Identification and molecular characterization of the nicotianamine synthase gene family in bread wheat

Transcriptome and biochemical analysis in hexaploid wheat with contrasting tolerance to iron deficiency pinpoints multi-layered molecular process

Iron (Fe) is an essential plant nutrient that is indispensable for many physiological activities. This study is an effort to identify the molecular and biochemical basis of wheat genotypes with contrasting tolerance towards Fe deficiency. Our physiological experiments performed at the early growth stage in cv. Kanchan (KAN) showed Fe deficiency tolerance, whereas cv. PBW343 (PBW) was susceptible. Under Fe deficient condition, KAN showed delayed chlorosis, high SPAD values, and low malondialdehyde content compared to PBW, indicative of Fe deficient condition. Comparative shoot transcriptomics revealed increased expression of photosynthetic pathway genes in PBW, further suggesting its sensitivity to Fe fluctuations. Under Fe deficiency, both the cultivars showed distinct molecular re-arrangements such as high expression of genes involved in Fe uptake (including membrane transporters) and its remobilization. Specifically, in KAN these changes lead to high root phytosiderophores (PS) biosynthesis and its release, resulting in enhanced Fe translocation index. Utilizing the non-transgenic TILLING (Targeting Induced Lesions in Genomes) technology, we identified TaZIFL4.2D as a putative PS efflux transporter. Characterization of the wheat TILLING lines indicated that TaZIFL4.2 functions in PS release and Fe acquisition, thereby imparting tolerance to Fe deficiency. Altogether, this work highlights the mechanistic insight into Fe deficiency tolerance of hexaploid wheat, thus enabling breeders to select suitable genotypes to utilize nutrients for maximum yields.

Molecular characterization of stable QTL and putative candidate genes for grain zinc and iron concentrations in two related wheat populations

KEY MESSAGE

Major QTL for grain zinc and iron concentrations were identified on the long arm of chromosomes 2D and 6D. Gene-based KASP markers were developed for putative candidate genes TaIPK1-2D and TaNAS10-6D. Micronutrient malnutrition is one of the most common public health problems in the world. Biofortification, the most attractive and sustainable solution to surmount malnutrition requires the development of micronutrient enriched new crop cultivars. In this study, two recombinant inbred line (RIL) populations, ZM175/XY60 and ZM175/LX987, were used to identify QTL for grain zinc concentration (GZnC), grain iron concentration (GFeC) and thousand grain weight (TGW). Eight QTL for GZnC, six QTL for GFeC and five QTL for TGW were detected. Three QTL on chromosomes 2DL and 4BS and chromosome 6A showed pleiotropic effects on all three traits. The 4BS and 6A QTL also increased plant height and might be Rht-B1a and Rht25a, respectively. The 2DL locus within a suppressed recombination region was identified in both RIL populations and the favorable allele simultaneously increasing GZnC, GFeC and TGW was contributed by XY60 and LX987. A QTL on chromosome 6DL associated only with GZnC was detected in ZM175/XY60 and was validated in JD8/AK58 RILs using kompetitive allele-specific PCR (KASP) marker K_AX-110119937. Both the 2DL and 6DL QTL were new loci for GZnC. Based on gene annotations, sequence variations and expression profiles, the phytic acid biosynthesis gene TaIPK1-2D and nicotianamine synthase gene TaNAS10-6D were predicted as candidate genes. Their gene-based KASP markers were developed and validated in a cultivar panel of 343 wheat accessions. This study investigated the genetic basis of GZnC and GFeC and provided valuable candidate genes and markers for breeding Zn- and Fe-enriched wheat.

Nicotianamine: A Key Player in Metal Homeostasis and Hyperaccumulation in Plants

Nicotianamine (NA) is a low-molecular-weight N-containing metal-binding ligand, whose accumulation in plant organs changes under metal deficiency or excess. Although NA biosynthesis can be induced in vivo by various metals, this non-proteinogenic amino acid is mainly involved in the detoxification and transport of iron, zinc, nickel, copper and manganese. This review summarizes the current knowledge on NA biosynthesis and its regulation, considers the mechanisms of NA secretion by plant roots, as well as the mechanisms of intracellular transport of NA and its complexes with metals, and its role in radial and long-distance metal transport. Its role in metal tolerance is also discussed. The NA contents in excluders, storing metals primarily in roots, and in hyperaccumulators, accumulating metals mainly in shoots, are compared. The available data suggest that NA plays an important role in maintaining metal homeostasis and hyperaccumulation mechanisms. The study of metal-binding compounds is of interdisciplinary significance, not only regarding their effects on metal toxicity in plants, but also in connection with the development of biofortification approaches to increase the metal contents, primarily of iron and zinc, in agricultural plants, since the deficiency of these elements in food crops seriously affects human health.

Interaction between selenium and essential micronutrient elements in plants: A systematic review

Nutrient imbalance (i.e., deficiency and toxicity) of microelements is an outstanding environmental issue that influences each aspect of ecosystems. Although the crucial roles of microelements in entire lifecycle of plants have been widely acknowledged, the effective control of microelements is still neglected due to the narrow safe margins. Selenium (Se) is an essential element for humans and animals. Although it is not believed to be indispensable for plants, many literatures have reported the significance of Se in terms of the uptake, accumulation, and detoxification of essential microelements in plants. However, most papers only concerned on the antagonistic effect of Se on metal elements in plants and ignored the underlying mechanisms. There is still a lack of systematic review articles to summarize the comprehensive knowledge on the connections between Se and microelements in plants. In this review, we conclude the bidirectional effects of Se on micronutrients in plants, including iron, zinc, copper, manganese, nickel, molybdenum, sodium, chlorine, and boron. The regulatory mechanisms of Se on these micronutrients are also analyzed. Moreover, we further emphasize the role of Se in alleviating element toxicity and adjusting the concentration of micronutrients in plants by altering the soil conditions (e.g., adsorption, pH, and organic matter), promoting microbial activity, participating in vital physiological and metabolic processes, generating element competition, stimulating metal chelation, organelle compartmentalization, and sequestration, improving the antioxidant defense system, and controlling related genes involved in transportation and tolerance. Based on the current understanding of the interaction between Se and these essential elements, future directions for research are suggested.

Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize

Anther development from stamen primordium to pollen dispersal is complex and essential to sexual reproduction. How this highly dynamic and complex developmental process is controlled genetically is not well understood, especially for genes involved in specific key developmental phases. Here we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize (Zea mays). Global transcriptome analyses revealed distinct phases of cell division and expansion, meiosis, pollen maturation, and mature pollen, for which we detected 50, 245, 42, and 414 phase-specific marker genes, respectively. Phase-specific transcription factor genes were significantly enriched in the phase of meiosis. The phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23, indicating they might have important roles in anther development. We explored a desiccation-related protein gene, ZmDRP1, which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage, by generating knockout mutants. Notably, mutants in ZmDRP1 were completely male-sterile, with abnormal Ubisch bodies and defective pollen exine. Our work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development.

Whole genome re-sequencing of indian wheat genotypes for identification of genomic variants for grain iron and zinc content

BACKGROUND

Whole-genome sequencing information which is of abundant significance for genetic evolution, and breeding of crops. Wheat (Triticum spp) is most widely grown and consumed crops globally. Micronutrients are very essential for healthy development of human being and their sufficient consumption in diet is essential for various metabolic functions. Biofortification of wheat grains with iron (Fe) and zinc (Zn) has proved the most reliable and effective way to combat micronutrient associated deficiency. Genetic variability for grain micronutrient could provide insight to dissect the traits.

METHODS AND RESULTS

In the current study, 1300 wheat lines were screened for grain Fe and Zn content, out of which only five important Indian wheat genotypes were selected on the basis of Fe and Zn contents. These lines were multiplied during at the National Agri-Food Biotechnology Institute (NABI) and re-sequenced to identify genomic variants in candidate genes for Fe and Zn between the genotypes. Whole genome sequencing generated ̴ 12 Gb clean data. Comparative genome analysis identified 254 genomic variants in the candidate genes associated with deleterious effect on protein function.

CONCLUSIONS

The present study demonstrated the fundamental in understanding the genomic variations for Fe and Zn enrichment to generate healthier wheat grains.

Organ-specific expression of genes involved in iron homeostasis in wheat mutant lines with increased grain iron and zinc content

Background

Iron deficiency is a well-known nutritional disorder, and the imbalance of trace-elements, specifically iron, is the most common nutrient deficiency of foods across the world, including in Kazakhstan. Wheat has significant nutritional relevance, especially in the provision of iron, however many bread wheat varieties have low iron despite the need for human nourishment. In this study, the expression profiles of wheat homologous genes related to iron homeostasis were investigated. The work resulted in the development of two new M₅ mutant lines of spring bread wheat through gamma-irradiation (200 Gy) with higher grain iron and zinc content, lower phytic acid content, and enhanced iron bioavailability compared to the parent variety. Mutant lines were also characterized by higher means of yield associated traits such as grain number per main spike, grain weight per main spike, grain weight per plant, and thousand-grain weight.

Methods

The homologous genes of bread wheat from several groups were selected for gene expression studies exploring the tight control of iron uptake, translocation rate and accumulation in leaves and roots, and comprised the following: (1) S-adenosylmethionine synthase (SAMS), nicotianamine synthase (NAS1), nicotianamine aminotransferase (NAAT), deoxymugineic acid synthetase (DMAS), involved in the synthesis and release of phytosiderophores; (2) transcription factor basic helix-loop-helix (bHLH); (3) transporters of mugineic acid (TOM), involved in long-distance iron transport; (4) yellow stripe-like (YSlA), and the vacuolar transporter (VIT2), involved in intracellular iron transport and storage; and lastly (5) natural resistance-associated macrophage protein (NRAMP) and ferritin (Fer1A).

Results

The wheat homologous genes TaSAMS, TaNAS1, and TaDMAS, were significantly up-regulated in the roots of both mutant lines by 2.1-4.7-fold compared to the parent variety. The combined over-expression of TaYSlA and TaVIT2 was also revealed in the roots of mutant lines by 1.3-2.7-fold. In one of the mutant lines, genes encoding intracellular iron transport and storage genes TaNRAMP and TaFer1A-D showed significant up-regulation in roots and leaves (by 1.4- and 3.5-fold, respectively). The highest expression was recorded in the transcription factor TabHLH, which was expressed 13.1- and 30.2-fold in the roots of mutant lines. Our research revealed that genotype-dependent and organ-specific gene expression profiles can provide new insights into iron uptake, translocation rate, storage, and regulation in wheat which aid the prioritization of gene targets for iron biofortification and bioavailability.

Improving Zinc and Iron Biofortification in Wheat through Genomics Approaches

Globally, about 20% of calories (energy) come from wheat. In some countries, it is more than 70%. More than 2 billion people are at risk for zinc deficiency and even more, people are at risk of iron deficiency, nearly a quarter of all children underage group of 5 are physically and cognitively stunted, and lack of dietary zinc is a major contributing factor. Biofortified wheat with elevated levels of zinc and iron has several potential advantages as a delivery vehicle for micronutrients in the diets of resource-poor consumers who depend on cereal-based diets. The conventional breeding strategies have been successful in the introduction of novel alleles for grain Zn and Fe that led to the release of competitive Zn enriched wheat varieties in South Asia. The major challenge over the next few decades will be to maintain the rates of genetic gains for grain yield along with increased grain Zn/Fe concentration to meet the food and nutritional security challenges. Therefore, to remain competitive, the performance of Zn-enhanced lines/varieties must be equal or superior to that of current non-biofortified elite lines/varieties. Since both yield and Zn content are invisible and quantitatively inherited traits except few intermediate effect QTL regions identified for grain Zn, increased breeding efforts and new approaches are required to combine them at high frequency, ensuring that Zn levels are steadily increased to the required levels across the breeding pipelines. The current review article provides a comprehensive list of genomic regions for enhancing grain Zn and Fe concentrations in wheat including key candidate gene families such NAS, ZIP, VLT, ZIFL, and YSL. Implementing forward breeding by taking advantage of the rapid cycling trait pipeline approaches would simultaneously introgress high Zn and Fe QTL into the high Zn and normal elite lines, further increasing Zn and Fe concentrations.

Combined morpho-physiological, ionomic and transcriptomic analyses reveal adaptive responses of allohexaploid wheat (Triticum aestivum L.) to iron deficiency

BACKGROUND

Plants worldwide are often stressed by low Fe availability around the world, especially in aerobic soils. Therefore, the plant growth, seed yield, and quality of crop species are severely inhibited under Fe deficiency. Fe metabolism in plants is controlled by a series of complex transport, storage, and regulatory mechanisms in cells. Allohexaploid wheat (Triticum aestivum L.) is a staple upland crop species that is highly sensitive to low Fe stresses. Although some studies have been previously conducted on the responses of wheat plants to Fe deficiency, the key mechanisms underlying adaptive responses are still unclear in wheat due to its large and complex genome.

RESULTS

Transmission electron microscopy showed that the chloroplast structure was severely damaged under Fe deficiency. Paraffin sectioning revealed that the division rates of meristematic cells were reduced, and the sizes of elongated cells were diminished. ICP-MS-assisted ionmics analysis showed that low-Fe stress significantly limited the absorption of nutrients, including N, P, K, Ca, Mg, Fe, Mn, Cu, Zn, and B nutrients. High-throughput transcriptome sequencing identified 378 and 2,619 genome-wide differentially expressed genes (DEGs) were identified in the shoots and roots between high-Fe and low-Fe conditions, respectively. These DEGs were mainly involved in the Fe chelator biosynthesis, ion transport, photosynthesis, amino acid metabolism, and protein synthesis. Gene coexpression network diagrams indicated that TaIRT1b-4A, TaNAS2-6D, TaNAS1a-6A, TaNAS1-6B, and TaNAAT1b-1D might function as key regulators in the adaptive responses of wheat plants to Fe deficiency.

CONCLUSIONS

These results might help us fully understand the morpho-physiological and molecular responses of wheat plants to low-Fe stress, and provide elite genetic resources for the genetic modification of efficient Fe use.

Strategies and Bottlenecks in Hexaploid Wheat to Mobilize Soil Iron to Grains

Our knowledge of iron (Fe) uptake and mobilization in plants is mainly based on Arabidopsis and rice. Although multiple players of Fe homeostasis have been elucidated, there is a significant gap in our understanding of crop species, such as wheat. It is, therefore, imperative not only to understand the different hurdles for Fe enrichment in tissues but also to address specifically the knowns/unknowns involved in the plausible mechanism of Fe sensing, signaling, transport, and subsequent storage in plants. In the present review, a unique perspective has been described in light of recent knowledge generated in wheat, an economically important crop. The strategies to boost efficient Fe uptake, transcriptional regulation, and long-distance mobilization in grains have been discussed, emphasizing recent biotechnological routes to load Fe in grains. This article also highlights the new elements of physiological and molecular genetics that underpin the mechanistic insight for the identified Fe-related genes and discusses the bottlenecks in unloading the Fe in grains. The information presented here will provide much-needed resources and directions to overcome challenges and design efficient strategies to enhance the Fe density in wheat grains.

Achieving nutritional security in India through iron and zinc biofortification in pearl millet (Pennisetum glaucum (L.) R. Br.)

The health problems caused by iron (Fe) and zinc (Zn) deficiency plague developing and underdeveloped countries. A vegetarian person mainly depends on cereal based diet with low quantity of Fe and Zn. Biofortification is an economical and sustainable approach to challenge the micronutrient malnutrition problem globally. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the nutri-cereals and mostly grown under hot, dry conditions on infertile soils of low water-holding capacity, where other crops generally fail. It contains anti-nutrient compounds like phytic acid and polyphenols which reduce the mineral bioavailability because of their chelating properties. Biofortification of pearl millet is like a double-edged sword which cuts down the economic burden and simultaneously supplies required nutrition to the poor, offering a great scope for food security as well as nutritional security. With this background, this review focus on biofortification of grain Fe and Zn content in pearl millet. Genetic research on Fe and Zn uptake and accumulation in pearl millet grain is crucial in identifying the 'bottlenecks' in biofortification. The review also reveals the need and strategies for increasing bioavailability of Fe and Zn in humans by increasing promoters and decreasing anti-nutritional factors in pearl millet.

Genome-wide analysis of the NAAT, DMAS, TOM, and ENA gene families in maize suggests their roles in mediating iron homeostasis

BACKGROUND

Nicotianamine (NA), 2'-deoxymugineic acid (DMA), and mugineic acid (MA) are chelators required for iron uptake and transport in plants. Nicotianamine aminotransferase (NAAT), 2'-deoxymugineic acid synthase (DMAS), transporter of MAs (TOM), and efflux transporter of NA (ENA) are involved in iron uptake and transport in rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare); however, these families have not been fully identified and comprehensively analyzed in maize (Zea mays L.).

RESULTS

Here, we identified 5 ZmNAAT, 9 ZmDMAS, 11 ZmTOM, and 2 ZmENA genes by genome mining. RNA-sequencing and quantitative real-time PCR analysis revealed that these genes are expressed in various tissues and respond differently to high and low iron conditions. In particular, iron deficiency stimulated the expression of ZmDMAS1, ZmTOM1, ZmTOM3, and ZmENA1. Furthermore, we determined protein subcellular localization by transient expression of green fluorescent protein fusions in maize mesophyll protoplasts. ZmNAAT1, ZmNAAT-L4, ZmDMAS1, and ZmDMAS-L1 localized in the cytoplasm, whereas ZmTOMs and ZmENAs targeted to plasma and tonoplast membranes, endomembranes, and vesicles.

CONCLUSIONS

Our results suggest that the different gene expression profiles and subcellular localizations of ZmNAAT, ZmDMAS, ZmTOM, and ZmENA family members may enable specific regulation of phytosiderophore metabolism in different tissues and under different external conditions, shedding light on iron homeostasis in maize and providing candidate genes for breeding iron-rich maize varieties.

Research and Progress on the Mechanism of Iron Transfer and Accumulation in Rice Grains

Iron (Fe) is one of the most important micronutrients for organisms. Currently, Fe deficiency is a growing nutritional problem and is becoming a serious threat to human health worldwide. A method that could help alleviate this “hidden hunger” is increasing the bioavailable Fe concentrations in edible tissues of major food crops. Therefore, understanding the molecular mechanisms of Fe accumulation in different crop tissues will help to develop crops with higher Fe nutritional values. Biofortification significantly increases the concentration of Fe in crops. This paper considers the important food crop of rice (Oryza sativa L.) as an example and highlights recent research advances on the molecular mechanisms of Fe uptake and allogeneic uptake in different tissues of rice. In addition, different approaches to the biofortification of Fe nutrition in rice and their outcomes are described and discussed. To address the problems that occur during the development and application of improving nutritional Fe in rice, technical strategies and long-term solutions are also proposed as a reference for the future improvement of staple food nutrition with micronutrients.

Subcellular dynamics studies of iron reveal how tissue-specific distribution patterns are established in developing wheat grains

Understanding the mechanisms of iron trafficking in plants is key to enhancing the nutritional quality of crops. Because it is difficult to image iron in transit, we currently have an incomplete picture of the route(s) of iron translocation in developing seeds and how the tissue-specific distribution is established. We have used a novel approach, combining iron-57 (⁵⁷ Fe) isotope labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), to visualize iron translocation between tissues and within cells in immature wheat grain, Triticum aestivum. This enabled us to track the main route of iron transport from maternal tissues to the embryo through the different cell types. Further evidence for this route was provided by genetically diverting iron into storage vacuoles, with confirmation provided by histological staining and transmission electron microscopy energy dispersive X-ray spectroscopy (TEM-EDS). Almost all iron in both control and transgenic grains was found in intracellular bodies, indicating symplastic rather than apoplastic transport. Furthermore, a new type of iron body, highly enriched in ⁵⁷ Fe, was observed in aleurone cells and may represent iron being delivered to phytate globoids. Correlation of the ⁵⁷ Fe enrichment profiles obtained by NanoSIMS with tissue-specific gene expression provides an updated model of iron homeostasis in cereal grains with relevance for future biofortification strategies.

Molecular Responses to Cadmium Exposure in Two Contrasting Durum Wheat Genotypes

Cadmium is a heavy metal that can be easily accumulated in durum wheat kernels and enter the human food chain. Two near-isogenic lines (NILs) with contrasting cadmium accumulation in grains, High-Cd or Low-Cd (H-Cd NIL and L-Cd NIL, respectively), were used to understand the Cd accumulation and transport mechanisms in durum wheat roots. Plants were cultivated in hydroponic solution, and cadmium concentrations in roots, shoots and grains were quantified. To evaluate the molecular mechanism activated in the two NILs, the transcriptomes of roots were analyzed. The observed response is complex and involves many genes and molecular mechanisms. We found that the gene sequences of two basic helix–loop–helix (bHLH) transcription factors (bHLH29 and bHLH38) differ between the two genotypes. In addition, the transporter Heavy Metal Tolerance 1 (HMT-1) is expressed only in the low-Cd genotype and many peroxidase genes are up-regulated only in the L-Cd NIL, suggesting ROS scavenging and root lignification as active responses to cadmium presence. Finally, we hypothesize that some aquaporins could enhance the Cd translocation from roots to shoots. The response to cadmium in durum wheat is therefore extremely complex and involves transcription factors, chelators, heavy metal transporters, peroxidases and aquaporins. All these new findings could help to elucidate the cadmium tolerance in wheat and address future breeding programs.

Functional mutants of Azospirillum brasilense elicit beneficial physiological and metabolic responses in Zea mays contributing to increased host iron assimilation

Iron (Fe), an essential element for plant growth, is abundant in soil but with low bioavailability. Thus, plants developed specialized mechanisms to sequester the element. Beneficial microbes have recently become a favored method to promote plant growth through increased uptake of essential micronutrients, like Fe, yet little is known of their mechanisms of action. Functional mutants of the epiphytic bacterium Azospirillum brasilense, a prolific grass-root colonizer, were used to examine mechanisms for promoting iron uptake in Zea mays. Mutants included HM053, FP10, and ipdC, which have varying capacities for biological nitrogen fixation and production of the plant hormone auxin. Using radioactive iron-59 tracing and inductively coupled plasma mass spectrometry, we documented significant differences in host uptake of Fe2+/3+ correlating with mutant biological function. Radioactive carbon-11, administered to plants as 11CO2, provided insights into shifts in host usage of 'new' carbon resources in the presence of these beneficial microbes. Of the mutants examined, HM053 exhibited the greatest influence on host Fe uptake with increased plant allocation of 11C-resources to roots where they were transformed and exuded as 11C-acidic substrates to aid in Fe-chelation, and increased C-11 partitioning into citric acid, nicotianamine and histidine to aid in the in situ translocation of Fe once assimilated.

Annotation and Molecular Characterisation of the TaIRO3 and TaHRZ Iron Homeostasis Genes in Bread Wheat (Triticum aestivum L.)

Effective maintenance of plant iron (Fe) homoeostasis relies on a network of transcription factors (TFs) that respond to environmental conditions and regulate Fe uptake, translocation, and storage. The iron-related transcription factor 3 (IRO3), as well as haemerythrin motif-containing really interesting new gene (RING) protein and zinc finger protein (HRZ), are major regulators of Fe homeostasis in diploid species like Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L.), but remain uncharacterised in hexaploid bread wheat (Triticum aestivum L.). In this study, we have identified, annotated, and characterised three TaIRO3 homoeologs and six TaHRZ1 and TaHRZ2 homoeologs in the bread wheat genome. Protein analysis revealed that TaIRO3 and TaHRZ proteins contain functionally conserved domains for DNA-binding, dimerisation, Fe binding, or polyubiquitination, and phylogenetic analysis revealed clustering of TaIRO3 and TaHRZ proteins with other monocot IRO3 and HRZ proteins, respectively. Quantitative reverse-transcription PCR analysis revealed that all TaIRO3 and TaHRZ homoeologs have unique tissue expression profiles and are upregulated in shoot tissues in response to Fe deficiency. After 24 h of Fe deficiency, the expression of TaHRZ homoeologs was upregulated, while the expression of TaIRO3 homoeologs was unchanged, suggesting that TaHRZ functions upstream of TaIRO3 in the wheat Fe homeostasis TF network.

Delineating the future of iron biofortification studies in rice: challenges and future perspectives

Iron (Fe) deficiency in humans is a widespread problem worldwide. Fe biofortification of rice (Oryza sativa) is a promising approach to address human Fe deficiency. Since its conceptualization, various biofortification strategies have been developed, some of which have resulted in significant increases in grain Fe concentration. However, there are still many aspects that have not yet been addressed in the studies to date. In this review, we first overview the important rice Fe biofortification strategies reported to date and the complications associated with them. Next, we highlight the key outstanding questions and hypotheses related to rice Fe biofortification. Finally, we make suggestions for the direction of future rice biofortification studies.

Changes in organic compounds secreted by roots in two Poaceae species (Hordeum vulgare and Polypogon monspenliensis) subjected to iron deficiency

Despite their economic and ecological interests, Poaceae are affected by the low availability of iron in calcareous soils. Several studies focused on the capacity of this family to secrete phytosiderophores and organic acids as a mechanism of tolerance to iron deficiency. This work aimed at studying the physiological responses of two Poaceae species; Hordeum vulgare (cultivated barley) and Polypogon monspenliensis (spontaneous species) to iron deficiency, and evaluate especially the release of phytosiderophores and organic acids. For this purpose, seedlings of these two species were cultivated in complete nutrient solution with or without iron. The biomass production, iron status, phytosiderophores and organic acids release by roots were studied. The results demonstrated that Polypogon monspenliensis was relatively more tolerant to iron deficiency than Hordeum vulgare. Polypogon monspenliensis had the ability to secrete a higher amount of phytosiderophores and organic acids, especially citric, acetic, oxalic and malic acids, compared to Hordeum vulgare. We propose this spontaneous species as a forage plant in calcareous soils and in intercropping systems with fruit trees to prevent iron chlorosis.

A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.

Dissection of Molecular Processes and Genetic Architecture Underlying Iron and Zinc Homeostasis for Biofortification: From Model Plants to Common Wheat

The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats.

Iron deficiency triggered transcriptome changes in bread wheat

A series of complex transport, storage and regulation mechanisms control iron metabolism and thereby maintain iron homeostasis in plants. Despite several studies on iron deficiency responses in different plant species, these mechanisms remain unclear in the allohexaploid wheat, which is the most widely cultivated commercial crop. We used RNA sequencing to reveal transcriptomic changes in the wheat flag leaves and roots, when subjected to iron limited conditions. We identified 5969 and 2591 differentially expressed genes (DEGs) in the flag leaves and roots, respectively. Genes involved in the synthesis of iron ligands i.e., nicotianamine (NA) and deoxymugineic acid (DMA) were significantly up-regulated during iron deficiency. In total, 337 and 635 genes encoding transporters exhibited altered expression in roots and flag leaves, respectively. Several genes related to MAJOR FACILITATOR SUPERFAMILY (MFS), ATP-BINDING CASSETTE (ABC) transporter superfamily, NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN (NRAMP) family and OLIGOPEPTIDE TRANSPORTER (OPT) family were regulated, indicating their important roles in combating iron deficiency stress. Among the regulatory factors, the genes encoding for transcription factors of BASIC HELIX-LOOP-HELIX (bHLH) family were highly up-regulated in both roots and the flag leaves. The jasmonate biosynthesis pathway was significantly altered but with notable expression differences between roots and flag leaves. Homoeologs expression and induction bias analysis revealed subgenome specific differential expression. Our findings provide an integrated overview on regulated molecular processes in response to iron deficiency stress in wheat. This information could potentially serve as a guideline for breeding iron deficiency stress tolerant crops as well as for designing appropriate wheat iron biofortification strategies.

Nicotianamine Synthesis by OsNAS3 Is Important for Mitigating Iron Excess Stress in Rice

Iron (Fe) toxicity in plants causes tissue damage and cellular homeostasis disorders, thereby affecting plant growth and development. Nicotianamine (NA) is a ubiquitous chelator of metal cations and is responsible for metal homeostasis. Rice has three NA synthase (NAS) genes, of which the expression of OsNAS1 and OsNAS2 but not of OsNAS3 is strongly induced in response to Fe deficiency. Recently, we found that OsNAS3 expression is strongly induced with excess Fe in most rice tissues, particularly old leaves, suggesting that it may play a vital role under excess Fe conditions. However, the mechanism by which OsNAS3 responds to excess Fe in rice remains poorly understood. In this study, we clarified the physiological response of OsNAS3 expression to excess Fe and the role of NA synthesis in this condition. Promoter GUS analyses revealed that OsNAS3 was widely expressed in roots, especially in vascular bundle, epidermis, exodermis, stem, and old leaf tissues under Fe excess compared to control plants. Nicotianamine and deoxymugineic acid (DMA; a type of phytosiderophore synthesized by Strategy II species) were present in roots and shoots under Fe excess likewise under control conditions. In addition, OsNAS3 knockout plants were sensitive to excess Fe, exhibiting inferior growth, reduced dry weight, severer leaf bronzing, and greater Fe accumulation in their leaves than non-transformants with excess Fe. We also observed that NA-overproducing rice was tolerant of excess Fe. These results show that NA synthesized by OsNAS3 under Fe excess condition is to mitigate excess Fe whereas NA synthesized by OsNAS1 and OsNAS2 under normal Fe condition is to enhance Fe translocation, suggesting the different roles and functions of the NA existence between these two conditions. Overall, these findings suggest that rice synthesizes NA with OsNAS3 under Fe excess in roots and shoots, and that NA and DMA within the plant body are important for mitigating excess Fe stress and alleviating other metal deficiencies in rice. This report will be important for the development of tolerant rice adapted to Fe-contaminated soils.

The Adaptive Mechanism of Plants to Iron Deficiency via Iron Uptake, Transport, and Homeostasis

Iron is an essential element for plant growth and development. While abundant in soil, the available Fe in soil is limited. In this regard, plants have evolved a series of mechanisms for efficient iron uptake, allowing plants to better adapt to iron deficient conditions. These mechanisms include iron acquisition from soil, iron transport from roots to shoots, and iron storage in cells. The mobilization of Fe in plants often occurs via chelating with phytosiderophores, citrate, nicotianamine, mugineic acid, or in the form of free iron ions. Recent work further elucidates that these genes’ response to iron deficiency are tightly controlled at transcriptional and posttranscriptional levels to maintain iron homeostasis. Moreover, increasing evidences shed light on certain factors that are identified to be interconnected and integrated to adjust iron deficiency. In this review, we highlight the molecular and physiological bases of iron acquisition from soil to plants and transport mechanisms for tolerating iron deficiency in dicotyledonous plants and rice.

Chloroplasts preferentially take up ferric-citrate over iron-nicotianamine complexes in Brassica napus

Fe uptake machinery of chloroplasts prefers to utilise Fe(III)-citrate over Fe-nicotianamine complexes. Iron uptake in chloroplasts is a process of prime importance. Although a few members of their iron transport machinery were identified, the substrate preference of the system is still unknown. Intact chloroplasts of oilseed rape (Brassica napus) were purified and subjected to iron uptake studies using natural and artificial iron complexes. Fe-nicotianamine (NA) complexes were characterised by 5 K, 5 T Mössbauer spectrometry. Expression of components of the chloroplast Fe uptake machinery was also studied. Fe(III)-NA contained a minor paramagnetic Fe(II) component (ca. 9%), a paramagnetic Fe(III) component exhibiting dimeric or oligomeric structure (ca. 20%), and a Fe(III) complex, likely being a monomeric structure, which undergoes slow electronic relaxation at 5 K (ca. 61%). Fe(II)-NA contained more than one similar chemical Fe(II) environment with no sign of Fe(III) components. Chloroplasts preferred Fe(III)-citrate compared to Fe(III)-NA and Fe(II)-NA, but also to Fe(III)-EDTA and Fe(III)-o,o'EDDHA, and the K_m value was lower for Fe(III)-citrate than for the Fe-NA complexes. Only the uptake of Fe(III)-citrate was light-dependent. Regarding the components of the chloroplast Fe uptake system, only genes of the reduction-based Fe uptake system showed high expression. Chloroplasts more effectively utilize Fe(III)-citrate, but hardly Fe-NA complexes in Fe uptake.

Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat

BACKGROUND

The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported.

RESULTS

In this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454-459, ZmbHLH099-101 and OsbHLH037 in root, TabHLH559-562, - 046, - 047 and ZmbHLH010, - 072, - 226 in leaf, TabHLH216-221, - 333, - 335, - 340 and OsbHLH005, - 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, - 047, ZmbHLH097, - 098, OsbHLH006 and - 185 were strongly induced, whereas TabHLH303, - 562, ZmbHLH155, - 154, OsbHLH152 and - 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation.

CONCLUSION

The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.

Activation of a gene network in durum wheat roots exposed to cadmium

BACKGROUND

Among cereals, durum wheat (Triticum turgidum L. subsp. durum) accumulates cadmium (Cd) at higher concentration if grown in Cd-polluted soils. Since cadmium accumulation is a risk for human health, the international trade organizations have limited the acceptable concentration of Cd in edible crops. Therefore, durum wheat cultivars accumulating low cadmium in grains should be preferred by farmers and consumers. To identify the response of durum wheat to the presence of Cd, the transcriptomes of roots and shoots of Creso and Svevo cultivars were sequenced after a 50-day exposure to 0.5 μM Cd in hydroponic solution.

RESULTS

No phytotoxic effects or biomass reduction was observed in Creso and Svevo plants at this Cd concentration. Despite this null effect, cadmium was accumulated in root tissues, in shoots and in grains suggesting a good cadmium translocation rate among tissues. The mRNA sequencing revealed a general transcriptome rearrangement after Cd treatment and more than 7000 genes were found differentially expressed in root and shoot tissues. Among these, the up-regulated genes in roots showed a clear correlation with cadmium uptake and detoxification. In particular, about three hundred genes were commonly up-regulated in Creso and Svevo roots suggesting a well defined molecular strategy characterized by the transcriptomic activation of several transcription factors mainly belonging to bHLH and WRKY families. bHLHs are probably the activators of the strong up-regulation of three NAS genes, responsible for the synthesis of the phytosiderophore nicotianamine (NA). Moreover, we found the overall up-regulation of the methionine salvage pathway that is tightly connected with NA synthesis and supply the S-adenosyl methionine necessary for NA biosynthesis. Finally, several vacuolar NA chelating heavy metal transporters were vigorously activated.

CONCLUSIONS

In conclusion, the exposure of durum wheat to cadmium activates in roots a complex gene network involved in cadmium translocation and detoxification from heavy metals. These findings are confident with a role of nicotianamine and methionine salvage pathway in the accumulation of cadmium in durum wheat.

Identification of nicotianamine synthase genes in Triticum monococcum and their expression under different Fe and Zn concentrations

In graminaceous plants, nicotianamine (NA) is an important component of metal acquisition. NA is synthesized from S-adenosyl-l-methionine (SAM) catalyzed by nicotianamine synthase (NAS). Here, eight Triticum monococcum NAS (TmNAS) genes were cloned and characterized. Amino acid sequence analysis showed that TmNAS genes had high sequence identity with those from Triticum aestivum, Zea mays, Oryza sativa and Hordeum vulgare. Phylogenetic analysis showed that NAS genes were classified into two distinct groups, e.g. group I and group II. Expression analysis demonstrated that two of the TmNAS genes in group II were highly expressed in shoot tissues, and the other six TmNAS genes in group I were expressed in root tissues. Further analysis indicated that root-specific TmNAS genes were up-regulated under conditions of Fe- or Zn-deficiency growth, while shoot-specific TmNAS genes were up-regulated under conditions of Fe- or Zn-sufficiency. These results help us understand the NAS genes in T. monococcum and provide novel genetic resources for improving Fe and Zn concentrations in common wheat.

Omics approaches revealed how arbuscular mycorrhizal symbiosis enhances yield and resistance to leaf pathogen in wheat

Besides improved mineral nutrition, plants colonised by arbuscular mycorrhizal (AM) fungi often display increased biomass and higher tolerance to biotic and abiotic stresses. Notwithstanding the global importance of wheat as an agricultural crop, its response to AM symbiosis has been poorly investigated. We focused on the role of an AM fungus on mineral nutrition of wheat, and on its potential protective effect against Xanthomonas translucens. To address these issues, phenotypical, molecular and metabolomic approaches were combined. Morphological observations highlighted that AM wheat plants displayed an increased biomass and grain yield, as well as a reduction in lesion area following pathogen infection. To elucidate the molecular mechanisms underlying the mycorrhizal phenotype, we investigated changes of transcripts and proteins in roots and leaves during the double (wheat-AM fungus) and tripartite (wheat-AM fungus-pathogen) interaction. Transcriptomic and proteomic profiling identified the main pathways involved in enhancing plant biomass, mineral nutrition and in promoting the bio-protective effect against the leaf pathogen. Mineral and amino acid contents in roots, leaves and seeds, and protein oxidation profiles in leaves, supported the omics data, providing new insight into the mechanisms exerted by AM symbiosis to confer stronger productivity and enhanced resistance to X. translucens in wheat.

Investigation of Baseline Iron Levels in Australian Chickpea and Evaluation of a Transgenic Biofortification Approach

Iron deficiency currently affects over two billion people worldwide despite significant advances in technology and society aimed at mitigating this global health problem. Biofortification of food staples with iron (Fe) represents a sustainable approach for alleviating human Fe deficiency in developing countries, however, biofortification efforts have focused extensively on cereal staples while pulses have been largely overlooked. In this study we describe a genetic engineering (GE) approach to biofortify the pulse crop, chickpea (Cicer arietinum L.), with Fe using a combination of the chickpea nicotianamine synthase 2 (CaNAS2) and soybean (Glycine max) ferritin (GmFER) genes which function in Fe transport and storage, respectively. This study consists of three main components: (1) the establishment for baseline Fe concentration of existing germplam, (2) the isolation and study of expression pattern of the novel CaNAS2 gene, and (3) the generation of GE chickpea overexpressing the CaNAS2 and GmFER genes. Seed of six commercial chickpea cultivars was collected from four different field locations in Australia and assessed for seed Fe concentration. The results revealed little difference between the cultivars assessed, and that chickpea seed Fe was negatively affected where soil Fe bioavailability is low. The desi cultivar HatTrick was then selected for further study. From it, the CaNAS2 gene was cloned and its expression in different tissues examined. The gene was found to be expressed in multiple vegetative tissues under Fe-sufficient conditions, suggesting that it may play a housekeeping role in systemic translocation of Fe. Two GE chickpea events were then generated and the overexpression of the CaNAS2 and GmFER transgenes confirmed. Analysis of nicotianamine (NA) and Fe levels in the GE seeds revealed that NA was nearly doubled compared to the null control while Fe concentration was not changed. Increased NA content in chickpea seed is likely to translate into increased Fe bioavailability and may thus overcome the effect of the bioavailability inhibitors found in pulses; however, further study is required to confirm this. This is the first known example of GE Fe biofortified chickpea; information gleaned from this study can feed into future pulse biofortification work to help alleviate global Fe deficiency.

Nanocarrier-mediated foliar zinc fertilization influences expression of metal homeostasis related genes in flag leaves and enhances gluten content in durum wheat

BACKGROUND

Wheat is the staple food for most of the world's population; however, it is a poor source of zinc. Foliar fertilization of zinc via zinc loaded chitosan nanocarriers (Zn-CNP) post-anthesis has proved to be a promising approach for grain zinc enhancement in durum wheat as evidenced in our earlier study. However, the molecular mechanism of uptake of zinc via Zn-CNP remains unclear.

METHODS/PRINCIPLE FINDINGS

Foliar application of Zn-CNP was performed at post anthesis stages in two durum wheat cultivars (MACS 3125 and UC1114, containing the Gpc-B1 gene), and expression levels of several metal-related genes were analyzed during early senescence. Zn-CNP application indeed caused changes in gene expression as revealed by qPCR data on representative genes involved in metal homeostasis, phloem transporters, and leaf senescence. Furthermore, zinc-regulated transporters and iron (Fe)-regulated transporter-like protein (ZIP) family [ZIP1, ZIP7, ZIP15], CA (carbonic anhydrase), and DMAS (2'-deoxymugineic acid synthase) in flag leaves exhibited significant correlation with zinc content in the seeds. The analysis of grain endosperm proteins showed enhancement of gamma gliadins while other gluten subunits decreased. Gene expression within ZIP family members varied with the type of cultivar mostly attributed to the Gpc-B1, concentration of external zinc ions as well as the type of tissue analyzed. Correlation analysis revealed the involvement of the selected genes in zinc enhancement.

CONCLUSION

At the molecular level, uptake of zinc via Zn-CNP nanocarrier was comparable to the uptake of zinc via common zinc fertilizers i.e. ZnSO4.

Iron homeostasis in plants - a brief overview

Iron plays a crucial role in biochemistry and is an essential micronutrient for plants and humans alike. Although plentiful in the Earth's crust it is not usually found in a form readily accessible for plants to use. They must therefore sense and interact with their environment, and have evolved two different molecular strategies to take up iron in the root. Once inside, iron is complexed with chelators and distributed to sink tissues where it is used predominantly in the production of enzyme cofactors or components of electron transport chains. The processes of iron uptake, distribution and metabolism are overseen by tight regulatory mechanisms, at the transcriptional and post-transcriptional level, to avoid iron concentrations building to toxic excess. Iron is also loaded into seeds, where it is stored in vacuoles or in ferritin. This is important for human nutrition as seeds form the edible parts of many crop species. As such, increasing iron in seeds and other tissues is a major goal for biofortification efforts by both traditional breeding and biotechnological approaches.

Characterisation of the nicotianamine aminotransferase and deoxymugineic acid synthase genes essential to Strategy II iron uptake in bread wheat (Triticum aestivum L.)

Iron (Fe) uptake in graminaceous plant species occurs via the release and uptake of Fe-chelating compounds known as mugineic acid family phytosiderophores (MAs). In the MAs biosynthetic pathway, nicotianamine aminotransferase (NAAT) and deoxymugineic acid synthase (DMAS) enzymes catalyse the formation of 2'-deoxymugineic acid (DMA) from nicotianamine (NA). Here we describe the identification and characterisation of six TaNAAT and three TaDMAS1 genes in bread wheat (Triticum aestivum L.). The coding sequences of all six TaNAAT homeologs consist of seven exons with ≥88.0% nucleotide sequence identity and most sequence variation present in the first exon. The coding sequences of the three TaDMAS1 homeologs consist of three exons with ≥97.8% nucleotide sequence identity. Phylogenetic analysis revealed that the TaNAAT and TaDMAS1 proteins are most closely related to the HvNAAT and HvDMAS1 proteins of barley and that there are two distinct groups of TaNAAT proteins-TaNAAT1 and TaNAAT2 -that correspond to the HvNAATA and HvNAATB proteins, respectively. Quantitative reverse transcription-PCR analysis revealed that the TaNAAT2 genes are expressed at highest levels in anther tissues whilst the TaNAAT1 and TaDMAS1 genes are expressed at highest levels in root tissues of bread wheat. Furthermore, the TaNAAT1, TaNAAT2 and TaDMAS1 genes were differentially regulated by plant Fe status and their expression was significantly upregulated in root tissues from day five onwards during a seven-day Fe deficiency treatment. The identification and characterization of the TaNAAT1, TaNAAT2 and TaDMAS1 genes provides a valuable genetic resource for improving bread wheat growth on Fe deficient soils and enhancing grain Fe nutrition.