Construction of a network describing asparagine metabolism in plants and its application to the identification of genes affecting asparagine metabolism in wheat under drought and nutritional stress

Degradation of FATTY ACID EXPORT PROTEIN1 by RHOMBOID-LIKE PROTEASE11 contributes to cold tolerance in Arabidopsis

Plants need to acclimate to different stresses to optimize growth under unfavorable conditions. In Arabidopsis (Arabidopsis thaliana), the abundance of the chloroplast envelope protein FATTY ACID EXPORT PROTEIN1 (FAX1) decreases after the onset of low temperatures. However, how FAX1 degradation occurs and whether altered FAX1 abundance contributes to cold tolerance in plants remains unclear. The rapid cold-induced increase in RHOMBOID-LIKE PROTEASE11 (RBL11) transcript levels, the physical interaction of RBL11 with FAX1, the specific FAX1 degradation after RBL11 expression, and the absence of cold-induced FAX1 degradation in rbl11 loss-of-function mutants suggest that this enzyme is responsible for FAX1 degradation. Proteomic analyses showed that rbl11 mutants have higher levels of FAX1 and other proteins involved in membrane lipid homeostasis, suggesting that RBL11 is a key element in the remodeling of membrane properties during cold conditions. Consequently, in the cold, rbl11 mutants show a shift in lipid biosynthesis toward the eukaryotic pathway, which coincides with impaired cold tolerance. To test whether cold sensitivity is due to increased FAX1 levels, we analyzed FAX1 overexpressors. The rbl11 mutants and FAX1 overexpressor lines show superimposable phenotypic defects upon exposure to cold temperatures. Our re-sults show that the cold-induced degradation of FAX1 by RBL11 is critical for Arabidop-sis to survive cold and freezing periods.

Different wheat loci are associated to heritable free asparagine content in grain grown under different water and nitrogen availability

KEY MESSAGE

Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential. The amount of free asparagine in grain of a wheat genotype determines its potential to form harmful acrylamide in derivative food products. Here, we explored the variation in the free asparagine, aspartate, glutamine and glutamate contents of 485 accessions reflecting wheat worldwide diversity to define the genetic architecture governing the accumulation of these amino acids in grain. Accessions were grown under high and low nitrogen availability and in water-deficient and well-watered conditions, and plant and grain phenotypes were measured. Free amino acid contents of grain varied from 0.01 to 1.02 mg g-1 among genotypes in a highly heritable way that did not correlate strongly with grain yield, protein content, specific weight, thousand-kernel weight or heading date. Mean free asparagine content was 4% higher under high nitrogen and 3% higher in water-deficient conditions. After genotyping the accessions, single-locus and multi-locus genome-wide association study models were used to identify several QTLs for free asparagine content located on nine chromosomes. Each QTL was associated with a single amino acid and growing environment, and none of the QTLs colocalised with genes known to be involved in the corresponding amino acid metabolism. This suggests that free asparagine content is controlled by several loci with minor effects interacting with the environment. We conclude that breeding for reduced asparagine content is feasible, but should be firmly based on multi-environment field trials.

KEY MESSAGE

Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential.

Protein biomarkers for root length and root dry mass on chromosomes 4A and 7A in wheat

Improving the wheat (Triticum aestivum L.) root system is important for enhancing grain yield and climate resilience. Total root length (RL) and root dry mass (RM) significantly contribute to water and nutrient acquisition directly impacting grain yield and stress tolerance. This study used label-free quantitative proteomics to identify proteins associated with RL and RM in wheat near-isogenic lines (NILs). NIL pair 6 had 113 and NIL pair 9 had 30 differentially abundant proteins (DAPs). Three of identified DAPs located within the targeted genomic regions (GRs) of NIL pairs 6 (qDT.4A.1) and 9 (QHtscc.ksu-7A), showed consistent gene expressions at the protein and mRNA transcription (qRT-PCR) levels for asparagine synthetase (TraesCS4A02G109900), signal recognition particle 19 kDa protein (TraesCS7A02G333600) and 3,4-dihydroxy-2-butanone 4-phosphate synthase (TraesCS7A02G415600). This study discovered, for the first time, the involvement of these proteins as candidate biomarkers for increased RL and RM in wheat. However, further functional validation is required to ascertain their practical applicability in wheat root breeding. SIGNIFICANCE OF THE STUDY: Climate change has impacted global demand for wheat (Triticum aestivum L.). Root traits such as total root length (RL) and root dry mass (RM) are crucial for water and nutrient uptake and tolerance to abiotic stresses such as drought, salinity, and nutrient imbalance in wheat. Improving RL and RM could significantly enhance wheat grain yield and climate resilience. However, breeding for these traits has been limited by lack of appropriate root phenotyping methods, advanced genotypes, and the complex nature of the wheat genome. In this study, we used a semi-hydroponic root phenotyping system to collect accurate root data, near-isogenic lines (NILs; isolines with similar genetic backgrounds but contrasting target genomic regions (GRs)) and label-free quantitative proteomics to explore the molecular mechanisms underlying high RL and RM in wheat. We identified differentially abundant proteins (DAPs) and their molecular pathways in NIL pairs 6 (GR: qDT.4A.1) and 9 (GR: QHtscc.ksu-7A), providing a foundation for further molecular investigations. Furthermore, we identified three DAPs within the target GRs of the NIL pairs with differential expression at the transcript level, as confirmed by qRT-PCR analysis which could serve as candidate protein biomarkers for RL and RM improvement.

Unveiling a differential metabolite modulation of sorghum varieties under increasing tunicamycin-induced endoplasmic reticulum stress

Plants trigger endoplasmic reticulum (ER) pathways to survive stresses, but the assistance of ER in plant tolerance still needs to be explored. Thus, we selected sensitive and tolerant contrasting abiotic stress sorghum varieties to test if they present a degree of tolerance to ER stress. Accordingly, this work evaluated crescent concentrations of tunicamycin (TM µg mL-1): control (0), lower (0.5), mild (1.5), and higher (2.5) on the initial establishment of sorghum seedlings CSF18 and CSF20. ER stress promoted growth and metabolism reductions, mainly in CSF18, from mild to higher TM. The lowest TM increased SbBiP and SbPDI chaperones, as well as SbbZIP60, and SbbIRE1 gene expressions, but mild and higher TM decreased it. However, CSF20 exhibited higher levels of SbBiP and SbbIRE1 transcripts. It corroborated different metabolic profiles among all TM treatments in CSF18 shoots and similarities between profiles of mild and higher TM in CSF18 roots. Conversely, TM profiles of both shoots and roots of CSF20 overlapped, although it was not complete under low TM treatment. Furthermore, ER stress induced an increase of carbohydrates (dihydroxyacetone in shoots, and cellobiose, maltose, ribose, and sucrose in roots), and organic acids (pyruvic acid in shoots, and butyric and succinic acids in roots) in CSF20, which exhibited a higher degree of ER stress tolerance compared to CSF18 with the root being the most affected plant tissue. Thus, our study provides new insights that may help to understand sorghum tolerance and the ER disturbance as significant contributor for stress adaptation and tolerance engineering.

Rhizobacteria-enhanced drought tolerance and post-drought recovery of creeping bentgrass involving differential modulation of leaf and root metabolism

Rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCd) that inhibits ethylene production may mitigate stress damages. The objectives of this study were to examine whether a novel strain of ACCd-producing bacteria, Paraburkholderia aspalathi "WSF23," promotes plant tolerance to drought stress and post-stress recovery and determine changes in metabolic profiles in leaves and roots associated with the positive ACCd-bacteria effects in cool-season perennial grass species. Creeping bentgrass (Agrostis Stolonifera L. cv. "Penncross") plants were inoculated with P. aspalathi "WSF23" and exposed to drought by withholding irrigation for 35 days, followed by re-watering for 15 days in growth chambers. Inoculated plants demonstrated increased turf quality, canopy density, and root growth during drought stress and more rapid re-growth upon re-watering. Metabolomic analysis demonstrated that inoculation with P. aspalathi "WSF 23" increased the content of metabolites in the metabolic pathways related to stress defense, including osmoregulation, cell wall stability, and antioxidant protection in both leaves and roots, as well as nitrogen metabolism in roots of creeping bentgrass exposed to drought stress. The promotion of post-stress recovery by P. aspalathi "WSF 23" was mainly associated with enhanced carbohydrate and pyrimidine metabolism and zeatin biosynthesis pathways in leaves and increased carbohydrates, biosynthesis of DNA and proteins, cellular metabolism, and TCA cycle activity in roots. These results provide insights into the metabolic pathways regulated by "WSF23," with the PGPR conferring improvements in drought stress tolerance and post-drought recovery in a perennial grass species.

Sugar Starvation Disrupts Lipid Breakdown by Inducing Autophagy in Embryonic Axes of Lupin (Lupinus spp.) Germinating Seeds

Under nutrient deficiency or starvation conditions, the mobilization of storage compounds during seed germination is enhanced to primarily supply respiratory substrates and hence increase the potential of cell survival. Nevertheless, we found that, under sugar starvation conditions in isolated embryonic axes of white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet) cultured in vitro for 96 h, the disruption of lipid breakdown occurs, as was reflected in the higher lipid content in the sugar-starved (-S) than in the sucrose-fed (+S) axes. We postulate that pexophagy (autophagic degradation of the peroxisome-a key organelle in lipid catabolism) is one of the reasons for the disruption in lipid breakdown under starvation conditions. Evidence of pexophagy can be: (i) the higher transcript level of genes encoding proteins of pexophagy machinery, and (ii) the lower content of the peroxisome marker Pex14p and its increase caused by an autophagy inhibitor (concanamycin A) in -S axes in comparison to the +S axes. Additionally, based on ultrastructure observation, we documented that, under sugar starvation conditions lipophagy (autophagic degradation of whole lipid droplets) may also occur but this type of selective autophagy seems to be restricted under starvation conditions. Our results also show that autophagy occurs at the very early stages of plant growth and development, including the cells of embryonic seed organs, and allows cell survival under starvation conditions.

Proteomics approach to investigating osmotic stress effects on pistachio

Osmotic stress can occur due to some stresses such as salinity and drought, threatening plant survival. To investigate the mechanism governing the pistachio response to this stress, the biochemical alterations and protein profile of PEG-treated plants was monitored. Also, we selected two differentially abundant proteins to validate via Real-Time PCR. Biochemical results displayed that in treated plants, proline and phenolic content was elevated, photosynthetic pigments except carotenoid decreased and MDA concentration were not altered. Our findings identified a number of proteins using 2DE-MS, involved in mitigating osmotic stress in pistachio. A total of 180 protein spots were identified, of which 25 spots were altered in response to osmotic stress. Four spots that had photosynthetic activities were down-regulated, and the remaining spots were up-regulated. The biological functional analysis of protein spots exhibited that most of them are associated with the photosynthesis and metabolism (36%) followed by stress response (24%). Results of Real-Time PCR indicated that two of the representative genes illustrated a positive correlation among transcript level and protein expression and had a similar trend in regulation of gene and protein. Osmotic stress set changes in the proteins associated with photosynthesis and stress tolerance, proteins associated with the cell wall, changes in the expression of proteins involved in DNA and RNA processing occur. Findings of this research will introduce possible proteins and pathways that contribute to osmotic stress and can be considered for improving osmotic tolerance in pistachio.

Hydropriming and Nutripriming of Bread Wheat Seeds Improved the Flour's Nutritional Value of the First Unprimed Offspring

Seed hydropriming or nutripriming has been used for wheat biofortification. Previously, the untreated S1 offspring of bread wheat S0 seeds hydro- and nutriprimed with FeSO₄.7H₂O and/or ZnSO₄.7H₂O showed improved yield relative to the offspring of untreated S0 seeds. We hypothesize that such improvement would have its origin in the higher quality of S1 seeds resulting from plants whose seeds were primed. In this work, we characterised biochemically the whole-wheat flour of unprimed S1 offspring whose S0 seeds were hydro- and nutriprimed with Fe and/or Zn and compared it to the offspring of untreated S0 seeds (control). We identified and quantified 16 free amino acids and five soluble sugars per offspring using high-performance liquid chromatography and the Association of Official Analytical Chemists (AOAC) methods. The most abundant amino acids were glutamic acid and glutamine, proline, and glycine, presenting their highest contents in the offspring of seeds nutriprimed with 8 ppm Zn (0.351 mmol∙g^-1), 8 ppm Fe + 8 ppm Zn (0.199 mmol∙g^-1), and (0.135 mmol∙g^-1), respectively. The highest contents of glucose (1.91 mg∙g^-1 sample), ash (24.90 g∙kg^-1 dry matter, DM), and crude protein (209.70 g∙kg^-1 DM) were presented by the offspring resulting from 4 ppm Fe + 4 ppm Zn, 8 ppm Zn, and 8 ppm Fe + 8 ppm Zn, respectively. The highest total starch content (630.10 g∙kg^-1 DM) was detected in the offspring of seeds soaked in 8 ppm Fe. The nutritional value of the flour of the S1 offspring resulting from nutripriming was significantly higher than the control. Overall, the novelty of our research is that seed priming can improve the quality of the wheat grain and flour, at least till the first offspring, without the need to repeat the presowing treatment. Beyond the study of subsequent generations, the unravelling of transgenerational mechanisms underlying the biochemical improvement of the offspring is approached.

The fate of secondary metabolites in plants growing on Cd-, As-, and Pb-contaminated soils-a comprehensive review

The study used scattered literature to summarize the effects of excess Cd, As, and Pb from contaminated soils on plant secondary metabolites/bioactive compounds (non-nutrient organic substances). Hence, we provided a systematic overview involving the sources and forms of Cd, As, and Pb in soils, plant uptake, mechanisms governing the interaction of these risk elements during the formation of secondary metabolites, and subsequent effects. The biogeochemical characteristics of soils are directly responsible for the mobility and bioavailability of risk elements, which include pH, redox potential, dissolved organic carbon, clay content, Fe/Mn/Al oxides, and microbial transformations. The radial risk element flow in plant systems is restricted by the apoplastic barrier (e.g., Casparian strip) and chelation (phytochelatins and vacuole sequestration) in roots. However, bioaccumulation is primarily a function of risk element concentration and plant genotype. The translocation of risk elements to the shoot via the xylem and phloem is well-mediated by transporter proteins. Besides the dysfunction of growth, photosynthesis, and respiration, excess Cd, As, and Pb in plants trigger the production of secondary metabolites with antioxidant properties to counteract the toxic effects. Eventually, this affects the quantity and quality of secondary metabolites (including phenolics, flavonoids, and terpenes) and adversely influences their antioxidant, antiinflammatory, antidiabetic, anticoagulant, and lipid-lowering properties. The mechanisms governing the translocation of Cd, As, and Pb are vital for regulating risk element accumulation in plants and subsequent effects on secondary metabolites.

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.

GraphML-SBGN bidirectional converter for metabolic networks

Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.

THP9 enhances seed protein content and nitrogen-use efficiency in maize

Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for this trait are unknown^1,2. Here we use trio binning to create a contiguous haplotype DNA sequence of a teosinte (Zea mays subsp. parviglumis) and, through map-based cloning, identify a major high-protein quantitative trait locus, TEOSINTE HIGH PROTEIN 9 (THP9), on chromosome 9. THP9 encodes an asparagine synthetase 4 enzyme that is highly expressed in teosinte, but not in the B73 inbred, in which a deletion in the tenth intron of THP9-B73 causes incorrect splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 significantly increased the seed protein content. Introgression of THP9-teosinte into modern maize inbreds and hybrids greatly enhanced the accumulation of free amino acids, especially asparagine, throughout the plant, and increased seed protein content without affecting yield. THP9-teosinte seems to increase nitrogen-use efficiency, which is important for promoting a high yield under low-nitrogen conditions.

Acrylamide in Corn-Based Thermally Processed Foods: A Review

Widely consumed thermally processed corn-based foods can have a great contribution to acrylamide dietary intake, thus bearing a high public health risk and requiring attention and application of strategies for its reduction. This paper reviews the literature on the acrylamide content of corn-based food products present in the market around the world. The potential of corn for acrylamide formation due to its content of free asparagine and reducing sugars is described. Human exposure to acrylamide from corn-based foods is also discussed. The content of acrylamide in corn/tortilla chips, popcorn, and corn flakes, as widely consumed products all over the world, is reported in the literature to be between 5 and 6360 μg/kg, between <LOD and 2220 μg/kg and between <LOD and 1186 μg/kg, respectively. Although these products are important acrylamide sources in the common diet of all age populations, higher intake values occurred among younger generations.

Metabolic Pathways Involved in the Drought Stress Response of Nitraria tangutorum as Revealed by Transcriptome Analysis

Drought resistance in plants is controlled by multiple genes. To identify the genes that mediate drought stress responses and to assess the associated metabolic pathways in the desert shrub Nitraria tangutorum, we conducted a transcriptome analysis of plants under control (maximum field capacity) and drought (20% of the maximum field capacity) conditions. We analyzed differentially expressed genes (DEGs) of N. tangutorum and their enrichment in the KEGG metabolic pathways database, and explored the molecular biological mechanisms underlying the answer to its drought tolerance. Between the control and drought groups, 119 classified metabolic pathways annotated 3047 DEGs in the KEGG database. For drought tolerance, nitrate reductase (NR) gene expression was downregulated, indicating that NR activity was decreased to improve drought tolerance. In ammonium assimilation, drought stress inhibited glutamine formation. Protochlorophyllide reductase (1.3.1.33) expression was upregulated to promote chlorophyll a synthesis, whereas divinyl reductase (1.3.1.75) expression was downregulated to inhibit chlorophyll-ester a synthesis. The expression of the chlorophyll synthase (2.5.1.62) gene was downregulated, which affected the synthesis of chlorophyll a and b. Overall, drought stress appeared to improve the ability to convert chlorophyll b into chlorophyll a. Our data serve as a theoretical foundation for further elucidating the growth regulatory mechanism of desert xerophytes, thereby facilitating the development and cultivation of new, drought-resistant genotypes for the purpose of improving desert ecosystems.

Understanding the Relationships between Free Asparagine in Grain and Other Traits to Breed Low-Asparagine Wheat

Since the discovery of acrylamide in food, and the identification of free asparagine as the key determinant of acrylamide concentration in wheat products, our understanding of how grain asparagine content is regulated has improved greatly. However, the targeted reduction in grain asparagine content has not been widely implemented in breeding programmes so far. Here we summarise how free asparagine concentration relates to other quality and agronomic traits and show that these relationships are unlikely to pose major issues for the breeding of low-asparagine wheat. We also outline the strategies that are possible for the breeding of low-asparagine wheat, using both natural and induced variation.

Mapping Resistance to Argentinean Fusarium (Graminearum) Head Blight Isolates in Wheat

Fusarium head blight (FHB) of wheat, caused by Fusarium graminearum (Schwabe), is a destructive disease worldwide, reducing wheat yield and quality. To accelerate the improvement of scab tolerance in wheat, we assessed the International Triticeae Mapping Initiative mapping population (ITMI/MP) for Type I and II resistance against a wide population of Argentinean isolates of F. graminearum. We discovered a total of 27 additive QTLs on ten different (2A, 2D, 3B, 3D, 4B, 4D, 5A, 5B, 5D and 6D) wheat chromosomes for Type I and Type II resistances explaining a maximum of 15.99% variation. Another four and two QTLs for thousand kernel weight in control and for Type II resistance, respectively, involved five different chromosomes (1B, 2D, 6A, 6D and 7D). Furthermore, three, three and five QTLs for kernel weight per spike in control, for Type I resistance and for Type II resistance, correspondingly, involved ten chromosomes (2A, 2D, 3B, 4A, 5A, 5B, 6B, 7A, 7B, 7D). We were also able to detect five and two epistasis pairs of QTLs for Type I and Type II resistance, respectively, in addition to additive QTLs that evidenced that FHB resistance in wheat is controlled by a complex network of additive and epistasis QTLs.

Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress

Drought tolerance in rice is controlled by several genes and is inherited quantitatively. Low genetic map density and the use of phenotypic traits that do not reflect the corresponding tolerance level have been obstacles in genetic analyses performed to identify genes that control drought-tolerant traits in rice. The current study aimed to construct a genetic map from high-density single-nucleotide polymorphism (SNP) markers generated from genome sequences of recombinant inbred lines (RILs), derived from IR64 × Hawara Bunar. Moreover, it sought to analyze the quantitative trait loci (QTL) and identify the drought tolerance candidate genes. A linkage map along 1980 cM on the 12 rice chromosomes was constructed employing 55,205 SNP markers resulting from the RIL genome sequences. A total of 175 morpho-physiological traits pertaining to drought stress were determined. A total of 41 QTLs were detected in 13 regions on rice chromosomes 1, 3, 6, 8, 9, and 12. Moreover, three hotspot QTL regions were found on chromosomes 6 and 8, along with two major QTL on chromosome 9. Differential gene expression for the loci within the QTL physical map intervals revealed many potential candidate genes. The markers tightly linked to the QTL and their candidate genes can potentially be used for pyramiding in marker-assisted breeding in order to achieve genetic improvement concerning the tolerance of rice to drought stress.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01095-y.

Potassium dependency of enzymes in plant primary metabolism

Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K⁺ ions). Several plant enzymes are also strictly K⁺-dependent, and this can be critical when plants are under K deficiency and thus intracellular K⁺ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K⁺ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K⁺-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K⁺. This information is instrumental to explain direct effects of low K⁺ content on metabolism and this is illustrated with recent metabolomics data.

Wheat with greatly reduced accumulation of free asparagine in the grain, produced by CRISPR/Cas9 editing of asparagine synthetase gene TaASN2

Free asparagine is the precursor for acrylamide, which forms during the baking, toasting and high-temperature processing of foods made from wheat. In this study, CRISPR/Cas9 was used to knock out the asparagine synthetase gene, TaASN2, of wheat (Triticum aestivum) cv. Cadenza. A 4-gRNA polycistronic gene was introduced into wheat embryos by particle bombardment and plants were regenerated. T1 plants derived from 11 of 14 T0 plants were shown to carry edits. Most edits were deletions (up to 173 base pairs), but there were also some single base pair insertions and substitutions. Editing continued beyond the T1 generation. Free asparagine concentrations in the grain of plants carrying edits in all six TaASN2 alleles (both alleles in each genome) were substantially reduced compared with wildtype, with one plant showing a more than 90 % reduction in the T2 seeds. A plant containing edits only in the A genome alleles showed a smaller reduction in free asparagine concentration in the grain, but the concentration was still lower than in wildtype. Free asparagine concentration in the edited plants was also reduced as a proportion of the free amino acid pool. Free asparagine concentration in the T3 seeds remained substantially lower in the edited lines than wildtype, although it was higher than in the T2 seeds, possibly due to stress. In contrast, the concentrations of free glutamine, glutamate and aspartate were all higher in the edited lines than wildtype. Low asparagine seeds showed poor germination but this could be overcome by exogenous application of asparagine.

The Arabidopsis Iron-Sulfur (Fe-S) Cluster Gene MFDX1 Plays a Role in Host and Nonhost Disease Resistance by Accumulation of Defense-Related Metabolites

Until recently, genes from the iron-sulfur (Fe-S) cluster pathway were not known to have a role in plant disease resistance. The Nitrogen Fixation S (NIFS)-like 1 (NFS1) and Mitochondrial Ferredoxin-1 (MFDX1) genes are part of a set of 27 Fe-S cluster genes induced after infection with host and nonhost pathogens in Arabidopsis. A role for AtNFS1 in plant immunity was recently demonstrated. In this work, we showed that MFDX1 is also involved in plant defense. More specifically, Arabidopsis mfdx1 mutants were compromised for nonhost resistance against Pseudomonas syringae pv. tabaci, and showed increased susceptibility to the host pathogen P. syringae pv. tomato DC3000. Arabidopsis AtMFDX1 overexpression lines were less susceptible to P. syringae pv. tomato DC3000. Metabolic profiling revealed a reduction of several defense-related primary and secondary metabolites, such as asparagine and glucosinolates in the Arabidopsis mfdx1-1 mutant when compared to Col-0. A reduction of 5-oxoproline and ornithine metabolites that are involved in proline synthesis in mitochondria and affect abiotic stresses was also observed in the mfdx1-1 mutant. In contrast, an accumulation of defense-related metabolites such as glucosinolates was observed in the Arabidopsis NFS1 overexpressor when compared to wild-type Col-0. Additionally, mfdx1-1 plants displayed shorter primary root length and reduced number of lateral roots compared to the Col-0. Taken together, these results provide additional evidence for a new role of Fe-S cluster pathway in plant defense responses.

Comparative Transcriptomics and Metabolomics Reveal an Intricate Priming Mechanism Involved in PGPR-Mediated Salt Tolerance in Tomato

Plant-associated beneficial strains inhabiting plants grown under harsh ecosystems can help them cope with abiotic stress factors by positively influencing plant physiology, development, and environmental adaptation. Previously, we isolated a potential plant growth promoting strain (AXSa06) identified as Pseudomonas oryzihabitans, possessing 1-aminocyclopropane-1-carboxylate deaminase activity, producing indole-3-acetic acid and siderophores, as well as solubilizing inorganic phosphorus. In this study, we aimed to further evaluate the effects of AXSa06 seed inoculation on the growth of tomato seedlings under excess salt (200 mM NaCl) by deciphering their transcriptomic and metabolomic profiles. Differences in transcript levels and metabolites following AXSa06 inoculation seem likely to have contributed to the observed difference in salt adaptation of inoculated plants. In particular, inoculations exerted a positive effect on plant growth and photosynthetic parameters, imposing plants to a primed state, at which they were able to respond more robustly to salt stress probably by efficiently activating antioxidant metabolism, by dampening stress signals, by detoxifying Na⁺, as well as by effectively assimilating carbon and nitrogen. The primed state of AXSa06-inoculated plants is supported by the increased leaf lipid peroxidation, ascorbate content, as well as the enhanced activities of antioxidant enzymes, prior to stress treatment. The identified signatory molecules of AXSa06-mediated salt tolerance included the amino acids aspartate, threonine, serine, and glutamate, as well as key genes related to ethylene or abscisic acid homeostasis and perception, and ion antiporters. Our findings represent a promising sustainable solution to improve agricultural production under the forthcoming climate change conditions.

Cereal asparagine synthetase genes

Asparagine synthetase catalyses the transfer of an amino group from glutamine to aspartate to form glutamate and asparagine. The accumulation of free (nonprotein) asparagine in crops has implications for food safety because free asparagine is the precursor for acrylamide, a carcinogenic contaminant that forms during high-temperature cooking and processing. Here we review publicly available genome data for asparagine synthetase genes from species of the Pooideae subfamily, including bread wheat and related wheat species (Triticum and Aegilops spp.), barley (Hordeum vulgare) and rye (Secale cereale) of the Triticeae tribe. Also from the Pooideae subfamily: brachypodium (Brachypodium dIstachyon) of the Brachypodiae tribe. More diverse species are also included, comprising sorghum (Sorghum bicolor) and maize (Zea mays) of the Panicoideae subfamily and rice (Oryza sativa) of the Ehrhartoideae subfamily. The asparagine synthetase gene families of the Triticeae species each comprise five genes per genome, with the genes assigned to four groups: 1, 2, 3 (subdivided into 3.1 and 3.2) and 4. Each species has a single gene per genome in each group, except that some bread wheat varieties (genomes AABBDD) and emmer wheat (Triticum dicoccoides; genomes AABB) lack a group 2 gene in the B genome. This raises questions about the ancestry of cultivated pasta wheat and the B genome donor of bread wheat, suggesting that the hybridisation event that gave rise to hexaploid bread wheat occurred more than once. In phylogenetic analyses, genes from the other species cluster with the Triticeae genes, but brachypodium, sorghum and maize lack a group 2 gene, while rice has only two genes, one group 3 and one group 4. This means that TaASN2, the most highly expressed asparagine synthetase gene in wheat grain, has no equivalent in maize, rice, sorghum or brachypodium. An evolutionary pathway is proposed in which a series of gene duplications gave rise to the five genes found in modern Triticeae species.

Metabolite profiling of semi-leafless pea (Pisum sativum L.) under progressive soil drought and subsequent re-watering

Four semi-leafless pea (Pisum sativum L.) cultivars at the vegetative stage of growth were exposed to progressive soil drought, which lasted for 18 days until the plants began to wilt, after which a 7-day period of the recovery from stress followed, when plant watering was resumed. The soil drought negatively affected plant growth, slowing down the rate of shoot elongation, decreasing the accumulation of fresh and dry weight, inhibiting the development of new leaves, and delaying the flowering of plants. Changes in the levels of 41 polar metabolites (identified by GC-MS) were established by the GC-FID method in the shoot tip, stem, stipules and tendrils, separately. Drought caused re-arrangement in the metabolism in all parts of the pea shoot, leading to a significant increase in the content of total polar metabolites. Although changes in most metabolites in the same parts of shoot were not identical among the pea cultivars studied, some metabolites were uniformly accumulated until 18th day of drought and decreased after recovery. They were i) proline and malate in all, while myo-inositol in most parts of shoot (of all the pea cultivars), ii) sucrose and glycine in the shoot tip, iii) homoserine in the stem and iv) GABA in stipules. These findings signify that the pea adjustment to progressive soil drought includes both accumulation of osmolytes and osmoprotectants and translocation of some of them (proline, sucrose, myo-inositol) to the shoot tip, thereby protecting the youngest tissues from damage caused by water deficit.

Genome-Wide Association Study and Identification of Candidate Genes for Nitrogen Use Efficiency in Barley (Hordeum vulgare L.)

Nitrogen (N) fertilizer is largely responsible for barley grain yield potential and quality, yet excessive application leads to environmental pollution and high production costs. Therefore, efficient use of N is fundamental for sustainable agriculture. In the present study, we investigated the performance of 282 barley accessions through hydroponic screening using optimal and low NH4NO3 treatments. Low-N treatment led to an average shoot dry weight reduction of 50%, but there were significant genotypic differences among the accessions. Approximately 20% of the genotypes showed high (>75%) relative shoot dry weight under low-N treatment and were classified as low-N tolerant, whereas 20% were low-N sensitive (≤55%). Low-N tolerant accessions exhibited well-developed root systems with an average increase of 60% in relative root dry weight to facilitate more N absorption. A genome-wide association study (GWAS) identified 66 significant marker trait associations (MTAs) conferring high nitrogen use efficiency, four of which were stable across experiments. These four MTAs were located on chromosomes 1H(1), 3H(1), and 7H(2) and were associated with relative shoot length, relative shoot and root dry weight. Genes corresponding to the significant MTAs were retrieved as candidate genes, including members of the asparagine synthetase gene family, several transcription factor families, protein kinases, and nitrate transporters. Most importantly, the high-affinity nitrate transporter 2.7 (HvNRT2.7) was identified as a promising candidate on 7H for root and shoot dry weight. The identified candidate genes provide new insights into our understanding of the molecular mechanisms driving nitrogen use efficiency in barley and represent potential targets for genetic improvement.

Constitutive expression of Asparaginase in Gossypium hirsutum triggers insecticidal activity against Bemisia tabaci

Whitefly infestation of cotton crop imparts enormous damage to cotton yield by severely affecting plant health, vigour and transmitting Cotton Leaf Curl Virus (CLCuV). Genetic modification of cotton helps to overcome both the direct whitefly infestation as well as CLCuV based cotton yield losses. We have constitutively overexpressed asparaginase (ZmASN) gene in Gossypium hirsutum to overcome the cotton yield losses imparted by whitefly infestation. We achieved 2.54% transformation efficiency in CIM-482 by Agrobacterium-mediated shoot apex transformation method. The relative qRT-PCR revealed 40-fold higher transcripts of asparaginase in transgenic cotton line vs. non-transgenic cotton lines. Metabolic analysis showed higher contents of aspartic acid and glutamic acid in seeds and phloem sap of the transgenic cotton lines. Phenotypically, the transgenic cotton lines showed vigorous growth and height, greater number of bolls, and yield. Among six representative transgenic cotton lines, line 14 had higher photosynthetic rate, stomatal conductance, smooth fiber surface, increased fiber convolutions (SEM analysis) and 95% whitefly mortality as compared to non-transgenic cotton line. The gene integration analysis by fluorescence in situ hybridization showed single copy gene integration at chromosome number 1. Collectively, asparaginase gene demonstrated potential to control whitefly infestation, post-infestation damages and improve cotton plant health and yield: a pre-requisite for farmer's community.

The Sulphur Response in Wheat Grain and Its Implications for Acrylamide Formation and Food Safety

Free (soluble, non-protein) asparagine concentration can increase many-fold in wheat grain in response to sulphur deficiency. This exacerbates a major food safety and regulatory compliance problem for the food industry because free asparagine may be converted to the carcinogenic contaminant, acrylamide, during baking and processing. Here, we describe the predominant route for the conversion of asparagine to acrylamide in the Maillard reaction. The effect of sulphur deficiency and its interaction with nitrogen availability is reviewed, and we reiterate our advice that sulphur should be applied to wheat being grown for human consumption at a rate of 20 kg per hectare. We describe the genetic control of free asparagine accumulation, including genes that encode metabolic enzymes (asparagine synthetase, glutamine synthetase, glutamate synthetase, and asparaginase), regulatory protein kinases (sucrose nonfermenting-1 (SNF1)-related protein kinase-1 (SnRK1) and general control nonderepressible-2 (GCN2)), and basic leucine zipper (bZIP) transcription factors, and how this genetic control responds to sulphur, highlighting the importance of asparagine synthetase-2 (ASN2) expression in the embryo. We show that expression of glutamate-cysteine ligase is reduced in response to sulphur deficiency, probably compromising glutathione synthesis. Finally, we describe unexpected effects of sulphur deficiency on carbon metabolism in the endosperm, with large increases in expression of sucrose synthase-2 (SuSy2) and starch synthases.

Yield and Metabolite Production of Pelargonium sidoides DC. in Response to Irrigation and Nitrogen Management

Competition for water between agricultural and non-agricultural economic sectors hampers agricultural production, especially in water-scarce regions. Understanding crop responses in terms of yield and quality to irrigation is an important factor in designing appropriate irrigation management for optimal crop production and quality. Pelargonium sidoides DC., often harvested from the wild, is in high demand in the informal market and for commercial formulations. Agricultural production of high-quality materials through cultivation can help reduce pressure on its wild populations. This study aimed at determining the effects of water and nitrogen on P. sidoides yield and metabolite production. The irrigation treatments applied were 30%, 50%, and 70% of an allowable depletion level (ADL), while the nitrogen (N) levels were 0 (control), 50, 100, and 150 kg ha⁻¹. The 30% ADL resulted in a significantly higher biomass and root yield. Nitrogen at 50 and 100 kg ha⁻¹ resulted in a significantly higher biomass yield, compared to the N control. An increase in sugars and citrate cycle components was observed for the well-watered 30% ADL treatment, whereas water-stressed (50% and 70% ADL) treatments increased alanine, aspartate, and glutamate metabolism, increasing levels of asparagine, 4-aminobutyrate, and arginine. The treatments had no significant effect on the root content of esculin, scopoletin, and umckalin. Water stress induced metabolite synthesis to mitigate the stress condition, whereas under no water stress primary metabolites were synthesized. Moreover, cultivation of P. sidoides as a conservation strategy can increase yield without affecting its bioactivity, while providing sustenance for the rural communities.

Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots

Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms.

Acrylamide in food: Progress in and prospects for genetic and agronomic solutions

Acrylamide is a processing contaminant and Group 2a carcinogen that was discovered in foodstuffs in 2002. Its presence in a range of popular foods has become one of the most difficult problems facing the food industry and its supply chain. Wheat, rye and potato products are major sources of dietary acrylamide, with biscuits, breakfast cereals, bread (particularly toasted), crispbread, batter, cakes, pies, French fries, crisps and snack products all affected. Here we briefly review the history of the issue, detection methods, the levels of acrylamide in popular foods and the risk that dietary acrylamide poses to human health. The pathways for acrylamide formation from free (non-protein) asparagine are described, including the role of reducing sugars such as glucose, fructose and maltose and the Maillard reaction. The evolving regulatory situation in the European Union and elsewhere is discussed, noting that food businesses and their suppliers must plan to comply not only with current regulations but with possible future regulatory scenarios. The main focus of the review is on the genetic and agronomic approaches being developed to reduce the acrylamide-forming potential of potatoes and cereals and these are described in detail, including variety selection, plant breeding, biotechnology and crop management. Obvious targets for genetic interventions include asparagine synthetase genes, and the asparagine synthetase gene families of different crop species are compared. Current knowledge on crop management best practice is described, including maintaining optimum storage conditions for potatoes and ensuring sulphur sufficiency and disease control for wheat.

Cell wall composition and transcriptomics in stem tissues of stinging nettle (Urtica dioica L.): Spotlight on a neglected fibre crop

Stinging nettle (Urtica dioica L.) produces silky cellulosic fibres, as well as bioactive molecules. To improve the knowledge on nettle and enhance its opportunities of exploitation, a draft transcriptome of the "clone 13" (a fibre clone) is here presented. The transcriptome of whole internodes sampled at the top and middle of the stem is then compared with the core and cortical tissues sampled at the bottom. Young internodes show an enrichment in genes involved in the biosynthesis of phytohormones (auxins and jasmonic acid) and secondary metabolites (flavonoids). The core of internodes collected at the bottom of the stem is enriched in genes partaking in different aspects of secondary cell wall formation (cellulose, hemicellulose, lignin biosynthesis), while the cortical tissues reveal the presence of a C starvation signal probably due to the UDP-glucose demand necessary for the thickening phase of bast fibres. Cell wall analysis indicates a difference in rhamnogalacturonan structure/composition of mature bast fibres, as evidenced by the higher levels of galactose measured, as well as the occurrence of more water-soluble pectins in elongating internodes. The targeted quantification of phenolics shows that the middle internode and the cortical tissues at the bottom have higher contents than top internodes. Ultrastructural analyses reveal the presence of a gelatinous layer in bast fibres with a lamellar structure. The data presented will be an important resource and reference for future molecular studies on a neglected fibre crop.

Physiological effects of nitrogen deficiency and recovery on the macroalga Gracilariopsis lemaneiformis (Rhodophyta)

Algal metabolites are the most promising feedstocks for bio-energy production. Gracilariopsis lemaneiformis seems to be a good candidate red alga for polysaccharide production, especially relating to the agar production industry. Nitrogen deficiency is an efficient environmental pressure used to increase the accumulation of metabolites in algae. However, there are no studies on the physiological effects of G. lemaneiformis in response to nitrogen deficiency and its subsequent recovery. Here we integrated physiological data with molecular studies to explore the response strategy of G. lemaneiformis under nitrogen deficiency and recovery. Physiological measurements indicated that amino acids and protein biosynthesis were decreased, while endogenous NH₄⁺ and soluble polysaccharides levels were increased under nitrogen stress. The expression of key genes involved in these pathways further suggested that G. lemaneiformis responded to nitrogen stress through up-regulation or down-regulation of genes related to nitrogen metabolism, and increased levels of endogenous NH₄⁺ to complement the deficiency of exogenous nitrogen. Consistent with the highest accumulation of soluble polysaccharides, the gene encoding UDP-glucose pyrophosphorylase, a molecular marker used to evaluate agar content, was dramatically up-regulated more than 4-fold compared to the relative expression of actin after 4 d of nitrogen recovery. The present data provide important information on the mechanisms of nutrient balance in macroalgae.

Contrasting gene expression patterns in grain of high and low asparagine wheat genotypes in response to sulphur supply

Background

Free asparagine is the precursor for acrylamide formation during cooking and processing of grains, tubers, beans and other crop products. In wheat grain, free asparagine, free glutamine and total free amino acids accumulate to high levels in response to sulphur deficiency. In this study, RNA-seq data were acquired for the embryo and endosperm of two genotypes of bread wheat, Spark and SR3, growing under conditions of sulphur sufficiency and deficiency, and sampled at 14 and 21 days post anthesis (dpa). The aim was to provide new knowledge and understanding of the genetic control of asparagine accumulation and breakdown in wheat grain.

Results

There were clear differences in gene expression patterns between the genotypes. Sulphur responses were greater at 21 dpa than 14 dpa, and more evident in SR3 than Spark. TaASN2 was the most highly expressed asparagine synthetase gene in the grain, with expression in the embryo much higher than in the endosperm, and higher in Spark than SR3 during early development. There was a trend for genes encoding enzymes of nitrogen assimilation to be more highly expressed in Spark than SR3 when sulphur was supplied. TaASN2 expression in the embryo of SR3 increased in response to sulphur deficiency at 21 dpa, although this was not observed in Spark. This increase in TaASN2 expression was accompanied by an increase in glutamine synthetase gene expression and a decrease in asparaginase gene expression. Asparagine synthetase and asparaginase gene expression in the endosperm responded in the opposite way. Genes encoding regulatory protein kinases, SnRK1 and GCN2, both implicated in regulating asparagine synthetase gene expression, also responded to sulphur deficiency. Genes encoding bZIP transcription factors, including Opaque2/bZIP9, SPA/bZIP25 and BLZ1/OHP1/bZIP63, all of which contain SnRK1 target sites, were also expressed. Homeologues of many genes showed differential expression patterns and responses, including TaASN2.

Conclusions

Data on the genetic control of free asparagine accumulation in wheat grain and its response to sulphur supply showed grain asparagine levels to be determined in the embryo, and identified genes encoding signalling and metabolic proteins involved in asparagine metabolism that respond to sulphur availability.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5991-8) contains supplementary material, which is available to authorized users.

Multi-trait analysis of domestication genes in Cicer arietinum - Cicer reticulatum hybrids with a multidimensional approach: Modeling wide crosses for crop improvement

Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by ˜100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid populations to delineate the genetic underpinnings of domestication traits. Two species of wild chickpea, C. reticulatum and C. echinospermum, were crossed with the elite, early flowering C. arietinum cultivar ICCV96029. KASP genotyping of F2 parents with an FT-linked molecular marker enabled selection of 284 F3 families with reduced phenological variation: 255 F3 families of C. arietinum x reticulatum (AR) derived from 17 diverse wild parents and 29 F3 families of C. arietinum x echinospermum (AE) from 3 wild parents. The combined 284 lineages were genotyped using a genotyping-by-sequencing strategy and phenotyped for agronomic traits. 50 QTLs in 11 traits were detected from AR and 35 QTLs in 10 traits from the combined data. Using hierarchical clustering to assign traits to six correlated groups and mixed model based multi-trait mapping, four pleiotropic loci were identified. Bayesian analysis further identified four inter-trait relationships controlling the duration of vegetative growth and seed maturation, for which the underlying pleiotropic genes were mapped. A random forest approach was used to explore the most extreme trait differences between AR and AE progenies, identifying traits most characteristic of wild species origin. Knowledge of the genomic basis of traits that segregate in wild-cultivated hybrid populations will facilitate chickpea improvement by linking genetic and phenotypic variation in a quantitative genetic framework.

Construction of a network describing asparagine metabolism in plants and its application to the identification of genes affecting asparagine metabolism in wheat under drought and nutritional stress

A detailed network describing asparagine metabolism in plants was constructed using published data from Arabidopsis (Arabidopsis thaliana) maize (Zea mays), wheat (Triticum aestivum), pea (Pisum sativum), soybean (Glycine max), lupin (Lupus albus), and other species, including animals. Asparagine synthesis and degradation is a major part of amino acid and nitrogen metabolism in plants. The complexity of its metabolism, including limiting and regulatory factors, was represented in a logical sequence in a pathway diagram built using yED graph editor software. The network was used with a Unique Network Identification Pipeline in the analysis of data from 18 publicly available transcriptomic data studies. This identified links between genes involved in asparagine metabolism in wheat roots under drought stress, wheat leaves under drought stress, and wheat leaves under conditions of sulfur and nitrogen deficiency. The network represents a powerful aid for interpreting the interactions not only between the genes in the pathway but also among enzymes, metabolites and smaller molecules. It provides a concise, clear understanding of the complexity of asparagine metabolism that could aid the interpretation of data relating to wider amino acid metabolism and other metabolic processes.