The genetics of phytate and phosphate accumulation in seeds and leaves of Arabidopsis thaliana, using natural variation

ANPS: machine learning based server for identification of anti-nutritional proteins in plants

Anti-nutrient factors are inherently present in almost all major crops, which impede the absorption of crucial vitamins and minerals upon human consumption. The commonly found anti-nutrients in food crops are saponins, tannins, lectins, and phytates etc. Currently, there is a lack of computational server for identification of proteins that encode for anti-nutritional factors in plants. Consequently, this study represents a computational approach aimed at distinguishing between proteins encoding anti-nutritional factors and those providing essential nutrients. In this work, machine learning algorithms have been employed to identify plant specific anti-nutrient factor proteins from protein sequences by using compositional features. Achieving a five-fold cross-validation training performance of 94.34% AUC-ROC and 94.13% AUC-PR with extreme gradient boosting surpasses the performance of other methods such as support vector machine, random forest, and adaptive boosting. These results suggest the proposed approach is highly reliable in predicting plant-specific anti-nutritional factor proteins. The resulting prediction models have led to the development of an online server named ANPS, freely available at https://nipb-bi.icar.gov.in .

Plant biochemical genetics in the multiomics era

Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.

Aspergillus niger Enhances Organic and Inorganic Phosphorus Release from Wheat Straw by Secretion of Degrading Enzymes and Oxalic Acid

To explore the mechanisms of crop straw degradation and phosphorus (P) release by phosphate-solubilizing fungi (PSF), a typical PSF Aspergillus niger (A. niger, ANG) was investigated for the degradation of wheat straw (WST) in this work. The results revealed that A. niger significantly increased wheat straw degradation (30%) compared with no A. niger treatment (7.7%). Meanwhile, more than 92% of total P was released from WST by A. niger, much higher than from WST treatment (69.5%). Although the ratios of inorganic P release between WST and WST + ANG treatments were similar (17.6 vs 19.7%), a significant difference occurred between their release of organic P, i.e., WST (51.9%) vs WST + ANG (72.5%). The high enzyme activity of β-1,4-glucanase and β-glucosidase produced by A. niger contributed to the wheat straw degradation and organic P release compared with no A. niger treatment. Oxalic acid secreted by A. niger dominated the release of inorganic P from WST. Our findings suggested that A. niger is an efficient microbial agent for crop straw degradation and P release, which could be a candidate in the pathway of straw return.

Genetic Control of Seed Phytate Accumulation and the Development of Low-Phytate Crops: A Review and Perspective

Breeding low phytic acid (lpa) crops is a strategy that has potential to both improve the nutritional quality of food and feed and contribute to the sustainability of agriculture. Here, we review the lipid-independent and -dependent pathways of phytate synthesis and their regulatory mechanisms in plants. We compare the genetic variation of the phytate concentration and distribution in seeds between dicot and monocot species as well as the associated temporal and spatial expression patterns of the genes involved in phytate synthesis and transport. Quantitative trait loci or significant single nucleotide polymorphisms for the seed phytate concentration have been identified in different plant species by linkage and association mapping, and some genes have been cloned from lpa mutants. We summarize the effects of various lpa mutations on important agronomic traits in crop plants and propose SULTR3;3 and SULTR3;4 as optimal target genes for lpa crop breeding.

Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate

Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 × 10⁶ single-nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27 kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low-phytate variety (LPA20) was significantly elevated compared with a high-phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favourable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.

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

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

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.

Effects of Interspecific Chromosome Substitution in Upland Cotton on Cottonseed Micronutrients

Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of chromosome or chromosome arm substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from chromosome substitution (CS) cotton lines. Our hypothesis was that interspecific chromosome substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in 2014 in Mississippi, USA). TM-1 (the recurrent parent of the CS line) and AM UA48 (cultivar) were used as control. The results showed significant variability among CS lines compared to the controls AM UA48 and TM-1. For example, in South Carolina (SC), B concentration in cottonseed ranged from 10.35 mg kg-1 in CS-M02 to 13.67 mg kg-1 in CS-T04. The concentration of Cu ranged from 4.81 mg kg-1 in CS-B08sh to 7.65 mg kg-1 in CS-T02, and CS-T02 was higher than both controls. The concentration of Fe ranged from 36.09 mg kg-1 to 56.69 mg kg-1 (an increase up to 57%), and six CS lines (CS-B02, CS-B08sh, CS-M02, CS-M04, CS-T02, and CS-T04) had higher concentration than both controls in 2013. In 2014 at the Mississippi location (MS), similar observation was found with CS lines for micronutrients content. The CS lines with higher concentrations of these micronutrients can be used as a genetic tool toward QTL identification for desired seed traits because these lines are genetically similar with TM-1, except the substituted chromosome or chromosome segment pairs from the alien species. Chromosome substitution provides an effective means for upland cotton improvement by targeted interspecific introgression, yielding CS lines that facilitate trait discovery, such as seed micronutritional qualities, due to increased isogenicity and markedly reduced complexity from epistatic interactions with non-target alien chromosomes. The positive correlation between B, Cu, and Fe at both locations, between Ni and Mn, between Zn and Cu, and between Zn and Ni at both locations signify the importance of a good agricultural and fertilizer management of these nutrients to maintain higher cottonseed nutrient content.

Genetic dissection of the shoot and root ionomes of Brassica napus grown with contrasting phosphate supplies

BACKGROUND AND AIMS

Mineral elements have many essential and beneficial functions in plants. Phosphorus (P) deficiency can result in changes in the ionomes of plant organs. The aims of this study were to characterize the effects of P supply on the ionomes of shoots and roots, and to identify chromosomal quantitative trait loci (QTLs) for shoot and root ionomic traits, as well as those affecting the partitioning of mineral elements between shoot and root in Brassica napus grown with contrasting P supplies.

METHODS

Shoot and root concentrations of 11 mineral elements (B, Ca, Cu, Fe, K, Mg, Mn, Na, P, S and Zn) were investigated by inductively coupled plasma optical emission spectrometry (ICP-OES) in a Brassica napus double haploid population grown at an optimal (OP) and a low phosphorus supply (LP) in an agar system. Shoot, root and plant contents, and the partitioning of mineral elements between shoot and root were calculated.

KEY RESULTS

The tissue concentrations of B, Ca, Cu, K, Mg, Mn, Na, P and Zn were reduced by P starvation, while the concentration of Fe was increased by P starvation in the BnaTNDH population. A total of 133 and 123 QTLs for shoot and root ionomic traits were identified at OP and LP, respectively. A major QTL cluster on chromosome C07 had a significant effect on shoot Mg and S concentrations at LP and was narrowed down to a 2.1 Mb region using an advanced backcross population.

CONCLUSIONS

The tissue concentration and partitioning of each mineral element was affected differently by P starvation. There was a significant difference in mineral element composition between shoots and roots. Identification of the genes underlying these QTLs will enhance our understanding of processes affecting the uptake and partitioning of mineral elements in Brassica napus.

Biotechnological mechanism for improving plant remobilization of phosphorus during leaf senescence

Phosphorus enrichment of aquatic ecosystems through diffuse source pollution is an ongoing issue worldwide. A potential solution lies in the use of fast-growing, multipurpose feedstocks, such as trees, to limit the flow of phosphorus into riparian areas through luxury consumption. However, the perennial nature of trees and their use of leaves as storage organs for excess phosphorus may reduce the effectiveness of contaminant removal during periods of leaf abscission. In an attempt to improve phosphorus remobilization during autumnal senescence, transgenic hybrid poplar P39 (Populus alba × Populus grandidentata) and Arabidopsis thaliana harbouring a constitutively expressed low-affinity potato phosphate transporter (35S::StPht1-1) were generated using Agrobacterium-mediated transformation. For both species, the highest expressing 35S::StPht1-1 lines were grown alongside wild-type plants and subjected to increasing phosphate applications. StPht1-1 expression in A. thaliana led to a reduction in biomass when grown under high-phosphate conditions and had no effect on phosphate remobilization during senescence. In contrast, StPht1-1 constitutive expression in P39 resulted in increased leaf phosphate content in the highest expressing transgenic line and minimal to no effect on P resorption efficiency. Surprisingly, sulphate resorption showed the greatest improvement in all three transgenic poplar lines, displaying a 31%-37% increase in resorption efficiency. These results highlight the complexity of nutrient resorption mechanisms in plants.

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.

QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana

BACKGROUND

Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability.

RESULTS

Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus.

CONCLUSION

We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .

Quantitative trait loci analysis of hormone levels in Arabidopsis roots

Quantitative trait loci (QTL) analyses for five groups of hormones, including cytokinins in Arabidopsis roots were performed using recombinant inbred lines (Ler×Cvi). Significant QTLs were detected for cytokinins, jasmonic acid and salicylic acid. Separate analysis of two sub-populations, viz., vegetative and flowering plants revealed that many of the QTLs were development-specific. Using near-isogenic lines, several significant QTLs were confirmed; three co-localized QTL regions were responsible for determining several cytokinin metabolites. Using a knock-out plant, a functional role of zeatin N-glucosyltransferase gene (UGT76C2) underlying a large-effect QTL for levels of tZ-N-glucosides and tZRMP was evaluated in the metabolism of cytokinins. Pleotropic effects of this gene were found for cytokinin levels in both roots and leaves, but significant changes of morphological traits were observed only in roots. Hormone QTL analysis reveals development-specific and organ-dependent aspects of the regulation of plant hormone content and metabolism.

Application of apigeninidin-rich red sorghum biocolorant in a fermented food improves product quality

BACKGROUND

The 'clean label' trend is pushing the food industry to replace synthetic colorants with plant-based colorants. However, technological efficacy and undesirable side effects restrict the use of plant-based colorants in industrial applications. This research studied the production of fermented maize dough coloured by apigeninidin-rich red sorghum biocolorant, as practised for centuries in West Africa, as a model to assess the impact of the biocolorant on nutritional and sensorial quality of foods.

RESULTS

A 3-day fermentation of a dyed maize dough (containing 327 µg g-1 dry matter of apigeninidin) by Pichia kudriavzevii and Lactobacillus fermentum led to a degradation of 69% of the apigeninidin content, causing a clearly visible colour difference (ΔE*00 17.4). The antioxidant activity of fermented dyed dough (DD) increased by 51% compared to fermented non-dyed dough (NDD). However, the phytate dephosphorylation and volatile organic compound concentrations were lower in DD than in NDD. This suggests a lower mineral solubility and change in the sensory quality of fermented DD.

CONCLUSION

Apigeninidin extract from sorghum leaf sheaths proved to be a bioactive red biocolorant with potential in fermented foods. The formation of new antioxidant compounds needs further investigation, as does the impact on the development of volatile compounds. © 2018 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Linking genes with ecological strategies in Arabidopsis thaliana

Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.

Systems, variation, individuality and plant hormones

Inter-individual variation in plants and particularly in hormone content, figures strongly in evolution and behaviour. Homo sapiens and Arabidopsis exhibit similar and substantial phenotypic and molecular variation. Whereas there is a very substantial degree of hormone variation in mankind, reports of inter-individual variation in plant hormone content are virtually absent but are likely to be as large if not larger than that in mankind. Reasons for this absence are discussed. Using an example of inter-individual variation in ethylene content in ripening, the article shows how biological time is compressed by hormones. It further resolves an old issue of very wide hormone dose response that result directly from negative regulation in hormone (and light) transduction. Negative regulation is used because of inter-individual variability in hormone synthesis, receptors and ancillary proteins, a consequence of substantial genomic and environmental variation. Somatic mosaics have been reported for several plant tissues and these too contribute to tissue variation and wide variation in hormone response. The article concludes by examining what variation exists in gravitropic responses. There are multiple sensing systems of gravity vectors and multiple routes towards curvature. These are an aspect of the need for reliability in both inter-individual variation and unpredictable environments. Plant hormone inter-individuality is a new area for research and is likely to change appreciation of the mechanisms that underpin individual behaviour.

Phytase overexpression in Arabidopsis improves plant growth under osmotic stress and in combination with phosphate deficiency

Engineering osmotolerant plants is a challenge for modern agriculture. An interaction between osmotic stress response and phosphate homeostasis has been reported in plants, but the identity of molecules involved in this interaction remains unknown. In this study we assessed the role of phytic acid (PA) in response to osmotic stress and/or phosphate deficiency in Arabidopsis thaliana. For this purpose, we used Arabidopsis lines (L7 and L9) expressing a bacterial beta-propeller phytase PHY-US417, and a mutant in inositol polyphosphate kinase 1 gene (ipk1-1), which were characterized by low PA content, 40% (L7 and L9) and 83% (ipk1-1) of the wild-type (WT) plants level. We show that the PHY-overexpressor lines have higher osmotolerance and lower sensitivity to abscisic acid than ipk1-1 and WT. Furthermore, PHY-overexpressors showed an increase by more than 50% in foliar ascorbic acid levels and antioxidant enzyme activities compared to ipk1-1 and WT plants. Finally, PHY-overexpressors are more tolerant to combined mannitol stresses and phosphate deficiency than WT plants. Overall, our results demonstrate that the modulation of PA improves plant growth under osmotic stress, likely via stimulation of enzymatic and non-enzymatic antioxidant systems, and that beside its regulatory role in phosphate homeostasis, PA may be also involved in fine tuning osmotic stress response in plants.

Manipulating the Phytic Acid Content of Rice Grain Toward Improving Micronutrient Bioavailability

Myo-inositol hexaphosphate, also known as phytic acid (PA), is the most abundant storage form of phosphorus in seeds. PA acts as a strong chelator of metal cations to form phytate and is considered an anti-nutrient as it reduces the bioavailability of important micronutrients. Although the major nutrient source for more than one-half of the global population, rice is a poor source of essential micronutrients. Therefore, biofortification and reducing the PA content of rice have arisen as new strategies for increasing micronutrient bioavailability in rice. Furthermore, global climate change effects, particularly rising atmospheric carbon dioxide concentration, are expected to increase the PA content and reduce the concentrations of most of the essential micronutrients in rice grain. Several genes involved in PA biosynthesis have been identified and characterized in rice. Proper understanding of the genes related to PA accumulation during seed development and creating the means to suppress the expression of these genes should provide a foundation for manipulating the PA content in rice grain. Low-PA rice mutants have been developed that have a significantly lower grain PA content, but these mutants also had reduced yields and poor agronomic performance, traits that challenge their effective use in breeding programs. Nevertheless, transgenic technology has been effective in developing low-PA rice without hampering plant growth or seed development. Moreover, manipulating the micronutrient distribution in rice grain, enhancing micronutrient levels and reducing the PA content in endosperm are possible strategies for increasing mineral bioavailability. Therefore, a holistic breeding approach is essential for developing successful low-PA rice lines. In this review, we focus on the key determinants for PA concentration in rice grain and discuss the possible molecular methods and approaches for manipulating the PA content to increase micronutrient bioavailability.

Genotypic difference in (137)Cs accumulation and transfer from the contaminated field in Fukushima to azuki bean (Vigna angularis)

The screening of mini-core collection of azuki bean accessions (Vigna angularis (Willd.) Ohwi & Ohashi) for comparative uptake of (137)Cs in their edible portions was done in field trials on land contaminated by the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident. Ninety seven azuki bean accessions including their wild relatives from a Japanese gene bank, were grown in a field in the Fukushima prefecture, which is located approximately 51 km north of FDNPP. The contamination level of the soil was 3665 ± 480 Bq kg(-1) dry weight ((137)Cs, average ± SD). The soil type comprised clay loam, where the sand: silt: clay proportion was 42:21:37. There was a significant varietal difference in the biomass production, radiocaesium accumulation and transfer factor (TF) of radiocaesium from the soil to edible portion. Under identical agricultural practice, the extent of (137)Cs accumulation by seeds differed between the accessions by as much as 10-fold. Inter-varietal variation was expressed at the ratio of the maximum to minimum observed (137)Cs transfer factor for seeds ranged from 0.092 to 0.009. The total biomass, time to flowering and maturity, and seed yield had negative relationship to (137)Cs activity concentration in seeds. The results suggest that certain variety/varieties of azuki bean which accumulated less (137)Cs in edible portion with preferable agronomic traits are suitable to reduce the (137)Cs accumulation in food chain on contaminated land.

Performance and Limitations of Phosphate Quantification: Guidelines for Plant Biologists

Phosphate (Pi) is a macronutrient that is essential for plant life. Several regulatory components involved in Pi homeostasis have been identified, revealing a very high complexity at the cellular and subcellular levels. Determining the Pi content in plants is crucial to understanding this regulation, and short real-time(33)Pi uptake imaging experiments have shown Pi movement to be highly dynamic. Furthermore, gene modulation by Pi is finely controlled by localization of this ion at the tissue as well as the cellular and subcellular levels. Deciphering these regulations requires access to and quantification of the Pi pool in the various plant compartments. This review presents the different techniques available to measure, visualize and trace Pi in plants, with a discussion of the future prospects.

The knowns and unknowns of phosphorus loading into grains, and implications for phosphorus efficiency in cropping systems

Inefficient use of phosphorus (P) in agriculture adds to production costs, increases the risk of eutrophication of waterways, and contributes to the rapid depletion of the world's non-renewable rock phosphate supplies. The removal of large quantities of P from fields in harvested grains is a major driver in the global P cycle, but opportunities exist to reduce the amount of P in harvested grains through plant breeding. Using rice (Oryza sativa L.) as a model crop, we examine our current understanding of the process of P loading into grain and its regulation by genetic and environmental factors. We expose a dearth of knowledge on the physiological processes involved in loading P into grains, poor resolution of the genes and networks involved in P mobilization from vegetative tissues to grains, and limited understanding of genetic versus environmental contributions to variation in grain P concentrations observed among genotypes. We discuss potential breeding strategies and highlight key research gaps that should be addressed to facilitate these breeding approaches. Given the strong economic and environmental incentives for a low grain P trait, we suggest that some of the investment and resources currently directed to determining the molecular regulation of P starvation responses in model plant species should be diverted to resolving the physiology, genetics, and molecular regulation of P loading into cereal grains.

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.

Certain Malvaceae Plants Have a Unique Accumulation of myo-Inositol 1,2,4,5,6-Pentakisphosphate

Methods used to quantify inositol phosphates in seeds lack the sensitivity and specificity necessary to accurately detect the lower concentrations of these compounds contained in the leaves of many plants. In order to measure inositol hexakisphosphate (InsP₆) and inositol pentakisphosphate (InsP₅) levels in leaves of different plants, a method was developed to concentrate and pre-purify these compounds prior to analysis. Inositol phosphates were extracted from leaves with diluted HCl and concentrated on small anion exchange columns. Reversed-phase solid phase extraction cartridges were used to remove compounds that give peaks that sometimes interfere during HPLC. The method permitted the determination of InsP₆ and InsP₅ concentrations in leaves as low as 10 µM and 2 µM, respectively. Most plants analyzed contained a high ratio of InsP₆ to InsP₅. In contrast, certain members of the Malvaceae family, such as cotton (Gossypium) and some hibiscus (Hibiscus) species, had a preponderance of InsP₅. Radiolabeling of cotton seedlings also showed increased amounts of InsP₅ relative to InsP₆. Why some Malvaceae species exhibit a reversal of the typical ratios of these inositol phosphates is an intriguing question for future research.

Accumulation of Phosphorus-Containing Compounds in Developing Seeds of Low-Phytate Pea (Pisum sativum L.) Mutants

Low phytic acid (lpa) crops are low in phytic acid and high in inorganic phosphorus (Pi). In this study, two lpa pea genotypes, 1-150-81, 1-2347-144, and their progenitor CDC Bronco were grown in field trials for two years. The lpa genotypes were lower in IP₆ and higher in Pi when compared to CDC Bronco. The total P concentration was similar in lpa genotypes and CDC Bronco throughout the seed development. The action of myo-inositol phosphate synthase (MIPS) (EC 5.5.1.4) is the first and rate-limiting step in the phytic acid biosynthesis pathway. Aiming at understanding the genetic basis of the lpa mutation in the pea, a 1530 bp open reading frame of MIPS was amplified from CDC Bronco and the lpa genotypes. Sequencing results showed no difference in coding sequence in MIPS between CDC Bronco and lpa genotypes. Transcription levels of MIPS were relatively lower at 49 days after flowering (DAF) than at 14 DAF for CDC Bronco and lpa lines. This study elucidated the rate and accumulation of phosphorus compounds in lpa genotypes. The data also demonstrated that mutation in MIPS was not responsible for the lpa trait in these pea lines.

Two inositol hexakisphosphate kinases drive inositol pyrophosphate synthesis in plants

Inositol pyrophosphates are unique cellular signaling molecules with recently discovered roles in energy sensing and metabolism. Studies in eukaryotes have revealed that these compounds have a rapid turnover, and thus only small amounts accumulate. Inositol pyrophosphates have not been the subject of investigation in plants even though seeds produce large amounts of their precursor, myo-inositol hexakisphosphate (InsP6 ). Here, we report that Arabidopsis and maize InsP6 transporter mutants have elevated levels of inositol pyrophosphates in their seed, providing unequivocal identification of their presence in plant tissues. We also show that plant seeds store a little over 1% of their inositol phosphate pool as InsP7 and InsP8 . Many tissues, including, seed, seedlings, roots and leaves accumulate InsP7 and InsP8 , thus synthesis is not confined to tissues with high InsP6 . We have identified two highly similar Arabidopsis genes, AtVip1 and AtVip2, which are orthologous to the yeast and mammalian VIP kinases. Both AtVip1 and AtVip2 encode proteins capable of restoring InsP7 synthesis in yeast mutants, thus AtVip1 and AtVip2 can function as bonafide InsP6 kinases. AtVip1 and AtVip2 are differentially expressed in plant tissues, suggesting non-redundant or non-overlapping functions in plants. These results contribute to our knowledge of inositol phosphate metabolism and will lay a foundation for understanding the role of InsP7 and InsP8 in plants.

Barley (Hordeum vulgare L.) low phytic acid 1-1: an endosperm-specific, filial determinant of seed total phosphorus

Inositol hexaphosphate (Ins P6 or "phytic acid") typically accounts for 75 (± 10%) of seed total phosphorus (P). In some cases, genetic blocks in seed Ins P6 accumulation can also alter the distribution or total amount of seed P. In nonmutant barley (Hordeum vulgare L.) caryopses, ~80% of Ins P6 and total P accumulate in the aleurone layer, the outer layer of the endosperm, with the remainder in the germ. In barley low phytic acid 1-1 (Hvlpa1-1) seed, both endosperm Ins P6 and total P are reduced (~45% and ~25%, respectively), but germs are phenotypically wild type. This translates into a net reduction in whole-seed total P of ~15%. Nutrient culture studies demonstrate that the reduction in endosperm total P is not due to a reduction in the uptake of P into the maternal plant. Genetic tests (analyses of testcross and F2 seed) reveal that the Hvlpa1-1 genotype of the filial seed conditions the seed total P reduction; sibling seed in the same head of barley that differ in their Hvlpa1-1 genotype (heterozygous vs. homozygous recessive) differ in their total P (normal vs. reduced, respectively). Therefore, Hvlpa1 functions as a seed-specific or filial determinant of barley endosperm total P.

Phytic acid in green leaves

Phytic acid or phytate, the free-acid form of myo-inositolhexakiphosphate, is abundant in many seeds and fruits, where it represents the major storage form of phosphorus. Although also known from other plant tissues, available reports on the occurrence of phytic acid, e.g. in leaves, have never been compiled, nor have they been critically reviewed. We found 45 published studies with information on phytic acid content in leaves. Phytic acid was almost always detected when studies specifically tried to detect it, and accounted for up to 98% of total P. However, we argue that such extreme values, which rival findings from storage organs, are dubious and probably result from measurement errors. Excluding these high values from further quantitative analysis, foliar phytic acid-P averaged 2.3 mg·g(-1) , and represented, on average, 7.6% of total P. Remarkably, the ratio of phytic acid-P to total P did not increase with total P, we even detected a negative correlation of the two variables within one species, Manihot esculenta. This enigmatic finding warrants further attention.

Combating Mineral Malnutrition through Iron and Zinc Biofortification of Cereals

 Iron and zinc are 2 important nutrients in the human diet. Their deficiencies in humans lead to a variety of health-related problems. Iron and zinc biofortification of cereals is considered a cost-effective solution to overcome the malnutrition of these minerals. Biofortification aims at either increasing accumulation of these minerals in edible parts, endosperm, or to increase their bioavailability. Iron and zinc fertilization management positively influence their accumulation in cereal grains. Regarding genetic strategies, quantitative genetic studies show the existence of ample variation for iron and zinc accumulation as well as inhibitors or promoters of their bioavailability in cereal grains. However, the genes underlying this variation have rarely been identified and never used in breeding programs. Genetically modified cereals developed by modulation of genes involved in iron and zinc homeostasis, or genes influencing bioavailability, have shown promising results. However, iron and zinc concentration were quantified in the whole grains during most of the studies, whereas a significant proportion of them is lost during milling. This makes it difficult to realistically assess the effectiveness of the different strategies. Moreover, modifications in the accumulation of toxic elements, like cadmium and arsenic, that are of concern for food safety are rarely determined. Trials in living organisms with iron- and zinc-biofortified cereals also remain to be undertaken. This review focuses on the common challenges and their possible solutions related to agronomic as well as genetic iron and zinc biofortification of cereals.

Increasing Phosphatidylinositol (4,5)-Bisphosphate Biosynthesis Affects Basal Signaling and Chloroplast Metabolism in Arabidopsis thaliana

One challenge in studying the second messenger inositol(1,4,5)-trisphosphate (InsP₃) is that it is present in very low amounts and increases only transiently in response to stimuli. To identify events downstream of InsP₃, we generated transgenic plants constitutively expressing the high specific activity, human phosphatidylinositol 4-phosphate 5-kinase Iα (HsPIPKIα). PIP5K is the enzyme that synthesizes phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P₂); this reaction is flux limiting in InsP₃ biosynthesis in plants. Plasma membranes from transgenic Arabidopsis expressing HsPIPKIα had 2-3 fold higher PIP5K specific activity, and basal InsP₃ levels in seedlings and leaves were >2-fold higher than wild type. Although there was no significant difference in photosynthetic electron transport, HsPIPKIα plants had significantly higher starch (2-4 fold) and 20% higher anthocyanin compared to controls. Starch content was higher both during the day and at the end of dark period. In addition, transcripts of genes involved in starch metabolism such as SEX1 (glucan water dikinase) and SEX4 (phosphoglucan phosphatase), DBE (debranching enzyme), MEX1 (maltose transporter), APL3 (ADP-glucose pyrophosphorylase) and glucose-6-phosphate transporter (Glc6PT) were up-regulated in the HsPIPKIα plants. Our results reveal that increasing the phosphoinositide (PI) pathway affects chloroplast carbon metabolism and suggest that InsP₃ is one component of an inter-organelle signaling network regulating chloroplast metabolism.

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.

High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities

BACKGROUND AND AIMS

Phosphate (Pi) deficiency in soils is a major limiting factor for crop growth worldwide. Plant growth under low Pi conditions correlates with root architectural traits and it may therefore be possible to select these traits for crop improvement. The aim of this study was to characterize root architectural traits, and to test quantitative trait loci (QTL) associated with these traits, under low Pi (LP) and high Pi (HP) availability in Brassica napus.

METHODS

Root architectural traits were characterized in seedlings of a double haploid (DH) mapping population (n = 190) of B. napus ['Tapidor' × 'Ningyou 7' (TNDH)] using high-throughput phenotyping methods. Primary root length (PRL), lateral root length (LRL), lateral root number (LRN), lateral root density (LRD) and biomass traits were measured 12 d post-germination in agar at LP and HP.

KEY RESULTS

In general, root and biomass traits were highly correlated under LP and HP conditions. 'Ningyou 7' had greater LRL, LRN and LRD than 'Tapidor', at both LP and HP availability, but smaller PRL. A cluster of highly significant QTL for LRN, LRD and biomass traits at LP availability were identified on chromosome A03; QTL for PRL were identified on chromosomes A07 and C06.

CONCLUSIONS

High-throughput phenotyping of Brassica can be used to identify root architectural traits which correlate with shoot biomass. It is feasible that these traits could be used in crop improvement strategies. The identification of QTL linked to root traits under LP and HP conditions provides further insights on the genetic basis of plant tolerance to P deficiency, and these QTL warrant further dissection.

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.

Identification of quantitative trait loci controlling fibre length and lignin content in Arabidopsis thaliana stems

Fibre properties and the biochemical composition of cell walls are important traits in many applications. For example, the lengths of fibres define the strength and quality of paper, and lignin content is a critical parameter for the use of biomass in biofuel production. Identifying genes controlling these traits is comparatively difficult in woody species, because of long generation times and limited amenability to high-resolution genetic mapping. To address this problem, this study mapped quantitative trait loci (QTLs) defining fibre length and lignin content in the Arabidopsis recombinant inbred line population Col-4 × Ler-0. Adapting high-throughput phenotyping techniques for both traits for measurements in Arabidopsis inflorescence stems identified significant QTLs for fibre length on chromosomes 2 and 5, as well as one significant QTL affecting lignin content on chromosome 2. For fibre length, total variation within the population was 208% higher than between parental lines and the identified QTLs explained 50.58% of the observed variation. For lignin content, the values were 261 and 26.51%, respectively. Bioinformatics analysis of the associated intervals identified a number of candidate genes for fibre length and lignin content. This study demonstrates that molecular mapping of QTLs pertaining to wood and fibre properties is possible in Arabidopsis, which substantially broadens the use of Arabidopsis as a model species for the functional characterization of plant genes.

Genetic diversity of thiamin and folate in primitive cultivated and wild potato (Solanum) species

Biofortification of staple crops like potato via breeding is an attractive strategy to reduce human micronutrient deficiencies. A prerequisite is metabolic phenotyping of genetically diverse material which can potentially be used as parents in breeding programs. Thus, the natural genetic diversity of thiamin and folate contents was investigated in indigenous cultivated potatoes (Solanum tuberosum group Andigenum) and wild potato species (Solanum section Petota). Significant differences were found among clones and species. For about 50% of the clones there were variations in thiamin and folate contents between years. Genotypes which contained over 2-fold the thiamin and 4-fold the folate content compared to the modern variety Russet Burbank were identified and should be useful material to integrate in breeding programs which aim to enhance the nutritional value of potato. Primitive cultivars and wild species with widely different amounts of thiamin and folate will also be valuable tools to explore their respective metabolic regulation.

A defective ABC transporter of the MRP family, responsible for the bean lpa1 mutation, affects the regulation of the phytic acid pathway, reduces seed myo-inositol and alters ABA sensitivity

• We previously identified the lpa1 (low phytic acid) 280-10 line that carries a mutation conferring a 90% reduction in phytic acid (InsP(6) ) content. In contrast to other lpa mutants, lpa1(280-10) does not display negative pleiotropic effects. In the present paper, we have identified the mutated gene and analysed its impact on the phytic acid pathway. • Here, we mapped the lpa1(280-10) mutation by bulk analysis on a segregating F(2) population, an then, by comparison with the soybean genome, we identified and sequenced a candidate gene. The InsP(6) pathway was analysed by gene expression and quantification of metabolites. • The mutated Pvmrp1(280-10) cosegregates with the lpa1(280-10) mutation, and the expression level of several genes of the InsP(6) pathway are reduced in the lpa1(280-10) mutant as well as the inositol and raffinosaccharide content. PvMrp2, a very similar paralogue of PvMrp1 was also mapped and sequenced. • The lpa1 mutation in beans is likely the result of a defective Mrp1 gene (orthologous to the lpa genes AtMRP5 and ZmMRP4), while its Mrp2 paralog is not able to complement the mutant phenotype in the seed. This mutation appears to down-regulate the InsP(6) pathway at the transcriptional level, as well as altering inositol-related metabolism and affecting ABA sensitivity.

Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.

Identification of genes necessary for wild-type levels of seed phytic acid in Arabidopsis thaliana using a reverse genetics approach

The majority of phosphorus (P) in seeds is found in phytic acid (InsP(6)) which accumulates as the mixed salt phytate. InsP(6) is generally considered to be an anti-nutrient and the development of low phytic acid (lpa) seed crops is of significant interest. We have employed a reverse genetics approach to examine the impact of disrupting genes involved in inositol phosphate metabolism on Arabidopsis seed InsP(6) levels. Our analysis revealed that knockout mutations in three genes (AtITPK1, AtITPK4, and AtMIK/At5g58730) reduced seed InsP(6) in addition to knockouts of four previously reported genes (AtIPK1, AtIPK2β, AtMRP5, and At5g60760). Seeds of these lpa mutants also exhibited reduced germination under various stress conditions. The greatest reduction in InsP(6) (>70%) was observed in atmrp5 seeds which were also among the least sensitive to the stresses examined. Expression analysis of the lpa genes revealed three distinct patterns in developing siliques consistent with their presumed roles. Disruption of each lpa gene resulted in changes in the expression in some of the other lpa genes indicating that transcription of lpa genes is modulated by other constituents of InsP(6) metabolism. While all the lpa genes represent possible targets for genetic engineering of low phytate seed crops, mutations in AtMRP5, AtMIK, and At5g60760 may be most successful for conventional approaches such as mutation breeding.

Identification of genes necessary for wild-type levels of seed phytic acid in Arabidopsis thaliana using a reverse genetics approach

The majority of phosphorus (P) in seeds is found in phytic acid (InsP(6)) which accumulates as the mixed salt phytate. InsP(6) is generally considered to be an anti-nutrient and the development of low phytic acid (lpa) seed crops is of significant interest. We have employed a reverse genetics approach to examine the impact of disrupting genes involved in inositol phosphate metabolism on Arabidopsis seed InsP(6) levels. Our analysis revealed that knockout mutations in three genes (AtITPK1, AtITPK4, and AtMIK/At5g58730) reduced seed InsP(6) in addition to knockouts of four previously reported genes (AtIPK1, AtIPK2β, AtMRP5, and At5g60760). Seeds of these lpa mutants also exhibited reduced germination under various stress conditions. The greatest reduction in InsP(6) (>70%) was observed in atmrp5 seeds which were also among the least sensitive to the stresses examined. Expression analysis of the lpa genes revealed three distinct patterns in developing siliques consistent with their presumed roles. Disruption of each lpa gene resulted in changes in the expression in some of the other lpa genes indicating that transcription of lpa genes is modulated by other constituents of InsP(6) metabolism. While all the lpa genes represent possible targets for genetic engineering of low phytate seed crops, mutations in AtMRP5, AtMIK, and At5g60760 may be most successful for conventional approaches such as mutation breeding.

Genetic and physiological analysis of iron biofortification in maize kernels

Background

Maize is a major cereal crop widely consumed in developing countries, which have a high prevalence of iron (Fe) deficiency anemia. The major cause of Fe deficiency in these countries is inadequate intake of bioavailable Fe, where poverty is a major factor. Therefore, biofortification of maize by increasing Fe concentration and or bioavailability has great potential to alleviate this deficiency. Maize is also a model system for genomic research and thus allows the opportunity for gene discovery. Here we describe an integrated genetic and physiological analysis of Fe nutrition in maize kernels, to identify loci that influence grain Fe concentration and bioavailability.

Methodology

Quantitative trait locus (QTL) analysis was used to dissect grain Fe concentration (FeGC) and Fe bioavailability (FeGB) from the Intermated B73 × Mo17 (IBM) recombinant inbred (RI) population. FeGC was determined by ion coupled argon plasma emission spectroscopy (ICP). FeGB was determined by an in vitro digestion/Caco-2 cell line bioassay.

Conclusions

Three modest QTL for FeGC were detected, in spite of high heritability. This suggests that FeGC is controlled by many small QTL, which may make it a challenging trait to improve by marker assisted breeding. Ten QTL for FeGB were identified and explained 54% of the variance observed in samples from a single year/location. Three of the largest FeGB QTL were isolated in sister derived lines and their effect was observed in three subsequent seasons in New York. Single season evaluations were also made at six other sites around North America, suggesting the enhancement of FeGB was not specific to our farm site. FeGB was not correlated with FeGC or phytic acid, suggesting that novel regulators of Fe nutrition are responsible for the differences observed. Our results indicate that iron biofortification of maize grain is achievable using specialized phenotyping tools and conventional plant breeding techniques.

Relationships between growth, growth response to nutrient supply, and ion content using a recombinant inbred line population in Arabidopsis

Growth is an integrative trait that responds to environmental factors and is crucial for plant fitness. A major environmental factor influencing plant growth is nutrient supply. In order to explore this relationship further, we quantified growth-related traits, ion content, and other biochemical traits (protein, hexose, and chlorophyll contents) of a recombinant inbred line population of Arabidopsis (Arabidopsis thaliana) grown on different levels of potassium and phosphate. Performing an all subsets multiple regression analyses revealed a link between growth-related traits and mineral nutrient content. Based on our results, up to 85% of growth variation can be explained by variation in ion content, highlighting the importance of ionomics for a broader understanding of plant growth. In addition, quantitative trait loci (QTLs) were detected for growth-related traits, ion content, further biochemical traits, and their responses to reduced supplies of potassium or phosphate. Colocalization of these QTLs is explored, and candidate genes are discussed. A QTL for rosette weight response to reduced potassium supply was identified on the bottom of chromosome 5, and its effects were validated using selected near isogenic lines. These lines retained over 20% more rosette weight in reduced potassium supply, accompanied by an increase in potassium content in their leaves.

Natural genetic variation in selected populations of Arabidopsis thaliana is associated with ionomic differences

Controlling elemental composition is critical for plant growth and development as well as the nutrition of humans who utilize plants for food. Uncovering the genetic architecture underlying mineral ion homeostasis in plants is a critical first step towards understanding the biochemical networks that regulate a plant's elemental composition (ionome). Natural accessions of Arabidopsis thaliana provide a rich source of genetic diversity that leads to phenotypic differences. We analyzed the concentrations of 17 different elements in 12 A. thaliana accessions and three recombinant inbred line (RIL) populations grown in several different environments using high-throughput inductively coupled plasma- mass spectroscopy (ICP-MS). Significant differences were detected between the accessions for most elements and we identified over a hundred QTLs for elemental accumulation in the RIL populations. Altering the environment the plants were grown in had a strong effect on the correlations between different elements and the QTLs controlling elemental accumulation. All ionomic data presented is publicly available at www.ionomicshub.org.

Quantitative trait loci affecting seed mineral concentrations in Brassica napus grown with contrasting phosphorus supplies

BACKGROUND AND AIMS

Phosphorus (P) deficiency is one of the major limitations for crop production. A significant relationship exists between plant P uptake from soils and the accumulation of P and other mineral elements in seeds. The aims of this study were to identify and characterize genetic loci (QTLs) controlling the accumulation of mineral elements in seeds of Brassica napus grown with contrasting P availabilities.

METHODS

A population of 124 recombinant inbred lines derived from a cross between P-inefficient 'B104-2' and P-efficient 'Eyou Changjia' was used for phenotypic investigation and QTL analysis. Two-year field trials were conducted with two P treatments. Concentrations of mineral elements (P, Ca, Mg, Fe, Zn, Cu and Mn) in seeds were determined and QTLs were identified by composite interval mapping.

KEY RESULTS

There was significant genetic variation in seed concentrations of all mineral elements, and correlations between most elements were observed. A total of 78 putative QTLs (45 under the normal-P conditions and 33 under the low-P conditions) were detected, covering 17 linkage groups and accounting for 7.84-18.1 % of the phenotypic variation. Sixteen of these QTLs were identified in at least two environments, and co-location of QTLs for different mineral traits was found on several linkage groups. By in silico mapping, 21 genes involved in ion homeostasis in Arabidopsis were mapped to the QTL intervals identified in B. napus.

CONCLUSIONS

The accumulation of mineral elements in seeds is controlled by multiple genes. Common physiological and molecular mechanisms could be involved in the accumulation of several mineral elements, and genes involved in these processes in B. napus are suggested. These results offer insights to the genetic basis of seed mineral accumulation across different P levels in B. napus.

In vitro solubility of calcium, iron and zinc in relation to phytic acid levels in rice-based consumer products in China

In vitro solubility of calcium, iron and zinc in relation to phytic acid (PA) levels in 30 commercial rice-based foods from China was studied. Solubility of minerals and molar ratios of PA to minerals varied with degrees of processing. In primary products, [PA]/[Ca] values were less than 5 and [PA]/[Fe] and [PA]/[Zn] similarly ranged between 5 and 74, with most values between 20 and 30. [PA]/[mineral] molar ratios in intensively processed products were lower. Solubility of calcium ranged from 0% to 87%, with the lowest in brown rice (12%) and the highest in infant foods (50%). Iron solubility in two-thirds of samples was lower than 30%, and that of zinc narrowly ranged from 6% to 30%. Solubility of minerals was not significantly affected by [PA]/[mineral]. At present, neither primary nor intensively processed rice-based products are good dietary sources of minerals. Improvements should be attempted by dephytinization, mineral fortification or, preferably, combination of both.

Transcriptional profile of genes involved in the biosynthesis of phytate and ferritin in Coffea

The present work aimed to study the control of the biosynthesis of the antinutritional factor phytate and its associated Fe-rich protein family, ferritin, in coffee. Phytate has the ability to chelate Fe, making it unavailable to human absorption. The Coffea genome databases were queried for genes associated with phytate metabolism and ferritin genes. The genetic framework for phytate biosynthesis and its reverse pathway was identified in silico analyses and indicate that Coffea phosphatidyl inositol kinase and monophosphatase families play nonredundant roles in phytate metabolism. The transcriptional profiles of phytate biosynthesis key-genes MYO-INOSITOL(3)P1 SYNTHASE, two genes coding for PHOSPHATIDYL INOSITOL KINASE, and three FERRITIN genes were temporally evaluated by qPCR in coffee seeds from two crop locations, Adamantina-SP and Ouro-Fino-MG, the last one traditionally associated with high-quality coffee beverage grain. A targeted metabolome profile of phytic acid contents throughout three fruit maturation stages in association with the transcriptional analysis was also obtained. Taken together, our data indicate that the investigated local conditions did not cause significant alterations in phytate biosynthesis. Futhermore, the temporal transcriptional profiling revealed that candidate gene expression is regulated independently of phytate accumulation. In contrast, the expression profile of ferritin-unit genes is affected by environmental conditions and genetic background. The roles of the investigated genes are discussed concerning the quality of coffee beverage.

Uncertainty analysis of the nonideal competitive adsorption-donnan model: effects of dissolved organic matter variability on predicted metal speciation in soil solution

Ion binding models such as the nonideal competitive adsorption-Donnan model (NICA-Donnan) and model VI successfully describe laboratory data of proton and metal binding to purified humic substances (HS). In this study model performance was tested in more complex natural systems. The speciation predicted with the NICA-Donnan model and the associated uncertainty were compared with independent measurements in soil solution extracts, including the free metal ion activity and fulvic (FA) and humic acid (HA) fractions of dissolved organic matter (DOM). Potentially important sources of uncertainty are the DOM composition and the variation in binding properties of HS. HS fractions of DOM in soil solution extracts varied between 14 and 63% and consisted mainly of FA. Moreover, binding parameters optimized for individual FA samples show substantial variation. Monte Carlo simulations show that uncertainties in predicted metal speciation, for metals with a high affinity for FA (Cu, Pb), are largely due to the natural variation in binding properties (i.e., the affinity) of FA. Predictions for metals with a lower affinity (Cd) are more prone to uncertainties in the fraction FA in DOM and the maximum site density (i.e., the capacity) of the FA. Based on these findings, suggestions are provided to reduce uncertainties in model predictions.

Natural variation in Arabidopsis adaptation to growth at low nitrogen conditions

Improving nutrient use efficiency of crop plants, especially at low input, is essential to ensure sustainable food production in the future. In order to address the genetic basis of nutrient use efficiency in a model system, growth of Arabidopsis ecotypes at normal and low nitrogen (N) supply was compared. The ecotypes differed significantly in the extent of growth reduction in limiting conditions. The fresh weight of Shahdara and Ws grown at 1mM nitrate was reduced by 30% compared to control, whereas Col-0 and Ga-0 were almost unaffected. Total N content was reduced in all ecotypes by 10-30%. The capacity to store nitrate correlated with the tolerance to low N; in Shahdara and Ws, but not in Col-0 and Ga-0, nitrate content on low N was significantly reduced compared to control nutrition. The mRNA levels for genes of nitrate uptake and assimilation were only moderately affected by the treatment. The transcript levels of nitrate reductase NIA1 and nitrite reductase were higher in the ecotypes tolerant to low N (Col-0 and Ga-0) with normal N nutrition but on low N they were reduced to a much higher extent than the sensitive ecotypes (Shahdara and Ws). It seems that a higher capacity to keep nitrate reserves at low N, perhaps due to the ability to turn down nitrate reduction rate, is responsible for a better tolerance of Col-0 and Ga-0 to low N supply.