combined use of ICP atomic emission and mass spectrometry enabled the determination of 29 major and trace elements (Ba, Bi, Ca, Cd, Co, Cr, Cu, Eu, Fe, Ga, K, Li, Mg, Mn, Mo, Na, P, Pb, Pt, Rb, S, Sb, Sn, Sr, Te, V, W, Y, and Zn) in different parts of the plants (roots, stems, and leaves), with high accuracy and precision. Multivariate data processing and study of element distribution patterns provided new information about the ionomic response of the target organism to chemical treatment or water stress. Genetic modification mainly affected the distribution of Bi, Cr, Mo, Na, and S, indicating that these elements were involved in biochemical processes controlled by the GR or rolC genes. Chemical stress strongly affected accumulation of several elements (Ba, Ca, Fe, Ga, K, Li, Mn, Mo, Na, P, Pb, Rb, S, Sn, Te, V, and Zn) in different ways; for Ca, Fe, K, Mn, Na, and P the effect was quite similar to that observed in other studies after treatment with other transition elements, for example Cu and Cd. The effect of water deficit was less evident, mainly consisting in a decrease of Ba, Cr, Na, and Sr in roots.

Large-scale plant ionomics

Large-scale phenotyping methods are at the heart of efficiently deciphering the functions of genes and gene networks in the postgenomic era. In order to obtain meaningful results when comparing natural variants, and mutants and wild-types during large-scale quantitative analyses, necessary precautions must be employed throughout the whole process. Here, we describe large-scale elemental profiling in Arabidopsis thaliana and other genetic model organisms using high-throughput analytical methodologies. We also include a description of workflow management and data storage systems.

Plant nutrition for sustainable development and global health

BACKGROUND

Plants require at least 14 mineral elements for their nutrition. These include the macronutrients nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) and sulphur (S) and the micronutrients chlorine (Cl), boron (B), iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), nickel (Ni) and molybdenum (Mo). These are generally obtained from the soil. Crop production is often limited by low phytoavailability of essential mineral elements and/or the presence of excessive concentrations of potentially toxic mineral elements, such as sodium (Na), Cl, B, Fe, Mn and aluminium (Al), in the soil solution.

SCOPE

This article provides the context for a Special Issue of the Annals of Botany on 'Plant Nutrition for Sustainable Development and Global Health'. It provides an introduction to plant mineral nutrition and explains how mineral elements are taken up by roots and distributed within plants. It introduces the concept of the ionome (the elemental composition of a subcellular structure, cell, tissue or organism), and observes that the activities of key transport proteins determine species-specific, tissue and cellular ionomes. It then describes how current research is addressing the problems of mineral toxicities in agricultural soils to provide food security and the optimization of fertilizer applications for economic and environmental sustainability. It concludes with a perspective on how agriculture can produce edible crops that contribute sufficient mineral elements for adequate animal and human nutrition.

Ionomics: The functional genomics of elements

Ionomics is the study of elemental accumulation in living systems using high-throughput elemental profiling. This approach has been applied extensively in plants for forward and reverse genetics, screening diversity panels, and modeling of physiological states. In this review, I will discuss some of the advantages and limitations of the ionomics approach as well as the important parameters to consider when designing ionomics experiments, and how to evaluate ionomics data.

Ionomics: studying the social network of mineral nutrients

The accumulation of a given element is a complex process controlled by a network of gene products critical for uptake, binding, transportation, and sequestration. Many of these genes and physiological processes affect more than one element. Therefore, to understand how elements are regulated, it is necessary to measure as many of the elements contained in a cell, tissue, or organism (the ionome) as possible. The elements that share components of their network vary depending on the species and genotype of the plants that are studied and environment they are grown in. Several recent papers describe high-throughput elemental profiling studies of how the ionome responds to the environment or explores the genetics that control the ionome. When combined with new genotyping technologies, ionomics provides a rapid way to identify genes that control elemental accumulation in plants.

Physiological functions of beneficial elements

Aluminum (Al), cobalt (Co), sodium (Na), selenium (Se), and silicon (Si) are considered beneficial elements for plants: they are not required by all plants but can promote plant growth and may be essential for particular taxa. These beneficial elements have been reported to enhance resistance to biotic stresses such as pathogens and herbivory, and to abiotic stresses such as drought, salinity, and nutrient toxicity or deficiency. The beneficial effects of low doses of Al, Co, Na and Se have received little attention compared to toxic effects that typically occur at higher concentrations. Better understanding of the effects of beneficial elements is important to improve crop productivity and enhance plant nutritional value for a growing world population.