Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thaliana

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar (Populus trichocarpa). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

The crucial elements for lettuce (Lactuca sativa L.) growth under DMA stress and the linkage with DMA behavior: A new application of ionome

Dimethylarsinic acid (DMA) is one of the common arsenic (As) species present in soil and is more toxic to plants than others. Identifying the crucial elements for plant growth under DMA stress is essential to enhance plant tolerance to DMA. Herein, we provided for the first time an ionome-based approach to address this issue. The phenotype, As species and concentrations of 11 essential elements in lettuce tissues were monitored under exposures of 0.1, 0.5, 1, 2, 5 mg L-1 DMA in hydroponic culture for 32 days. Lettuces remained normal (no significant difference in phenotype from the control) under 0.1-2 mg L-1 DMA stress, and were inhibited with fresh weights of leaf and root under 5 mg L-1 DMA stress. Integrating the difference in ionome profiles between the two growth states (normal and inhibited) and the responses of the individual element, Mg and S were clarified as the most possible candidates for the crucial elements for lettuce growth under DMA stress. Under 5 mg L-1 DMA stress, the accumulation of Mg and S declined, yet their BCF values were significantly increased, which was consistent with the change in BCF of DMA. Based on the physiological functions of Mg and S and the toxicity of DMA, it could be inferred that the enhanced transfer of Mg and S to leaves should be induced by the potential damage caused by the increased DMA accumulation in leaves, and would result in a shortage of both elements in roots as well as the growth inhibition.

Genetic analysis of the variation for mineral accumulation in the leaves and seeds of natural germplasm of Brassica rapa L. (AA) and the its derived forms extracted from an allotetraploid B.juncea L.(AABB)

Brassica rapa L. (2n = 20; AA) is a vegetable and oilseed crop that is grown all over the world. Its leaves, shoots, and seeds store significant amounts of minerals. We used inductively coupled plasma-optical emission spectroscopy (ICP-OES) to determine the concentrations of eleven minerals in the leaves and seeds of 195 advanced generation inbred lines, of which 92 represented natural (NR) B. rapa and the remaining 103 were derived (DR) from a set of mother genotypes originally extracted from an allotetraploid B. juncea (2n = 36; AABB). The inbred lines differed for the composition of leaf and seed minerals. Leaf concentrations of N, K, Zn, and Se were higher in the DR subpanel as compared to NR subpanel, along with high seed accumulations of K and Se. DArT genotyping and genome wide association mapping led to the identification of SNPs associated with leaf and seed mineral compositions. Chromosomes A03, A05, and A10 harboured the most associated loci. Annotations of the regions adjacent to respective GWAS peaks allowed prediction of genes known for acquisition, transport, and accumulation of minerals and heavy metal detoxification. Transcriptome analysis revealed differential expression patterns of the predicted candidates, with most genes either down-regulated in derived genotypes relative to natural forms or their expression being comparable between the two. General downregulation may be a consequence of extracting B. rapa from allotetraploid B. juncea through genome resection. Some of the identified SNPs may be used as DNA markers for breeding programmes designed to modify the leaf and seed mineral compositions.

Natural variation of nutrient homeostasis among laboratory and field strains of Chlamydomonas reinhardtii

Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macronutrients have a wide range of functions in photosynthetic organisms, and mineral nutrition thus plays a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, 24 Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared with autotrophy and nine deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, and -S) and micronutrients (-Cu, -Fe, -Mn, and -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.

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.

Transient Nutrient Deficiencies in Pea: Consequences on Nutrient Uptake, Remobilization, and Seed Quality

Legume plants, such as peas, are of significant nutritional interest for both humans and animals. However, plant nutrition and thus, seed composition, depends on soil mineral nutrient availability. Understanding the impact of their deprivation on the plant mineral nutrient content, net uptake, and remobilization is of key importance but remains complex as the elements of the plant ionome are linked in intricate networks, one element deprivation impacting uptake and remobilization of other nutrients. To get a better insight into pea mineral nutrition, the transitory deprivations of 13 mineral nutrients were imposed during the vegetative growth phase. Thereafter, plants were grown under optimal mineral conditions until physiological maturity. Plant nutritional status and seed quality impacts caused by the deprivations were characterized using measurement of mineral nutrient concentration and plant biomass allocation. Our results highlight: (i) the preferential allocation of dry weight and elements to shoots at the expense of the roots under non-limiting conditions, and more particularly to the tendrils in comparison to the other shoot organs, (ii) the positive and/or negative impact of one mineral nutrient deprivation on other elements of the ionome, (iii) four different remobilization strategies for eight mineral nutrients, and (iv) possible strategies to improve seed quality via fine control of fertilization during a period of mineral nutrient deficiency.

Potato biofortification: an effective way to fight global hidden hunger

Hidden hunger is leading to extensive health problems in the developing world. Several strategies could be used to reduce the micronutrient deficiencies by increasing the dietary uptake of essential micronutrients. These include diet diversification, pharmaceutical supplementation, food fortification and crop biofortification. Among all, crop biofortification is the most sustainable and acceptable strategy to overcome the global issue of hidden hunger. Since most of the people suffering from micronutrient deficiencies, have monetary issues and are dependent on staple crops to fulfil their recommended daily requirements of various essential micronutrients. Therefore, increasing the micronutrient concentrations in cost effective staple crops seems to be an effective solution. Potato being the world's most consumed non-grain staple crop with enormous industrial demand appears to be an ideal candidate for biofortification. It can be grown in different climatic conditions, provide high yield, nutrition and dry matter in lesser time. In addition, huge potato germplasm have natural variations related to micronutrient concentrations, which can be utilized for its biofortification. This review discuss the current scenario of micronutrient malnutrition and various strategies that could be used to overcome it. The review also shed a light on the genetic variations present in potato germplasm and suggest effective ways to incorporate them into modern high yielding potato varieties.

Genomic analysis of ionome-related QTLs in Arabidopsis thaliana

Ionome contributes to maintain cell integrity and acts as cofactors for catalyzing regulatory pathways. Identifying ionome contributing genomic regions provides a practical framework to dissect the genetic architecture of ionomic traits for use in biofortification. Meta-QTL (MQTL) analysis is a robust method to discover stable genomic regions for traits regardless of the genetic background. This study used information of 483 QTLs for ionomic traits identified from 12 populations for MQTL analysis in Arabidopsis thaliana. The selected QTLs were projected onto the newly constructed genetic consensus map and 33 MQTLs distributed on A. thaliana chromosomes were identified. The average confidence interval (CI) of the drafted MQTLs was 1.30 cM, reduced eight folds from a mean CI of 10.88 cM for the original QTLs. Four MQTLs were considered as stable MQTLs over different genetic backgrounds and environments. In parallel to the gene density over the A. thaliana genome, the genomic distribution of MQTLs over the genetic and physical maps indicated the highest density at non- and sub-telomeric chromosomal regions, respectively. Several candidate genes identified in the MQTLs intervals were associated with ion transportation, tolerance, and homeostasis. The genomic context of the identified MQTLs suggested nine chromosomal regions for Zn, Mn, and Fe control. The QTLs for potassium (K) and phosphorus (P) were the most frequently co-located with Zn (78.3%), Mn (76.2%), and Fe (88.2% and 70.6%) QTLs. The current MQTL analysis demonstrates that meta-QTL analysis is cheaper than, and as informative as genome-wide association study (GWAS) in refining the known QTLs.

GWAS with a PCA uncovers candidate genes for accumulations of microelements in maize seedlings

Microelements are necessary for plant growth and development, they control key processes of physiological metabolism. Herein, we evaluated three accumulation-related performances for each of the four microelements (Fe, Zn, Cu, and Mn) among 305 inbred maize lines. Quantification of these microelements in maize roots and shoots revealed abundant phenotypic variations in the association panel, with the variation coefficients ranging from 0.31 to 0.76. Principal component analysis (PCA) of the three related traits (concentration in root, concentration in shoot, and transport coefficient) showed that PC1 and PC2 explained >95% of phenotypic variations for each element. The scores of PC1 and PC2 were thereby used for a genome-wide association study by combining 44,134 SNPs of this panel. A total of 27, 1, 5, and 3 SNPs were significantly (P < .05) associated with Zn-PC1, Zn-PC2, Cu-PC1, and Mn-PC2, respectively, with 11 genes closely linked (r²  > 0.8) to these SNPs. Of them, GRMZM2G142870, GRMZM2G045531, and GRMZM2G143512 were individually annotated as ABC transporter C family member 14, zinc transporter 3, and heavy metal ATPase10. A candidate gene association analysis further verified that GRMZM2G142870 and GRMZM2G045531 affect Zn and Mn accumulations, respectively. Evaluation of contrasting allele ratios in elite lines indicated that the majority of the alleles correlating with higher Zn or Cu had not been utilized in maize breeding. Integration of more "higher-accumulation" alleles in the elite lines will be practical for improving Zn and Cu accumulations in maize. Our findings contribute to genetic revelation and molecular marker-assisted selection of microelement accumulations in maize.

Investigation of Genotype by Environment Interactions for Seed Zinc and Iron Concentration and Iron Bioavailability in Common Bean

Iron and zinc malnutrition are global public health concerns afflicting mostly infants, children, and women in low- and middle-income countries with widespread consumption of plant-based diets. Common bean is a widely consumed staple crop around the world and is an excellent source of protein, fiber, and minerals including iron and zinc. The development of nutrient-dense common bean varieties that deliver more bioavailable iron and zinc with a high level of trait stability requires a measurement of the contributions from genotype, environment, and genotype by environment interactions. In this research, we investigated the magnitude of genotype by environment interaction for seed zinc and iron concentration and seed iron bioavailability (FeBIO) using a set of nine test genotypes and three farmers' local check varieties. The research germplasm was evaluated for two field seasons across nine on-farm locations in three agro-ecological zones in Uganda. Seed zinc concentration ranged from 18.0 to 42.0 μg g^-1 and was largely controlled by genotype, location, and the interaction between location and season [28.0, 26.2, and 14.7% of phenotypic variability explained (PVE), respectively]. Within a genotype, zinc concentration ranged on average 12 μg g^-1 across environments. Seed iron concentration varied from 40.7 to 96.7 μg g^-1 and was largely controlled by genotype, location, and the interaction between genotype, location, and season (25.7, 17.4, and 13.7% of PVE, respectively). Within a genotype, iron concentration ranged on average 28 μg g^-1 across environments. Seed FeBIO ranged from 8 to 116% of Merlin navy control and was largely controlled by genotype (68.3% of PVE). The red mottled genotypes (Rozi Koko and Chijar) accumulated the most seed zinc and iron concentration, while the yellow (Ervilha and Cebo Cela) and white (Blanco Fanesquero) genotypes had the highest seed FeBIO and performed better than the three farmers' local check genotypes (NABE-4, NABE-15, and Masindi yellow). The genotypes with superior and stable trait performance, especially the Manteca seed class which combine high iron and zinc concentrations with high FeBIO, would serve as valuable parental materials for crop improvement breeding programs aimed at enhancing the nutritional value of the common bean.

Two chemically distinct root lignin barriers control solute and water balance

Lignin is a complex polymer deposited in the cell wall of specialised plant cells, where it provides essential cellular functions. Plants coordinate timing, location, abundance and composition of lignin deposition in response to endogenous and exogenous cues. In roots, a fine band of lignin, the Casparian strip encircles endodermal cells. This forms an extracellular barrier to solutes and water and plays a critical role in maintaining nutrient homeostasis. A signalling pathway senses the integrity of this diffusion barrier and can induce over-lignification to compensate for barrier defects. Here, we report that activation of this endodermal sensing mechanism triggers a transcriptional reprogramming strongly inducing the phenylpropanoid pathway and immune signaling. This leads to deposition of compensatory lignin that is chemically distinct from Casparian strip lignin. We also report that a complete loss of endodermal lignification drastically impacts mineral nutrients homeostasis and plant growth.

1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana

Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.

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.

The maize shoot ionome: Its interaction partners, predictive power, and genetic determinants

An improved understanding of how to manipulate the accumulation and enrichment of mineral elements in aboveground plant tissues holds promise for future resource efficient and sustainable crop production. The objectives of this study were to (a) evaluate the influence of Fe regimes on mineral element concentrations and contents in the maize shoot as well as their correlations, (b) examine the predictive ability of physiological and morphological traits of individual genotypes of the IBM population from the concentration of mineral elements, and (c) identify genetic factors influencing the mineral element composition within and across Fe regimes. We evaluated the concentration and content of 12 mineral elements in shoots of the IBM population grown in sufficient and deficient Fe regimes and found for almost all mineral elements a significant (α = 0.05) genotypic variance. Across all mineral elements, the variance of genotype*Fe regime interactions was on average even more pronounced. High prediction abilities indicated that mineral elements are powerful predictors of morphological and physiological traits. Furthermore, our results suggest that ZmHMA2/3 and ZmMOT1 are major players in the natural genetic variation of Cd and Mo concentrations and contents of maize shoots, respectively.

Natural variation on whole-plant form in the wild is influenced by multivariate soil nutrient characteristics: natural selection acts on root traits

PREMISE

In the complex soil nutrient environments of wild populations of annual plants, in general, low nutrient availability restricts growth and alters root-shoot relationships. However, our knowledge of natural selection on roots in field settings is limited. We sought to determine whether selection acts directly on root traits and to identify which components of the soil environment were potential agents of selection.

METHODS

We studied wild native populations of Arabidopsis thaliana across 4 years, measuring aboveground and belowground traits and analyzing soil nutrients. Using multivariate methods, we examined patterns of natural selection and identified soil attributes that contributed to whole-plant form. In a common garden experiment at two field sites with contrasting soil texture, we examined patterns of selection on root and shoot traits.

RESULTS

In wild populations, we uncovered selection for above- and belowground size and architectural traits. We detected variation through time and identified soil components that influenced fruit production. In the garden experiment, we detected a distinct positive selection for total root length at the site with greater water-holding capacity and negative selection for measures of root architecture at the field site with reduced nutrient availability and water holding capacity.

CONCLUSIONS

Patterns of natural selection on belowground traits varied through time, across field sites and experimental gardens. Simultaneous investigations of above- and belowground traits reveal trait functional relationships on which natural selection can act, highlighting the influence of edaphic features on evolutionary processes in wild annual plant populations.

Ionomic and transcriptomic analyses of two cotton cultivars (Gossypium hirsutum L.) provide insights into the ion balance mechanism of cotton under salt stress

Soil salinity is a major abiotic stress factor that limits cotton production worldwide. To improve salt tolerance in cotton, an in-depth understanding of ionic balance is needed. In this study, a pot experiment using three levels of soil salinity (0%, 0.2%, and 0.4%, represented as CK, SL, and SH, respectively) and two cotton genotypes (salt-tolerant genotype: L24; salt-sensitive genotype: X45) was employed to investigate how sodium chloride (NaCl) stress effects cotton growth, ion distribution, and transport, as well as to explore the related mechanism. The results showed that SL treatment mainly inhibited shoot growth, while SH treatment caused more extensive impairment to roots and shoots. The growth inhibition ratio of NaCl stress on X45 was more marked than that of L24. Under NaCl stress, the Na concentration in the roots, stems and leaves significantly increased, whereas the K, Cu, B, and Mo concentration in roots, as well as Mg and S concentrations in the leaves, significantly decreased. Under salt stress conditions, salt-tolerant cotton plants can store Na in the leaves, and as a result, a larger amount of minerals (e.g., Cu, Mo, Si, P, and B) tend to transport to the leaves. By contrast, salt-sensitive varieties tend to accumulate certain minerals (e.g., Ca, P, Mg, S, Mn, Fe, Cu, B, Mo, and Si) in the roots. Most genes related to ion transport and homeostasis were upregulated in L24, but not in X45. The expression level of GhSOS1 in X45 was higher than L24, but GhNHX1 in L24 was higher than X45. Our findings suggest that the two varieties response to salt stress differently; for X45 (salt-sensitive), the response is predominantly governed by Na+ efflux, whereas for L24 (salt-tolerant), vacuolar sequestration of Na+ is the major mechanism. The expression changes of the genes encoding the ion transporters may partially explain the genotypic difference in leaf ion accumulation under salt stress conditions.

Genetic mapping of ionomic quantitative trait loci in rice grain and straw reveals OsMOT1;1 as the putative causal gene for a molybdenum QTL qMo8

Rice is a major dietary source of essential mineral nutrients and toxic elements (aka ionome) for humans. However, the genetic basis underlying the variation in ionome is still largely unknown. Here, we mapped 51 and 61 quantitative trait loci (QTLs) controlling the concentrations of 13 and 15 elements in rice (Oryza sativa L.) grain and straw, respectively, using a recombinant inbred lines (RILs) that were grown at three different field sites in 3 years. Several QTLs were repeatedly detected in both grain and straw or in multiple years; the resulting 87 unique QTLs with 17 of them (20%) were co-localized with previously reported corresponding QTLs and 70 were novel ionomic QTLs. At least, 14 genomic clusters that controlled the concentrations of multiple elements were identified. Furthermore, we identified a molybdate transporter gene OsMOT1;1 as the putative causal gene for a QTL controlling molybdenum concentration in both straw and grain. QTL analyses based on the concentrations of multiple elements in both grain and straw of RIL population grown in three field sites in 3 years allow us to identify tissue common QTLs and reproducible QTLs that were validated in multiple years. The identification of ionomic QTLs will be useful in revealing the molecular mechanisms underlying the accumulation of elements in rice and providing the opportunity to reduce the accumulation of toxic elements and enrich the accumulation of beneficial elements in rice grain.

The Intensity of Manganese Deficiency Strongly Affects Root Endodermal Suberization and Ion Homeostasis

Manganese (Mn) deficiency affects various processes in plant shoots. However, the functions of Mn in roots and the processes involved in root adaptation to Mn deficiency are largely unresolved. Here, we show that the suberization of endodermal cells in barley (Hordeum vulgare) roots is altered in response to Mn deficiency, and that the intensity of Mn deficiency ultimately determines whether suberization increases or decreases. Mild Mn deficiency increased the length of the unsuberized zone close to the root tip, and increased the distance from the root tip at which the fully suberized zone developed. By contrast, strong Mn deficiency increased suberization closer to the root tip. Upon Mn resupply, suberization was identical to that seen on Mn-replete plants. Bioimaging and xylem sap analyses suggest that the reduced suberization in mildly Mn-deficient plants promotes radial Mn transport across the endodermis at a greater distance from the root tip. Less suberin also favors the inwards radial transport of calcium and sodium, but negatively affects the potassium concentration in the stele. During strong Mn deficiency, Mn uptake was directed toward the root tip. Enhanced suberization provides a mechanism to prevent absorbed Mn from leaking out of the stele. With more suberin, the inward radial transport of calcium and sodium decreases, whereas that of potassium increases. We conclude that changes in suberization in response to the intensity of Mn deficiency have a strong effect on root ion homeostasis and ion translocation.

Applications of Abscisic Acid and Increasing Concentrations of Calcium Affect the Partitioning of Mineral Nutrients between Tomato Leaf and Fruit Tissue

This study examined how abscisic acid (ABA) and calcium (Ca) concentrations in nutrient solution affect concentrations of mineral nutrients in tomato leaves and fruit. Tomato plants were grown in a greenhouse at 25/20 °C (day/night) under a 16 h photoperiod. Plants were treated with different concentrations of ABA and Ca. Calcium was applied via the irrigation lines at 60, 90, or 180 mg·L−1. ABA was applied as a combination of foliar sprays and root applications. For foliar ABA applications, treatments consisted of deionized (DI) water control (0.0 mg·L−1 ABA) or 500 mg·L−1 ABA. For ABA root applications, treatments consisted of no ABA control (0.0 mg·L−1 ABA) or 50 mg·L−1 ABA applied via the irrigation lines. Results indicate that mineral nutrient concentrations in tomato leaf and fruit tissue varied in connection with each exogenous application of ABA. Variability in mineral nutrient concentration depended on if ABA was applied to the leaf or root tissue. Additionally, increasing Ca treatment concentrations either decreased or did not change mineral nutrients in tomato and fruit tissue. Thus, tomato plants react to acquiring mineral nutrients in numerous mechanisms and, depending on how the applications of exogenous ABA are applied, can have varying effects on these mechanisms.

Survey of 17 elements, including rare earth elements, in chilled and non-chilled cauliflower cultivars

This study investigated if genetic diversity among cauliflower cultivars (white 'Xenia' F1, green 'Vitaverde' F1, purple 'Graffiti' F1, orange 'Sunset' F1, romanesco 'Celio' F1) and transplant chilling are reflected in the content of 17 elements in mature curds. Transplants at 40 days after sowing were exposed to 4 °C (chilling) and 18 °C (control) for 7 days and then planted in the field till harvest maturity. The lowest Ag, Al, Co, and Li contents were found in 'Celio' F1 cauliflower, which also had the highest Ba and Sr levels. Orange curds of 'Sunset' F1 were the richest in Al, and high in Li, Sc, and Sn. Chilling applied to the transplants increased Ag, Ba, Co, Sc, Sr, and Tb, and decreased the Y content of mature curds. Transplant chilling can permanently alter plant metabolism, and subsequently may affect the mineral composition of the curds.

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.

Identification of Novel Genomic Loci Associated with Soybean Shoot Tissue Macro- and Micronutrient Concentrations

The mineral composition of crop shoot tissues is important for yield formation and nutrient remobilization to seeds. The natural diversity that exists within crop species can be used to investigate mechanisms that define plant mineral composition and to identify important genomic loci for these processes. The objective of this study was to determine shoot mineral nutrient concentrations in genetically diverse soybean [ (L.) Merr.] genotypes and to identify genomic regions associated with concentrations of different nutrients in shoot tissue. The genotypes were grown at two locations in 2 yr and characterized for macronutrient (Ca, Mg, P, K, and S) and micronutrient (B, Cu, Fe, Mn, and Zn) concentrations in shoot tissues. Genome-wide association studies were conducted with 31,748 single nucleotide polymorphisms (SNPs) via a unified mixed model to identify SNPs associated with macro- and micronutrient concentrations. The number of putative loci identified for the macronutrients ranged from 11 for Ca to 20 for K. For the micronutrients, the number ranged from 10 for Mn to 24 for Fe. In addition to colocated loci for multiple nutrients, 22 individual SNPs were associated with more than one nutrient such that 11 different nutrient combinations were encompassed by these SNPs. Ultimately, the putative loci identified in this study will need to be confirmed and are expected to aid in the identification of new sources of variation for use in soybean breeding programs as well as for mechanistic studies aimed at understanding the regulation of mineral nutrient uptake, translocation, and shoot tissue concentrations.

Variation in the angiosperm ionome

The ionome is defined as the elemental composition of a subcellular structure, cell, tissue, organ or organism. The subset of the ionome comprising mineral nutrients is termed the functional ionome. A 'standard functional ionome' of leaves of an 'average' angiosperm, defined as the nutrient composition of leaves when growth is not limited by mineral nutrients, is presented and can be used to compare the effects of environment and genetics on plant nutrition. The leaf ionome of a plant is influenced by interactions between its environment and genetics. Examples of the effects of the environment on the leaf ionome are presented and the consequences of nutrient deficiencies on the leaf ionome are described. The physiological reasons for (1) allometric relationships between leaf nitrogen and phosphorus concentrations and (2) linear relationships between leaf calcium and magnesium concentrations are explained. It is noted that strong phylogenetic effects on the mineral composition of leaves of angiosperm species are observed even when sampled from diverse environments. The evolutionary origins of traits including (1) the small calcium concentrations of Poales leaves, (2) the large magnesium concentrations of Caryophyllales leaves and (3) the large sulphur concentrations of Brassicales leaves are traced using phylogenetic relationships among angiosperm orders, families and genera. The rare evolution of hyperaccumulation of toxic elements in leaves of angiosperms is also described. Consequences of variation in the leaf ionome for ecology, mineral cycling in the environment, strategies for phytoremediation of contaminated land, sustainable agriculture and the nutrition of livestock and humans are discussed.

Nutritional variation in baobab (Adansonia digitata L.) fruit pulp and seeds based on Africa geographical regions

Baobab (Adansonia digitata L.) is an indigenous fruit tree associated with the Savannah drylands of sub-Saharan Africa. Local communities mainly utilize the leaves, pulp, and seeds of baobab as a source of food and for income generation. The present study was conducted to determine the nutritive attributes of baobab fruit pulp and seeds across provenances in east, west, and southern Africa and to determine whether the nutrient content varied with the provenance of origin. Pulp and seed proximate composition and mineral element concentration were determined using the AOAC 1984 methods and inductively coupled plasma atomic emission spectroscopy (ICP-AES), respectively. The results showed that there exist significant variation (p < .05) in pulp moisture, protein, fiber, ash, and elemental content among provenances. The highest mean pulp crude fiber (8.68 g 100 g-1 dw) was recorded in Kenya. At country level, Malawi had the highest mean pulp potassium (22.2 mg g-1), calcium (4,300 mg kg-1), magnesium (2,300 mg kg-1), sodium (1,000 mg kg-1), and phosphorus (1,100 mg kg-1) levels. Kenya had the highest mean pulp iron (57.4 μg g-1) and manganese (27.2 μg g-1) content, while Mali had the lowest iron (13.1 μg g-1) and manganese (8.6 μg g-1). At country level, the mean seed calcium content was highest (3,200 mg kg-1) in Malawi and lowest (2,000 mg kg-1) in Kenya. The highest mean iron content of 63.7 μg g-1 was recorded in seeds from Kenya, while the lowest (25.8 μg g-1) was in Mali. Baobab seed mineral and proximate content varied significantly (p < .001) among the selected countries. Overall, baobab fruit pulp and seeds contain significant amounts of nutritionally essential minerals and proximate components but the amounts varied significantly among the selected countries. This variation offers opportunities for selecting provenances to concentrate on during germplasm collection for conservation and domestication of baobab.

Mineral composition of durum wheat grain and pasta under increasing atmospheric CO2 concentrations

The concentrations of 10 minerals were investigated in the grain of 12 durum wheat genotypes grown under free air CO₂ enrichment conditions, and in four of their derived pasta samples, using inductively coupled plasma mass spectrometry. Compared to ambient CO₂ (400ppm; AMB), under elevated CO₂ (570ppm; ELE), the micro-element and macro-element contents showed strong and significant decreases in the grain: Mn, -28.3%; Fe, -26.7%; Zn, -21.9%; Mg, -22.7%; Mo, -40.4%; K, -22.4%; and Ca, -19.5%. These variations defined the 12 genotypes as sensitive or non-sensitive to ELE. The pasta samples under AMB and ELE showed decreased mineral contents compared to the grain. Nevertheless, the contributions of the pasta to the recommended daily allowances remained relevant, also for the micro-elements under ELE conditions (range, from 18% of the recommended daily allowance for Zn, to 70% for Mn and Mo).

Natural variation in Arabidopsis thaliana reveals shoot ionome, biomass, and gene expression changes as biomarkers for zinc deficiency tolerance

Zinc (Zn) is an essential nutrient for plants, with a crucial role as a cofactor for many enzymes. Approximately one-third of the global arable land area is Zn deficient, leading to reduced crop yield and quality. To improve crop tolerance to Zn deficiency, it is important to understand the mechanisms plants have adopted to tolerate suboptimal Zn supply. In this study, physiological and molecular aspects of traits related to Zn deficiency tolerance were examined in a panel of 19 Arabidopsis thaliana accessions. Accessions showed a larger variation for shoot biomass than for Zn concentration, indicating that they have different requirements for their minimal Zn concentration required for growth. Accessions with a higher tolerance to Zn deficiency showed an increased expression of the Zn deficiency-responsive genes ZIP4 and IRT3 in comparison with Zn deficiency-sensitive accessions. Changes in the shoot ionome, as a result of the Zn treatment of the plants, were used to build a multinomial logistic regression model able to distinguish plants regarding their Zn nutritional status. This set of biomarkers, reflecting the A. thaliana response to Zn deficiency and Zn deficiency tolerance, can be useful for future studies aiming to improve the performance and Zn status of crop plants grown under suboptimal Zn concentrations.

Ionomic and transcriptomic analysis provides new insight into the distribution and transport of cadmium and arsenic in rice

To identify the key barrier parts and relevant elements during Cd/As transport into brown rice, 16 elements were measured in 14 different parts of 21 rice genotypes; moreover, transcriptomic of different nodes was analyzed. Cd/As contents in root and nodes were significantly higher than those other parts. Node I had the highest Cd content among nodes, leading an increase in gene expressions involved in glycolytic and Cd detoxification. The Cu/Zn/Co distribution and transport to various parts was similar to that of Cd, and Fe/Sb distribution and transport to various parts was similar to that of As. Moreover, Cu/Zn/Co/Mg was correlated with Cd in root and nodes, as well as Fe with As. Besides, the ionomic profile showed the different parts of an organ were closely related, and the spatial distribution of different organs was consistent with the growth morphology of rice. Therefore, root and nodes are two key barriers to Cd/As transport into brown rice. Moreover, Node I has the highest Cd accumulation capacities among nodes. The ionomic profile reflects relationships among plant parts and correlations between the elements, suggesting that nodes are hubs for element distribution, as well as the correlation between Cd with Zn/Cu/Co/Mg, between Fe with As.

Chemical element accumulation in tree bark grown in volcanic soils of Cape Verde-a first biomonitoring of Fogo Island

Barks from Prosopis juliflora (acacia) were collected in 12 sites of different geological contexts over the volcanic Fogo Island (Cape Verde). Elemental contents of Ba, Br, Co, Cr, Fe, K, Na, Zn and some rare earth elements (REE)-La, Ce, Sm, Eu, Tb, Yb, and Lu, were obtained for biological samples and topsoils by using k ₀-standardized and comparative method of instrumental neutron activation analysis (INAA), aiming the evaluation of chemical elements uptake by acacia bark. This first biomonitoring study of Fogo Island showed that, in general, significant accumulations of trace elements present in high amounts in these soils occur. This can be partially explained by the semi-arid climate with a consequent bioavailability of chemical elements when rain drops fall in this non-polluted environment. REE enrichment factors (EFs) increase with the decrease of ionic radius. Heavy REE (HREE) are significantly enriched in bark, which agrees with their release after the primary minerals breakdown and the formation of more soluble compounds than the other REE, and uptake by plants. Among the potential harmful chemical elements, Cr appears to be partially retained in nanoparticles of iron oxides. The high EFs found in tree barks of Fogo Island are certainly of geogenic origin rather than anthropogenic input since industry and the use of fertilizers is scarce.

Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri

Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation.

Accumulation of trace elements in edible crops and poplar grown on a titanium ore landfill

Urban gardening has recently experienced rapid development; however, the risk of the transfer of toxic elements from neighboring industry needs to be evaluated. We performed a multi-elemental analysis with several common edible crops (cucumber, pepper, cabbage, and lettuce) and poplar grown directly on a titanium ore landfill as a maximized scenario of exposure. Despite elevated concentrations of soil Ca, Fe, Mn, and Ti resulting from the industrial process, we did not register higher accumulation of these elements in the edible parts of crops or in poplar leaves grown on red gypsum compared with the control soil. Only S concentrations were higher in plants grown on the red gypsum, especially for cabbage. The principal component analysis among elements for plants grown on red gypsum indicated that S and Mn were accumulated by different plant species than Cd, Cu, and Zn. The poplar clone had a significantly higher transfer of S and Cr than the control and is a suitable tree species for monitoring element transfer to vegetation in this industrial context. By comparing our data with tolerable daily intake (TDI) recommendations, we demonstrated the low risk of cultivating edible crops directly on an industrial substrate in a maximized scenario of exposure, except for Cr, for which the toxicity depends on the bioavailable form. However, we did not consider the cumulative effects of the various elements because there are no current guidelines, and further research is needed to address this question.

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.

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity

Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal 'short-term stress memory' with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.

Natural Genetic Variation of Seed Micronutrients of Arabidopsis thaliana Grown in Zinc-Deficient and Zinc-Amended Soil

The quality of edible seeds for human and animal nutrition is crucially dependent on high zinc (Zn) and iron (Fe) seed concentrations. The micronutrient bioavailability is strongly reduced by seed phytate that forms complexes with seed cations. Superior genotypes with increased seed Zn concentrations had been identified, but low micronutrient seed levels often prevail when the plants are grown in Zn-deficient soils, which are globally widespread and correlate with human Zn-deficiency. Here, seed Zn concentrations of Arabidopsis accessions grown in Zn-deficient and Zn-amended conditions were measured together with seed Fe and manganese (Mn), in a panel of 108 accessions. By applying genome-wide association, de novo candidate genes potentially involved in the seed micronutrient accumulation were identified. However, a candidate inositol 1,3,4-trisphosphate 5/6-kinase 3 gene (ITPK3), located close to a significant nucleotide polymorphism associated with relative Zn seed concentrations, was dispensable for seed micronutrients accumulation in Col-0. Loss of this gene in itpk3-1 did neither affect phytate seed levels, nor seed Zn, Fe, and Mn. It is concluded that large natural variance of micronutrient seed levels is identified in the population and several accessions maintain high seed Zn despite growth in Zn-deficient conditions.

The Review of Nuclear Microscopy Techniques: An Approach for Nondestructive Trace Elemental Analysis and Mapping of Biological Materials

The properties of many biological materials often depend on the spatial distribution and concentration of the trace elements present in a matrix. Scientists have over the years tried various techniques including classical physical and chemical analyzing techniques each with relative level of accuracy. However, with the development of spatially sensitive submicron beams, the nuclear microprobe techniques using focused proton beams for the elemental analysis of biological materials have yielded significant success. In this paper, the basic principles of the commonly used microprobe techniques of STIM, RBS, and PIXE for trace elemental analysis are discussed. The details for sample preparation, the detection, and data collection and analysis are discussed. Finally, an application of the techniques to analysis of corn roots for elemental distribution and concentration is presented.

The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance

Genome-wide association (GWA) analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean. More rarely, loci have also been detected based on variance differences between genotypes. Several hypotheses have been proposed to explain the possible genetic mechanisms leading to such variance signals. However, little is known about what causes these signals, or whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, fine-mapping of this association reveals that the vGWA emerges from the effects of three independent genetic polymorphisms that all are in strong LD with the markers displaying the genetic variance-heterogeneity. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation or “missing heritability”. Two of the three polymorphisms underlying the genetic variance-heterogeneity are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of MOT1. Use of a T-DNA knockout allele highlights Copper Transporter 6; COPT6 (AT2G26975) as a strong candidate gene for this association. Our results show that an extended LD across a complex locus including multiple functional alleles can lead to a variance-heterogeneity between genotypes in natural populations. Further, they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.

Most biological traits vary in natural populations, and understanding the genetic basis of this variation remains an important challenge. Genome-wide association (GWA) studies have emerged as a powerful tool to address this challenge by dissecting the genetic architecture of trait variation into the contribution of individual genes. This contribution has traditionally been measured as the difference in the phenotypic means between groups of individuals with alternative genotypes at one, or multiple loci. However, instead of altering the trait mean, certain loci alter the variability of the trait. Here, we describe the genetic dissection of one such variance-controlling locus that drives variation in leaf molybdenum concentrations amongst natural accessions of Arabidopsis thaliana. The variance-controlling locus was found to result from the contributions of multiple alleles at multiple loci that are closely linked on the chromosome and is a major contributor to the “missing heritability” for this trait identified in previous studies. This illustrates that multi-allelic genetic architectures can hide large amounts of additive genetic variation, and that it is possible to uncover this hidden variation using the appropriate experimental designs and statistical methods described here.

Shoot ionome to predict the synergism and antagonism between nutrients as affected by substrate and physiological status

The elemental composition of a tissue or organism is defined as ionome. However, the combined effects on the shoot ionome determined by the taxonomic character, the nutrient status and different substrates have not been investigated. This study tests the hypothesis that phylogenetic variation of monocots and dicots grown in iron deficiency can be distinguished by the shoot ionome. We analyzed 18 elements in barley, cucumber and tomato and in two substrates (hydroponic vs soil) with different nutritional regimes. Multivariate analysis evidenced a clear separation between the species. In hydroponic conditions the main drivers separating the species are non essential-nutrients as Ti, Al, Na and Li, which were positively correlated with macro- (P, K) and micronutrients (Fe, Zn, Mo, B). The separation between species is confirmed when plants are grown on soil, but the distribution is determined especially by macronutrients (S, P, K, Ca, Mg) and micronutrients (B). A number of macro (Mg, Ca, S, P, K) and micronutrients (Fe, Mn, Zn, Cu, Mo, B) contribute to plant growth and several other important physiological and metabolic plant activities. The results reported here confirmed that the synergism and antagonism between them and other non-essential elements (Ti, Al, Si, Na) define the plant taxonomic character. The ionome profile might thus be exploited as a tool for the diagnosis of plants physiological/nutritional status but also in defining biofortification strategies to optimize both mineral enrichment of staple food crops and the nutrient input as fertilizers.

Comprehensive phenotypic analysis and quantitative trait locus identification for grain mineral concentration, content, and yield in maize (Zea mays L.)

Understanding the correlations of seven minerals for concentration, content and yield in maize grain, and exploring their genetic basis will help breeders to develop high grain quality maize. Biofortification by enhanced mineral accumulation in grain through genetic improvement is an efficient way to solve global nutrient malnutrition, in which one key step is to detect the underlying quantitative trait loci (QTL). Herein, a maize recombinant inbred population (RIL) was field grown to maturity across four environments (two locations × two years). Phenotypic data for grain mineral concentration, content and yield were determined for copper (Cu), iron (Fe), manganese (Mn), zinc (Zn), magnesium (Mg), potassium (K) and phosphorus (P). Significant effects of genotype, location and year were observed for all investigated traits. The strongest location effects were found for Zn accumulation traits probably due to distinct soil Zn availabilities across locations. Heritability (H (2)) of different traits varied with higher H (2) (72-85 %) for mineral concentration and content, and lower (48-63 %) for mineral yield. Significant positive correlations for grain concentration were revealed between several minerals. QTL analysis revealed 28, 25, and 12 QTL for mineral concentration, content and yield, respectively; and identified 8 stable QTL across at least two environments. All these QTL were assigned into 12 distinct QTL clusters. A cluster at chromosome Bin 6.07/6.08 contained 6 QTL for kernel weight, mineral concentration (Mg) and content (Zn, K, Mg, P). Another cluster at Bin 4.05/4.06 contained a stable QTL for Mn concentration, which were previously identified in other maize and rice RIL populations. These results highlighted the phenotypic and genetic performance of grain mineral accumulation, and revealed two promising chromosomal regions for genetic improvement of grain biofortification in maize.

Interactions between Cs, Sr, and other nutrients and trace element accumulation in Amaranthus shoot in response to variety effect

Aiming at clarifying the interactions between Cs, Sr, and other mineral elements in the genus Amaranthus, this study adopted 33 different varieties of Amaranthus and investigated the concentrations of 23 mineral elements in shoots grown in the fields of Iino in Fukushima prefecture. Significant varietal effects were detected for all elements except Se, and degree of interspecies variation was highly element dependent. Among 23 elements, amaranths were less sensitive to the accumulation of Cs and Sr than most other mineral elements to the species level. There are six elements showing significant correlation with Cs, positive correlations between As, Rb, Al, Fe, Ni, and Cs, and negative correlation between Ba and Cs. Significant correlations between Ca, Mg, Mn, Zn, B, Ba, Cd, and Sr were detected, and all of the coefficients were positive. Cs and Sr did not present significant correlation, but they were both significantly correlated with Ba. By principal component analysis (PCA), the first and second principal components (PC1 and PC2) accounted for 23.2 and 20.3% of the total variance and associated with Cs and Sr, respectively. Both of the two species took up more Cs by promoting the influx of elements positively correlated with Cs into shoot, but at the same time, Amaranthus hypochondriacus (L.) Mapes 847 decreased the K and Ba uptake and Amaranthus powellii (S. Wats) subsp. Powellii inhibited the accumulation of Rb, Sr, and significantly correlated elements of Sr in shoot. This study is the first to pave the way for comprehension on ionome in amaranth shoot at the variety level. The results of this research provide the ionomic basis for implementing countermeasures in the field against the translocation of Cs (and potentially Sr) toward crops and food.

Genome-wide association mapping identifies a new arsenate reductase enzyme critical for limiting arsenic accumulation in plants

Inorganic arsenic is a carcinogen, and its ingestion through foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content 1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit both its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1-encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots, causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Furthermore, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic-containing food such as rice.

Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis species range

Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis (Arabidopsis thaliana) accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction, and its reduced activity in the loss-of-function allele apr2-1 and the two Arabidopsis accessions Hodonín and Shahdara leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Shahdara accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by 4 orders of magnitude across the Arabidopsis species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.

Soil organic matter and salinity affect copper bioavailability in root zone and uptake by Vicia faba L. plants

Processes that control the mobility, transformation and toxicity of metals in soil are of special importance in the root-developing zone. For this reason, there is a considerable interest in understanding trace elements (TEs) behavior in soil, emphasising the processes by which plants take them up. Increased root-zone salinity can affect plant TEs uptake and accumulation in plant tissue. Furthermore, copper (Cu) complexation by soil organic matter (SOM) is an effective mechanism of Cu retention in soils, controlling thus its bioavailability. Therefore, a greenhouse pot experiment was conducted to study the effects of soil Cu contamination in a saline environment on faba bean (Vicia faba L.) element uptake. Treatment with NaCl salinity was applied (control, 50 mM NaCl and 100 mM NaCl) on faba bean plants grown in a control and in a soil spiked with Cu (250 and 500 mg kg(-1)). Low and high SOM content trial variants were studied. Cu accumulation occurred in faba bean leaf, pod and seed. Cu contamination affected plant element concentrations in leaves (Na, Ca, Mg, Mn), pod (Zn, Mn) and seed (Mn, Mo, Zn). Root-zone salinity also affected faba bean element concentrations. Furthermore, Cu contamination-salinity and salinity-SOM interactions were significant for pod Cu concentration, suggesting that Cu phytoavailability could be affected by these interactions. Future research will be focused on the mechanisms of Cu translocation in plant and adaptation aspects of abiotic stress.

An update on magnesium homeostasis mechanisms in plants

Worldwide, nearly two-thirds of the population do not consume the recommended amount of magnesium (Mg) in their diet. Furthermore, low Mg status (hypomagnesaemia) is known to contribute to a number of human chronic disease conditions. Because the principal dietary Mg source is of plant origin, agronomic and genetic biofortification strategies are aimed at improving nutritional Mg content in food crops to overcome this mineral deficiency in humans. This update incorporates the contributions of annotated permeases involved in Mg uptake, storage and recycling with a schematic model of Mg movement at the organ and cellular levels in the model species Arabidopsis thaliana. Furthermore, approaches using mutagenesis or natural ionomic variation to identify loci involved in Mg homeostasis in roots, leaves and seeds will be summarised. A brief overview will be presented on how Arabidopsis research can help to develop strategies for biofortification of crops.

Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain

QTLs controlling the concentrations elements in rice grain were identified in two mapping populations. The QTLs were clustered such that most genomic regions were associated with more than one element. In this study, quantitative trait loci (QTLs) affecting the concentrations of 16 elements in whole, unmilled rice (Oryza sativa L.) grain were identified. Two rice mapping populations, the ‘Lemont’ × ‘TeQing’ recombinant inbred lines (LT-RILs), and the TeQing-into-Lemont backcross introgression lines (TILs) were used. To increase opportunity to detect and characterize QTLs, the TILs were grown under two contrasting field conditions, flooded and irrigated-but-unflooded. Correlations between the individual elements and between each element with grain shape, plant height, and time of heading were also studied. Transgressive segregation was observed among the LT-RILs for all elements. The 134 QTLs identified as associated with the grain concentrations of individual elements were found clustered into 39 genomic regions, 34 of which were found associated with grain element concentration in more than one population and/or flooding treatment. More QTLs were found significant among flooded TILs (92) than among unflooded TILs (47) or among flooded LT-RILs (40). Twenty-seven of the 40 QTLs identified among the LT-RILs were associated with the same element among the TILs. At least one QTL per element was validated in two or more population/environments. Nearly all of the grain element loci were linked to QTLs affecting additional elements, supporting the concept of element networks within plants. Several of the grain element QTLs co-located with QTLs for grain shape, plant height, and days to heading; but did not always differ for grain elemental concentration as predicted by those traits alone. A number of interesting patterns were found, including a strong Mg–P–K complex.

Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain

QTLs controlling the concentrations elements in rice grain were identified in two mapping populations. The QTLs were clustered such that most genomic regions were associated with more than one element. In this study, quantitative trait loci (QTLs) affecting the concentrations of 16 elements in whole, unmilled rice (Oryza sativa L.) grain were identified. Two rice mapping populations, the ‘Lemont’ × ‘TeQing’ recombinant inbred lines (LT-RILs), and the TeQing-into-Lemont backcross introgression lines (TILs) were used. To increase opportunity to detect and characterize QTLs, the TILs were grown under two contrasting field conditions, flooded and irrigated-but-unflooded. Correlations between the individual elements and between each element with grain shape, plant height, and time of heading were also studied. Transgressive segregation was observed among the LT-RILs for all elements. The 134 QTLs identified as associated with the grain concentrations of individual elements were found clustered into 39 genomic regions, 34 of which were found associated with grain element concentration in more than one population and/or flooding treatment. More QTLs were found significant among flooded TILs (92) than among unflooded TILs (47) or among flooded LT-RILs (40). Twenty-seven of the 40 QTLs identified among the LT-RILs were associated with the same element among the TILs. At least one QTL per element was validated in two or more population/environments. Nearly all of the grain element loci were linked to QTLs affecting additional elements, supporting the concept of element networks within plants. Several of the grain element QTLs co-located with QTLs for grain shape, plant height, and days to heading; but did not always differ for grain elemental concentration as predicted by those traits alone. A number of interesting patterns were found, including a strong Mg–P–K complex.

A chemometrics as a powerful tool in the elucidation of the role of metals in the biosynthesis of volatile organic compounds in Hungarian thyme samples

The volatile fraction of the leaves of Thymus pannonicus All. (Lamiaceae) was analyzed by headspace extraction followed by GC-FID and GC-MS analysis. The different headspace profiles were recognized, with citral and with monoterpene hydrocarbons as dominant compounds. In addition, the determination of Cr, Co, Ni, Mo, Cu, Zn, Mn, Fe, Mg, Ca, K and Na was conducted by spectroscopic techniques (FAAS, GFAAS and ICP-OES). In order to evaluate the relationship between volatile organic compounds and metals, a chemometrics approach was applied. The data obtained by analysis of the headspace and elemental content were subjected to correlation analysis, factor analysis, principal component analysis and cluster analysis. A number of significant correlations of metals with plant volatiles were found. Correlation of Zn with citral, Mn with oxygenated monoterpenes and Mg with β-bourbonene, could be explained by involvement of metals in the biosynthesis of volatile organic compounds.

Magnesium deficiency phenotypes upon multiple knockout of Arabidopsis thaliana MRS2 clade B genes can be ameliorated by concomitantly reduced calcium supply

Plant MRS2 membrane protein family members have been shown to play important roles in magnesium uptake and homeostasis. Single and double knockouts for two Arabidopsis thaliana genes, AtMRS2-1 and AtMRS2-5, have previously not shown significant phenotypes even under limiting Mg(2+) supply although both are strongly expressed already in early seedlings. Together with AtMRS2-10, these genes form clade B of the AtMRS2 gene family. We now succeeded in obtaining homozygous AtMRS2-1/10 double and AtMRS2-1/5/10 triple knockout lines after selection under increased magnesium supply. Although wilting early, both new mutant lines develop fully and are also fertile under standard magnesium supply, but show severe developmental retardation under limiting Mg(2+) concentrations. To investigate nutrient dependency of germination and seedling development under various conditions, including variable supplies of Mg(2+), Ca(2+), Zn(2+), Mn(2+), Co(2+), Cd(2+) and Cu(2+), in a reproducible and economical way, we employed a small-scale liquid culturing system in 24-well plate set-ups. This allowed the growth and monitoring of individual plantlets of different mutant lines under several nutritional conditions in parallel, and the scoring and statistical evaluation of developmental stages and biomass accumulation. Detrimental effects of higher concentrations of these elements were similar in mutants and the wild type. However, growth retardation phenotypes seen upon hydroponic cultivation under low Mg(2+) could be ameliorated when Ca(2+) concentrations were concomitantly lowered, supporting indications for an important interplay of these two most abundant divalent cations in the nutrient homeostasis of plants.

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.