Ionomic, metabolomic and proteomic analyses reveal molecular mechanisms of root adaption to salt stress in Tibetan wild barley

OsCaM1-1 Is Responsible for Salt Tolerance by Regulating Na+/K+ Homoeostasis in Rice

Calmodulin, a highly conserved calcium-binding protein, plays a crucial role in response to salt stress. Previous studies investigated sequence and function of calmodulin members in some plants, but their roles in rice have not been fully elucidated. Three OsCaM1 genes namely OsCaM1-1/2/3 encode the same OsCaM1 protein. Here, we found that OsCaM1-1 had significantly higher expression than the other two genes under salt stress. After 4 weeks of exposure to 75 mM NaCl, OsCaM1-1 overexpressed mutants showed higher salt tolerance, while knocked-out mutants exhibited lower salt tolerance, compared to the wild type. Moreover, the oscam1-1 mutants had higher Na+ concentration and Na+/K+ ratio in both shoots and roots, less instantaneous K+ and Ca2+ fluxes in roots, compared to wild type under salt stress, indicating the involvement of OsCaM1-1 in regulation of Na+ and K+ homoeostasis via Ca2+ signal. RNA-seq analysis identified 452 differentially expressed genes (DEGs) regulated by OsCaM1-1 and salt stress, and they were mainly enriched in nucleus DNA-binding activities, including ABI5, WRKY76, WRKY48 and bHLH120 transcription factors. Knockout of OsCaM1-1 also modulated the expression of Na+ transporters, including HKT1;1, HKT1;5, SOS1, NHX1 and NHX4. In conclusion, OsCaM1-1 positively regulates salt tolerance in rice through mediating ion homoeostasis.

Bacillus altitudinis AD13-4 Enhances Saline-Alkali Stress Tolerance of Alfalfa and Affects Composition of Rhizosphere Soil Microbial Community

Saline and alkaline stresses limit plant growth and reduce crop yield. Soil salinization and alkalization seriously threaten the sustainable development of agriculture and the virtuous cycle of ecology. Biofertilizers made from plant growth-promoting rhizobacteria (PGPR) not only enhance plant growth and stress tolerance, but also are environmentally friendly and cost-effective. There have been many studies on the mechanisms underlying PGPRs enhancing plant salt resistance. However, there is limited knowledge about the interaction between PGPR and plants under alkaline-sodic stress. To clarify the mechanisms underlying PGPR's improvement of plants' tolerance to alkaline-sodic stress, we screened PGPR from the rhizosphere microorganisms of local plants growing in alkaline-sodic land and selected an efficient strain, Bacillus altitudinis AD13-4, as the research object. Our results indicate that the strain AD13-4 can produce various growth-promoting substances to regulate plant endogenous hormone levels, cell division and differentiation, photosynthesis, antioxidant capacity, etc. Transcriptome analysis revealed that the strain AD13-4 significantly affected metabolism and secondary metabolism, signal transduction, photosynthesis, redox processes, and plant-pathogen interactions. Under alkaline-sodic conditions, inoculation of the strain AD13-4 significantly improved plant biomass and the contents of metabolites (e.g., soluble proteins and sugars) as well as secondary metabolites (e.g., phenols, flavonoids, and terpenoids). The 16S rRNA gene sequencing results indicated that the strain AD13-4 significantly affected the abundance and composition of the rhizospheric microbiota and improved soil activities and physiochemical properties. Our study provides theoretical support for the optimization of saline-alkali-tolerant PGPR and valuable information for elucidating the mechanism of plant alkaline-sodic tolerance.

Heat shock protein HvHSP16.9 from wild barley enhances tolerance to salt stress

Heat shock proteins (HSPs) are known to play a crucial role in the response of plants to environmental stress, particularly heat stress. Nevertheless, the function of HSPs in salt stress tolerance in plants, especially in barley, remains largely unexplored. Here, we aimed to investigate and compare the salt tolerance mechanisms between wild barley EC_S1 and cultivated barley RGT Planet through a comprehensive analysis of physiological parameters and transcriptomic profiles. Results demonstrated that the number of differentially expressed genes (DEGs) in EC_S1 was significantly higher than in RGT Planet, indicating that wild barley gene regulation is more adaptive to salt stress. KEGG enrichment analysis revealed that DEGs were mainly enriched in the processes of photosynthesis, plant hormone signal transduction, and reactive oxygen species metabolism. Furthermore, the application of weighted gene correlation network analysis (WGCNA) enabled the identification of a set of key genes, including small heat shock protein (sHSP), Calmodulin-like proteins (CML), and protein phosphatases 2C (PP2C). Subsequently, a novel sHSP gene, HvHSP16.9 encoding a protein of 16.9 kDa, was cloned from wild barley, and its role in plant response to salt stress was elucidated. In Arabidopsis, overexpression of HvHSP16.9 increased the salt tolerance. Meanwhile, barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) of HvHSP16.9 significantly reduced the salt tolerance in wild barley. Overall, this study offers a new theoretical framework for comprehending the tolerance and adaptation mechanisms of wild barley under salt stress. It provides valuable insights into the salt tolerance function of HSP, and identifies new candidate genes for enhancing cultivated barley varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01455-4.

Ecophysiological responses of Phragmites australis populations to a tidal flat gradient in the Yangtze River Estuary, China

Phragmites australis is a prevalent species in the Chongming Dongtan wetland and is capable of thriving in various tidal flat environments, including high salinity habitats. P. australis population displays inconsistent ecological performances, highlighting the need to uncover their survival strategies and mechanisms in tidal flats with diverse soil salinities. Upon comparing functional traits of P. australis at multiple tidal flats (low, middle, and high) and their responses to soil physicochemical properties, this study aimed to clarify the salt-tolerant strategy of P. australis and the corresponding mechanisms. These results showed that leaf characteristics, such as specific leaf area and leaf dry matter content, demonstrated more robust stability to soil salinity than shoot height and dry weight. Furthermore, as salt stress intensified, the activities of superoxide dismutase (SOD), catalase (CAT) and peroxisome (POD) in P. australis leaves at low tidal flat exhibited an increased upward trend compared to those at other tidal flats. The molecular mechanism of salt tolerance in Phragmites australis across various habitats was investigated using transcriptome sequencing. Weighted correlation network analysis (WGCNA) combined with differentially expressed genes (DEGs) screened out 3 modules closely related to high salt tolerance and identified 105 core genes crucial for high salt tolerance. Further research was carried out on the few degraded populations at low tidal flat, and 25 core genes were identified by combining WGCNA and DEGs. A decrease in the activity of ferroptosis marker gonyautoxin-4 and an increase in the content of Fe3+ in the degenerated group were observed, indicating that ferroptosis might participate in degradation. Furthermore, correlation analysis indicated a possible regulatory network between salt tolerance and ferroptosis. In short, this study provided new insights into the salt tolerance mechanism of P. australis population along tidal flats.

Integrated physiological and transcriptomic analyzes reveal the duality of TiO2 nanoparticles on alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.) is a feed crop due to its rich nutrition and high productivity. The utilization of titanium oxide nanoparticles (TiO2 NPs) brings benefits to agricultural production but also has potential hazards. To investigate the duality and related mechanism of TiO2 NPs on alfalfa, its different doses including 0, 50, 100, 200, 500, and 1000 mg L- 1 (CK, Ti-50, Ti-100, Ti-200, Ti-500, and Ti-1000) were sprayed on leaves. The results showed that greater doses of TiO2 NPs (500 and 1000 mg L-1) negatively affected the physiological parameters, including morphology, biomass, leaf ultrastructure, stomata, photosynthesis, pigments, and antioxidant ability. However, 100 mg L-1 TiO2 NPs revealed an optimal positive effect; compared with the CK, it dramatically increased plant height, fresh weight, and dry weight by 22%, 21%, and 41%, respectively. Additionally, TiO2 NPs at low doses significantly protected leaf tissue, promoted stomatal opening, and enhanced the antioxidant system; while higher doses had phytotoxicity. Hence, TiO2 NPs are dose-dependent on alfalfa. The transcriptomic analysis identified 4625 and 2121 differentially expressed genes (DEGs) in the comparison of CK vs. Ti-100 and CK vs. Ti-500, respectively. They were mainly enriched in photosynthesis, chlorophyll metabolism, and energy metabolism. Notably, TiO2 NPs-induced phytotoxicity on photosynthetic parameters happened concurrently with the alterations of the genes involved in the porphyrin and chlorophyll metabolism and carbon fixation in photosynthetic organisms in the KEGG analysis. Similarly, it affected the efficiency of alfalfa energy transformation processes, including pyruvate metabolism and chlorophyll synthesis. Several key related genes in these pathways were validated. Therefore, TiO2 NPs have positive and toxic effects by regulating morphology, leaf ultrastructure, stomata, photosynthesis, redox homeostasis, and genes related to key pathways. It is significant to understand the duality of TiO2 NPs and cultivate varieties resistant to nanomaterial pollution.

Investigation of the response of Platycodongrandiflorus (Jacq.) A. DC to salt stress using combined transcriptomics and metabolomics

BACKGROUND

Platycodon grandiflorus (Jacq.) A. DC is a famous traditional Chinese medicine in China and an authentic medicine in Inner Mongolia. It has been traditionally used as an expectorant in cough and also has anti-inflammatory and other pharmacological effects. As a homologous plant of medicine and food, P. grandiflorus is widely planted in Northeast China. Soil salinity isa limiting factor for its cultivation. In this study, we comprehensively described the physiological characteristics of P. grandiflorus and combined transcriptomics and metabolomics to study the response of roots of P. grandiflorus to salt stress.

RESULTS

Overall, 8,988 differentially expressed genes were activated and significantly altered the metabolic processes. In total, 428 differentially abundant metabolites were affected by salt stress. After moderate and severe salt stress, most of the differentially abundant metabolites were enriched in the L-phenylalanine metabolic pathway. Through the comprehensive analysis of the interaction between key genes and metabolites, the main pathways such as lignin compound biosynthesis and triterpene saponin biosynthesis were completed. The relative content of compounds related to lignin biosynthesis, such as caffeic acid, coniferin, and syringing, increased under salt stress, and the related genes such as PAL, C4H, and the key enzyme gene UGT72E2 were activated to adapt to the salt stress. Platycodon saponin is one of the major triterpene saponins in P. grandiflorus, and Platycodin D is its most abundant major bioactive component. Under severe salt stress, Platycodin D level increased by nearly 1.77-fold compared with the control group. Most of the genes involved insynthetic pathway of Platycodin D, such as HMGCR, GGPS, SE, and LUP, were upregulated under salt stress.

CONCLUSION

Salt stress led to a decrease in the biomass and affected the activities of antioxidant enzymes and contents of osmotic regulators in the plant. These results provided not only novel insights into the underlying mechanisms of response of P. grandiflorus to salt stress but also a foundation for future studies on the function of genes related to salt tolerance in the triterpenoid saponin biosynthesis pathway.

Time-Course Transcriptome Analysis of Aquilegia vulgaris Root Reveals the Cell Wall's Roles in Salinity Tolerance

Salt stress has a considerable impact on the development and growth of plants. The soil is currently affected by salinisation, a problem that is becoming worse every year. This means that a significant amount of salt-tolerant plant material needs to be added. Aquilegia vulgaris has aesthetically pleasing leaves, unique flowers, and a remarkable tolerance to salt. In this study, RNA-seq technology was used to sequence and analyse the transcriptome of the root of Aquilegia vulgaris seedlings subjected to 200 mM NaCl treatment for 12, 24, and 48 h. In total, 12 Aquilegia vulgaris seedling root transcriptome libraries were constructed. At the three time points of salt treatment compared with the control, 3888, 1907, and 1479 differentially expressed genes (DEGs) were identified, respectively. Various families of transcription factors (TFs), mainly AP2, MYB, and bHLH, were identified and might be linked to salt tolerance. Gene Ontology (GO) analysis of DEGs revealed that the structure and composition of the cell wall and cytoskeleton may be crucial in the response to salt stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs showed a significant enrichment of the pentose and glucuronate interconversion pathway, which is associated with cell wall metabolism after 24 and 48 h of salt treatment. Based on GO and KEGG analyses of DEGs, the pentose and glucuronate interconversion pathway was selected for further investigation. AP2, MYB, and bHLH were found to be correlated with the functional genes in this pathway based on a correlation network. This study provides the groundwork for understanding the key pathways and gene networks in response to salt stress, thereby providing a theoretical basis for improving salt tolerance in Aquilegia vulgaris.

Acetylation of GhCaM7 enhances cotton resistance to Verticillium dahliae

Protein lysine acetylation is an important post-translational modification mechanism involved in cellular regulation in eukaryotes. Calmodulin (CaM) is a ubiquitous Ca²⁺ sensor in eukaryotes and is crucial for plant immunity, but it is so far unclear whether acetylation is involved in CaM-mediated plant immunity. Here, we found that GhCaM7 is acetylated upon Verticillium dahliae (V. dahliae) infection and a positive regulator of V. dahliae resistance. Overexpressing GhCaM7 in cotton and Arabidopsis enhances V. dahliae resistance and knocking-down GhCaM7 makes cotton more susceptible to V. dahliae. Transgenic Arabidopsis plants overexpressing GhCaM7 with mutation at the acetylation site are more susceptible to V. dahliae than transgenics overexpressing the wild-type GhCaM7, implying the importance of the acetylated GhCaM7 in response to V. dahliae infection. Yeast two-hybrid, bimolecular fluorescent complementation, luciferase complementation imaging, and coimmunoprecipitation assays demonstrated interaction between GhCaM7 and an osmotin protein GhOSM34 that was shown to have a positive role in V. dahliae resistance. GhCaM7 and GhOSM34 are co-localized in the cell membrane. Upon V. dahliae infection, the Ca²⁺ content reduces almost instantly in plants with downregulated GhCaM7 or GhOSM34. Down regulating GhOSM34 enhances accumulation of Na⁺ and increases cell osmotic pressure. Comparative transcriptomic analyses between cotton plants with an increased or reduced expression level of GhCaM7 and wild-type plants indicate the involvement of jasmonic acid signaling pathways and reactive oxygen species in GhCaM7-enabled disease resistance. Together, these results demonstrate the involvement of CaM protein in the interaction between cotton and V. dahliae, and more importantly, the involvement of the acetylated CaM in the interaction.

Metabolomic analysis reveals the molecular responses to copper toxicity in rice (Oryza sativa)

Copper (Cu) is one of the essential microelements and widely participates in various pathways in plants, but excess Cu in plant cells could induce oxidative stress and harm plant growth. Rice (Oryza sativa) is a main crop food worldwide. The molecular mechanisms of rice in response to copper toxicity are still not well understood. In this study, two-week-old seedlings of the rice cultivar Nipponbare were treated with 100 μM Cu²⁺ (CuSO₄) in the external solution for 10 days. Physiological analysis showed that excess Cu significantly inhibited the growth and biomass of rice seedlings. After Cu treatment, the contents of Mn and Zn were significantly reduced in the roots and shoots, while the Fe content was significantly increased in the roots. Meanwhile, the activities of antioxidant enzymes including SOD and POD were dramatically enhanced after Cu treatment. Based on metabolomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods, 695 metabolites were identified in rice roots. Among these metabolites, 123 metabolites were up-regulated and 297 were down-regulated, respectively. The differential metabolites (DMs) include carboxylic acids and derivatives, benzene and substituted derivatives, carbonyl compounds, cinnamic acids and derivatives, fatty acyls and organ nitrogen compounds. KEGG analysis showed that these DMs were mainly enriched in TCA cycle, purine metabolism and starch and sucrose metabolism pathways. Many intermediates in the TCA cycle and purine metabolism were down-regulated, indicating a perturbed carbohydrate and nucleic acid metabolism. Taken together, the present study provides new insights into the mechanism of rice roots to Cu toxicity.

Abiotic Stress in Crop Production

The vast majority of agricultural land undergoes abiotic stress that can significantly reduce agricultural yields. Understanding the mechanisms of plant defenses against stresses and putting this knowledge into practice is, therefore, an integral part of sustainable agriculture. In this review, we focus on current findings in plant resistance to four cardinal abiotic stressors—drought, heat, salinity, and low temperatures. Apart from the description of the newly discovered mechanisms of signaling and resistance to abiotic stress, this review also focuses on the importance of primary and secondary metabolites, including carbohydrates, amino acids, phenolics, and phytohormones. A meta-analysis of transcriptomic studies concerning the model plant Arabidopsis demonstrates the long-observed phenomenon that abiotic stressors induce different signals and effects at the level of gene expression, but genes whose regulation is similar under most stressors can still be traced. The analysis further reveals the transcriptional modulation of Golgi-targeted proteins in response to heat stress. Our analysis also highlights several genes that are similarly regulated under all stress conditions. These genes support the central role of phytohormones in the abiotic stress response, and the importance of some of these in plant resistance has not yet been studied. Finally, this review provides information about the response to abiotic stress in major European crop plants—wheat, sugar beet, maize, potatoes, barley, sunflowers, grapes, rapeseed, tomatoes, and apples.

Integrated metabolome, transcriptome analysis, and multi-flux full-length sequencing offer novel insights into the function of lignin biosynthesis as a Sesuvium portulacastrum response to salt stress

Sesuvium portulacastrum is a typical halophyte. However, few studies have investigated its salt-tolerant molecular mechanism. In this study, metabolome, transcriptome, and multi-flux full-length sequencing analysis were conducted to investigate the significantly different metabolites (SDMs) and differentially expressed genes (DEGs) of S. portulacastrum samples under salinity. The complete-length transcriptome of S. portulacastrum was developed, which contained 39,659 non-redundant unigenes. RNA-seq results showed that 52 DEGs involved in lignin biosynthesis may be responsible for S. portulacastrum salt tolerance. Furthermore, 130 SDMs were identified, and the salt response could be attributed to the p-coumaryl alcohol-rich in lignin biosynthesis. The co-expression network that was constructed after comparing the different salt treatment processes showed that the p-Coumaryl alcohol was linked to 30 DEGs. Herein, 8 structures genes, i.e., Sp4CL, SpCAD, SpCCR, SpCOMT, SpF5H, SpCYP73A, SpCCoAOMT, and SpC3'H were identified as significant factors in regulating lignin biosynthesis. Further investigation revealed that 64 putative transcription factors (TFs) may interact with the promoters of the above-mentioned genes. Together, the data revealed a potential regulatory network comprising important genes, putative TFs, and metabolites involved in the lignin biosynthesis of S. portulacastrum roots under salt stress, which could serve as a rich useful genetic resource for breeding excellent salt-tolerant plants.

Integrated Transcriptome and Metabolome Analysis of Rice Leaves Response to High Saline-Alkali Stress

Rice (Oryza sativa) is one of the most important crops grown worldwide, and saline-alkali stress seriously affects the yield and quality of rice. It is imperative to elucidate the molecular mechanisms underlying rice response to saline-alkali stress. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the effects of long-term saline-alkali stress on rice. High saline-alkali stress (pH > 9.5) induced significant changes in gene expression and metabolites, including 9347 differentially expressed genes (DEGs) and 693 differentially accumulated metabolites (DAMs). Among the DAMs, lipids and amino acids accumulation were greatly enhanced. The pathways of the ABC transporter, amino acid biosynthesis and metabolism, glyoxylate and dicarboxylate metabolism, glutathione metabolism, TCA cycle, and linoleic acid metabolism, etc., were significantly enriched with DEGs and DAMs. These results suggest that the metabolites and pathways play important roles in rice's response to high saline-alkali stress. Our study deepens the understanding of mechanisms response to saline-alkali stress and provides references for molecular design breeding of saline-alkali resistant rice.

Physiological and Biochemical Responses of Solanum lycopersicum L. to Benzo[a]pyrene Contaminated Soils

Benzo[a]pyrene (BaP) is noted as one of the main cancer-causing pollutants in human beings and may damage the development of crop plants. The present work was designed to explore more insights into the toxic effects of BaP on Solanum lycopersicum L. at various doses (20, 40, and 60 MPC) spiked in Haplic Chernozem. A dose-dependent response in phytotoxicity were noted, especially in the biomass of the roots and shoots, at doses of 40 and 60 MPC BaP and the accumulation of BaP in S. lycopersicum tissues. Physiological and biochemical response indices were severely damaged based on applied doses of BaP. During the histochemical analysis of the localization of superoxide in the leaves of S. lycopersicum, formazan spots were detected in the area near the leaf's veins. The results of a significant increase in malondialdehyde (MDA) from 2.7 to 5.1 times, proline 1.12- to 2.62-folds, however, a decrease in catalase (CAT) activity was recorded by 1.8 to 1.1 times. The activity of superoxide dismutase (SOD) increased from 1.4 to 2, peroxidase (PRX) from 2.3 to 5.25, ascorbate peroxidase (APOX) by 5.8 to 11.5, glutathione peroxidase (GP) from 3.8 to 7 times, respectively. The structure of the tissues of the roots and leaves of S. lycopersicum in the variants with BaP changed depending on the dose: it increased the intercellular space, cortical layer, and the epidermis, and the structure of the leaf tissues became looser.

Quantitative Proteomics Analysis Reveals Proteins Associated with High Melatonin Content in Barley Seeds under NaCl-Induced Salt Stress

Soil salinization limits hull-less barley cultivation in the Qinghai-Tibet Plateau of China. However, some wild hull-less barley seeds accumulate high melatonin (MEL) during germination with improved salt tolerance; but the mechanism of melatonin-mediated salt tolerance in hull-less barley is not well understood at the protein level. This study investigated proteome changes resulting in high melatonin content in germinating hull-less barley seeds under high saline conditions. The proteome profiles of seed treatment with 240 mM-NaCl (N), water (H), and control (C) taken 7 days after germination were compared using the TMT-based quantitative proteomics. Our results indicate that salt stress-induced global changes in the proteomes of germinating hull-less barley seeds, altering the expression and abundance of proteins related to cell cycle and control, carbohydrate and energy metabolism, and amino acid transport and metabolism including proteins related to melatonin production. Furthermore, proteins associated with cellular redox homeostasis, osmotic stress response, and secondary metabolites derived primarily from amino acid metabolism, purine degradation, and shikimate pathways increased significantly in abundance and may contribute to the high melatonin content in seeds under salt stress. Consequently, triggering the robust response to oxidative stress occasioned by the NaCl-induced salt stress, improved seed germination and strong adaptation to salt stress.

Comparative Ionomics and Metabolic Responses and Adaptive Strategies of Cotton to Salt and Alkali Stress

Soil salinization and alkalization severely inhibit agriculture. However, the response mechanisms of cotton to salt stress or alkali stress are unclear. Ionomics and metabolomics were used to investigate salt and alkali stresses in cotton roots and leaves. Compared with the control, salt-treated and alkali-treated cotton plants showed 51.8 and 53.0% decreases in biomass, respectively. Under salt stress, the concentration of N decreased in roots but increased in leaves, and the concentrations of P and K increased in roots but decreased in leaves. Salt stress inhibited Ca, B, N, and Fe uptake and Mg, K, P, S, and Cu transport, but promoted Mo, Mn, Zn, Mg, K, P, S, and Cu uptake and Mo, Mn, Zn, B, N, and Fe transport. Under alkali stress, the concentrations of N and P in roots and leaves decreased, while the concentrations of K in roots and leaves increased. Alkali stress inhibited P, Ca, S, N, Fe, and Zn uptake and N, P, Mg and B transport, but promoted K, Mn, Cu, Mo, Mg, and B uptake and K, Mn, Cu, Mo, Fe, and Zn transport. Under salt stress in the leaves, 93 metabolites increased, mainly organic acids, amino acids, and sugars, increased in abundance, while 6 decreased. In the roots, 72 metabolites increased, mainly amino acids, organic acids, and sugars, while 18 decreased. Under alkali stress, in the leaves, 96 metabolites increased, including organic acids, amino acids, and sugars, 83 metabolites decreased, including organic acids, amino acids, and sugars; In the roots, 108 metabolites increased, including organic acids, amino acids, and sugars. 83 metabolites decreased, including organic acids and amino acids. Under salt stress, cotton adapts to osmotic stress through the accumulation of organic acids, amino acids and sugars, while under alkali stress, osmoregulation was achieved via inorganic ion accumulation. Under salt stress, significant metabolic pathways in the leaves and roots were associated with amino acid and organic acid metabolism, sugar metabolism was mainly used as a source of energy, while under alkali stress, the pathways in the leaves were related to amino acid and linoleic acid metabolism, β-Oxidation, TCA cycle, and glycolysis were enhanced to provide the energy needed for life activities. Enhancing organic acid accumulation and metabolism in the roots is the key response mechanism of cotton to alkalinity.

Genome-Wide Identification, Expression Pattern and Sequence Variation Analysis of SnRK Family Genes in Barley

Sucrose non-fermenting 1 (SNF1)-related protein kinase (SnRK) is a large family of protein kinases that play a significant role in plant stress responses. Although intensive studies have been conducted on SnRK members in some crops, little is known about the SnRK in barley. Using phylogenetic and conserved motif analyses, we discovered 46 SnRK members scattered across barley’s 7 chromosomes and classified them into 3 sub-families. The gene structures of HvSnRKs showed the divergence among three subfamilies. Gene duplication and synteny analyses on the genomes of barley and rice revealed the evolutionary features of HvSnRKs. The promoter regions of HvSnRK family genes contained many ABRE, MBS and LTR elements responding to abiotic stresses, and their expression patterns varied with different plant tissues and abiotic stresses. HvSnRKs could interact with the components of ABA signaling pathway to respond to abiotic stress. Moreover, the haplotypes of HvSnRK2.5 closely associated with drought tolerance were detected in a barley core collection. The current results could be helpful for further exploration of the HvSnRK genes responding to abiotic stress tolerance in barley.

Metabolic and Physiological Changes in the Roots of Two Oat Cultivars in Response to Complex Saline-Alkali Stress

Saline-alkali stress is a major abiotic stress factor in agricultural productivity. Oat (Avena sativa L.) is a saline-alkali tolerant crop species. However, molecular mechanisms of saline-alkali tolerance in oats remain unclear. To understand the physiological and molecular mechanisms underlying seedling saline-alkali tolerance in oats, the phenotypic and metabolic responses of two oat cultivars, Baiyan7 (BY, tolerant cultivar) and Yizhangyan4 (YZY, sensitive cultivar), were characterized under saline-alkali stress conditions. Compared with YZY, BY showed better adaptability to saline-alkali stress. A total of 151 and 96 differential metabolites induced by saline-alkali stress were identified in roots of BY and YZY, respectively. More detailed analyses indicated that enhancements of energy metabolism and accumulations of organic acids were the active strategies of oat roots, in response to complex saline-alkali stress. The BY utilized sugars via sugar consumption more effectively, while amino acids strengthened metabolism and upregulated lignin and might be the positive responses of BY roots to saline-alkali stress, which led to a higher osmotic adjustment of solute concentrations and cell growth. The YZY mainly used soluble sugars and flavonoids combined with sugars to form glycosides, as osmotic regulatory substances or antioxidant substances, to cope with saline-alkali stress. The analyses of different metabolites of roots of tolerant and sensitive cultivars provided an important theoretical basis for understanding the mechanisms of saline-alkali tolerance and increased our knowledge of plant metabolism regulation under stress. Meanwhile, some related metabolites, such as proline, betaine, and p-coumaryl alcohol, can also be used as candidates for screening saline-alkali tolerant oat cultivars.

Vacuolar H+-pyrophosphatase HVP10 enhances salt tolerance via promoting Na+ translocation into root vacuoles

Vacuolar H+-pumping pyrophosphatases (VPs) provide a proton gradient for Na+ sequestration in the tonoplast; however, the regulatory mechanisms of VPs in developing salt tolerance have not been fully elucidated. Here, we cloned a barley (Hordeum vulgare) VP gene (HVP10) that was identified previously as the HvNax3 gene. Homology analysis showed VP10 in plants had conserved structure and sequence and likely originated from the ancestors of the Ceramiales order of Rhodophyta (Cyanidioschyzon merolae). HVP10 was mainly expressed in roots and upregulated in response to salt stress. After salt treatment for 3 weeks, HVP10 knockdown (RNA interference) and knockout (CRISPR/Cas9 gene editing) barley plants showed greatly inhibited growth and higher shoot Na+ concentration, Na+ transportation rate and xylem Na+ loading relative to wild-type (WT) plants. Reverse transcription quantitative polymerase chain reaction and microelectronic Ion Flux Estimation results indicated that HVP10 likely modulates Na+ sequestration into the root vacuole by acting synergistically with Na+/H+ antiporters (HvNHX1 and HvNHX4) to enhance H+ efflux and K+ maintenance in roots. Moreover, transgenic rice (Oryza sativa) lines overexpressing HVP10 also showed higher salt tolerance than the WT at both seedling and adult stages with less Na+ translocation to shoots and higher grain yields under salt stress. This study reveals the molecular mechanism of HVP10 underlying salt tolerance and highlights its potential in improving crop salt tolerance.

Integrated physiological, proteomic, and metabolomic analyses of pecan cultivar 'Pawnee' adaptation to salt stress

The pecan is a salt-alkali-tolerant plant, and its fruit and wood have high economic value. This study aimed to explore the molecular mechanisms responsible for salt stress tolerance in the pecan grown under hydroponic conditions to simulate salt stress. The results showed that the photosynthetic rate (Pn) was reduced in response to salt stress, while the intercellular carbon dioxide concentrations (Ci) increased. The response of the pecan to salt stress was measured using iTRAQ (isobaric tags for relative or absolute quantitation) and LC/MS (liquid chromatography and mass spectrometry) non-targeted metabolomics technology. A total of 198 differentially expressed proteins (65 down-regulated and 133 up-regulated) and 538 differentially expressed metabolites (283 down-regulated and 255 up-regulated) were identified after exposure to salt stress for 48 h. These genes were associated with 21 core pathways, shown by Kyoto Encyclopedia of Genes and Genomes annotation and enrichment, including the metabolic pathways involved in nucleotide sugar and amino sugar metabolism, amino acid biosynthesis, starch and sucrose metabolism, and phenylpropane biosynthesis. In addition, analysis of interactions between the differentially expressed proteins and metabolites showed that two key nodes of the salt stress regulatory network, L-fucose and succinate, were up-regulated and down-regulated, respectively, suggesting that these metabolites may be significant for adaptations to salt stress. Finally, several key proteins were further verified by parallel reaction monitoring. In conclusion, this study used physiological, proteomic, and metabolomic methods to provide an important preliminary foundation for improving the salt tolerance of pecans.

Coordination of root growth with root morphology, physiology and defense functions in response to root pruning in Platycladus orientalis

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A growth‒defense tradeoff following root pruning.

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Root growth lagged behind root physiology after root pruning.

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The growth–defense tradeoff was induced by indole-3-acetic acid.

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Proteomic analysis supported a growth–defense tradeoff.

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Root pruning altered the expression of genes at the protein and mRNA levels.

Introduction

Root pruning is commonly used to facilitate seedling transplantation for the restoration of degraded or damaged ecosystems. However, little is known about how root growth coordinates morphology, physiology and defense functions following root pruning.

Objectives

We aim to elucidate whether and how root growth trades off with defense functioning after pruning.

Methods

Seedlings of Platycladus orientalis, a tree species widely used in forest restoration, were subjected to root pruning treatment. A suite of root growth, morphological and physiological traits were measured after pruning in combination with proteomic analysis.

Results

Root growth was insensitive to pruning until at 504 h with a significant increase of 16.8%, whereas root physiology was activated rapidly after pruning. Key root morphological traits, such as root diameter, specific root length and root tissue density, showed no response to the pruning treatment. Plant defense syndromes such as reactive oxygen species-scavenging enzymes and defensive phytohormones such as jasmonic acid and abscisic acid, were recruited at six hours after pruning and recovered to the unpruned levels at 504 h. Compared with the controls, 271, 360 and 106 proteins were differentially expressed at 6, 72 and 504 h after root pruning, respectively. These proteins, associated with defense function, showed temporal patterns similar to the above defense syndromes.

Conclusion

Our results suggest a root growth-defense tradeoff following root pruning in P. orientalis. This tradeoff was potentially due to the significant increase of indole-3-acetic acid, the phytohormone stimulating root branching, which occurred soon after pruning. Together, these results provide a holistic understanding of how root growth is coordinated with root morphology, physiology, and defense in response to root pruning.

Physiological and Transcriptome Indicators of Salt Tolerance in Wild and Cultivated Barley

Barley is used as a model cereal to decipher salt tolerance mechanisms due to its simpler genome than wheat and enhanced salt tolerance compared to rice and wheat. In the present study, RNA-Seq based transcriptomic profiles were compared between salt-tolerant wild (Hordeum spontaneum, genotype no. 395) genotype and salt-sensitive cultivated (H. vulgare, 'Mona' cultivar) subjected to salt stress (300 mM NaCl) and control (0 mM NaCl) conditions. Plant growth and physiological attributes were also evaluated in a separate experiment as a comparison. Wild barley was significantly less impacted by salt stress than cultivated barley in growth and physiology and hence was more stress-responsive functionally. A total of 6,048 differentially expressed genes (DEGs) including 3,025 up-regulated and 3,023 down-regulated DEGs were detected in the wild genotype in salt stress conditions. The transcripts of salt-stress-related genes were profoundly lower in the salt-sensitive than the tolerant barley having a total of 2,610 DEGs (580 up- and 2,030 down-regulated). GO enrichment analysis showed that the DEGs were mainly enriched in biological processes associated with stress defenses (e.g., cellular component, signaling network, ion transporter, regulatory proteins, reactive oxygen species (ROS) scavenging, hormone biosynthesis, osmotic homeostasis). Comparison of the candidate genes in the two genotypes showed that the tolerant genotype contains higher functional and effective salt-tolerance related genes with a higher level of transcripts than the sensitive one. In conclusion, the tolerant genotype consistently exhibited better tolerance to salt stress in physiological and functional attributes than did the sensitive one. These differences provide a comprehensive understanding of the evolved salt-tolerance mechanism in wild barley. The shared mechanisms between these two sub-species revealed at each functional level will provide more reliable insights into the basic mechanisms of salt tolerance in barley species.

GWAS and transcriptomic integrating analysis reveals key salt-responding genes controlling Na+ content in barley roots

Salt stress is one of the major environmental restricts for crop production and food safety. Barley (Hordeum vulgare L.) is the most salt-tolerant cereal crop, which could be the pioneer for shifting agricultural crop production to marginal saline lands. However, probably due to high genetic complexity of salinity tolerance trait, the progress in the identification of salt-tolerant locus or genes of barley roots moves slowly. Here, we determined physiological and ionic changes in mini-core barley accessions under salt conditions. Na⁺ content was lower in whole-plant but higher in roots of the salt tolerant genotypes than sensitive ones under salt stress. Genome-wide association study (GWAS) analysis identified 43 significant SNPs out of 12,564 SNPs and 215 candidate genes (P < 10^-3) in the roots of worldwide barley accessions, highly associated with root relative dry weight (RDW) and Na⁺ content after hydroponic salinity in greenhouse and growth chamber. Meanwhile, transcriptomic analysis (RNA-Seq) identified 3217 differentially expression genes (DEGs) in barley roots induced by salt stress, mainly enriched in metabolism and transport processes. After GWAS and RNA-Seq integrating analysis, 39 DEGs were verified by qRT-PCR as salt-responding genes, including CYPs, LRR-KISS and CML genes, mostly related to the signal regulation. Taken together, current results provide genetic map-based genes or new locus useful for improving salt tolerance in crop and contributing to the utilization of saline soils.

Synthesis of trans- methyl ferulate bearing an oxadiazole ether as potential activators for controlling plant virus

A series of new ferulic acid derivatives bearing an oxadiazole ether was synthesized by introducing a structure of oxadiazole into trans-ferulic acid via an ether linkage. The synthesized target compounds were evaluated in vivo for their anti-TMV (tobacco mosaic virus) activity, which indicated that some synthesized compounds displayed strong activity for controlling TMV. For protective activity, compounds 6f and 6h had the most activities of 65% and 69.8% at 500 mg L^-1, respectively. Compounds 6a, 6b, 6e, 6f and 6h showed > 60% curative activities at 500 mg L^-1. Preliminary proteomics analysis showed that compound 6h could regulate the phenylpropanoid biosynthesis pathway and chloroplast function. These results indicated that synthesized novel ferulic acid derivatives could be used for controlling TMV.

The barley SHN1-type transcription factor HvSHN1 imparts heat, drought and salt tolerances in transgenic tobacco

The APETAL2/Ethylene Responsive Factor (AP2/ERF) family was the subject of intensive research which led to the identification of several members involved in different stress responses such as salinity, drought and high temperature. The SHN/WIN clade of AP2/ERF participates in many important processes such as cutin and wax biosynthesis, ethylene signaling and gene expression. Here, we report the functional analysis of SHN1-type transcription factor, HvSHN1, from barely. The overexpression of HvSHN1 under the control of the duplicated 35S promoter in transgenic tobacco plants improved tolerance to salt, water stress and heat stress. Transgenic lines exhibited altered permeability of the cuticle and decreased stomatal density. Under heat stress, HvSHN1 transgenic lines exhibited higher superoxide dismutase (SOD) and catalase (CAT) activity and lower MDA and H2O2 contents than did WT. The overexpression of HvSHN1 upregulated different genes involved in osmotic stress, oxidative stress, sugar metabolism, and wax biosynthesis. To understand the involvement of HvSHN1 in heat stress tolerance, promoter regions of two tobacco genes homologous to Arabidopsis genes HSP90.1 and RAP2.6 were analyzed and DRE cis-elements; binding sites of HvSHN1, were found. Interaction network of HvSHN1, predicted using STRING software, contained proteins with predicted functions related to lipids metabolism and a gene encoding Cyclin-Dependent Kinase. These results suggest that HvSHN1 is an interesting candidate for the improvement of abiotic stress tolerance especially in the context of climate change.

Integrative analysis of transcriptome and metabolome reveal mechanism of tolerance to salt stress in oat (Avena sativa L.)

Soil salinity is among the crucial factors that impact on crop productivity, including oat (Avena sativa L.). Herein, we used two distinct oat cultivars with varied salt tolerance levels to unravel adaptive responses to salt stress by metabolomic and transcriptomic characterization. Metabolomic profiling revealed 201 metabolites, including saccharides, amino acids, organic acids, and secondary metabolites. The levels of most saccharides and amino acids were elevated in Baiyan 2 (BY2) as well as in Baiyan 5 (BY5) exposed to salt stress. In the tolerant cultivar BY2 exposed to 150 mM NaCl, concentrations of most of the metabolites increased significantly, with sucrose increased by 38.34-fold, Sophorose increased by 314.15-fold and Isomaltose 2 increased by 25.76-fold. In the sensitive cultivar BY5, the concentrations of most metabolites increased after the plant was exposed to 150 mM NaCl but decreased after the plant was exposed to 300 mM NaCl. Transcriptomic analysis revealed that gene expressions in BY5 were significantly affected under exposure to 300 mM NaCl (34040 genes up-regulated and 14757 genes down-regulated). Assessment of metabolic pathways as well as KEGG enrichment revealed that salt stress interferes with the biosynthesis of two oat cultivars, including capacity expenditure and sugar metabolism. Most of the BY2 genes enhanced energy consumption (for example, glycolysis) and biosynthesis (for instance, starch and sugar metabolism) under salt stress. In contrast, genes in BY5 were found to be down-regulated, leading to the inhibition of energy consumption and biosynthesis, which may also be attributed to salt sensitivity in BY5. In addition, the modified Na⁺/K⁺ transporter genes expression is associated with the predominant ionic responses in BY2, which leads low concentration of Na⁺ and high K⁺ when exposed to high salt situations. These findings suggest that the varied defensive capacities of these two oat cultivars in response to salt stress are due to their variations in energy-expenditure strategy, synthesis of energy substances and ion transport in roots. Our present study offers a crucial reference for oat cultivation under saline soil.

Carbon Assimilation, Isotope Discrimination, Proline and Lipid Peroxidation Contribution to Barley (Hordeum vulgare) Salinity Tolerance

Barley (Hordeum vulgare L.) exhibits great adaptability to salt tolerance in marginal environments because of its great genetic diversity. Differences in main biochemical, physiological, and molecular processes, which could explain the different tolerance to soil salinity of 16 barley varieties, were examined during a two-year field experiment. The study was conducted in a saline soil with an electrical conductivity ranging from 7.3 to 11.5 dS/m. During the experiment, a number of different physiological and biochemical characteristics were evaluated when barley was at the two- to three-nodes growing stage (BBCH code 32–33). The results indicated that there were significant (p < 0.001) effects due to varieties for tolerance to salinity. Carbon isotopes discrimination was higher by 11.8% to 16.0% in salt tolerant varieties than that in the sensitive ones. Additionally, in the tolerant varieties, assimilation rates of CO₂ and proline concentration were 200% and up to 67% higher than the sensitive varieties, respectively. However, in sensitive varieties, hydrogen peroxide and lipid peroxidation were enhanced, indicating an increased lipid peroxidation. The expression of the genes Hsdr4, HvA1, and HvTX1 did not differ among barley varieties tested. This study suggests that the increased carbon isotopes discrimination, increased proline concentration (play an osmolyte source role), and decreased lipid peroxidation are traits that are associated with barley tolerance to soil salinity. Moreover, our findings that proline improves salt tolerance by up-regulating stress-protective enzymes and reducing oxidation of lipid membranes will encourage our hypothesis that there are specific mechanisms that can be co-related with the salt sensitivity or the tolerance of barley. Therefore, further research is needed to ensure the tolerance mechanisms that exclude NaCl in salt tolerant barley varieties and diminish accumulation of lipid peroxides through adaptive plant responses.

Metabolics and ionomics responses of tea leaves (Camellia sinensis (L.) O. Kuntze) to fluoride stress

Tea plant (Camellia sinensis (L.) O. Kuntze) is known to accumulate high concentrations of fluoride (F) in its leaves; however, the underlying mechanism of F accumulation remains unclear. The main objective of this study was to investigate the homeostatic self-defense mechanisms of tea leaves to F supplementation (0, 5, 20, and 50 mgL^-1) by metabolomics and ionomics. We identified a total of 96 up-regulated and 40 down-regulated metabolites in tea leaves treated with F. Of these different compounds, minor polypeptides, carbohydrates and amino acids played valuable roles in the F-tolerating mechanism of tea plant. After F treatments, the concentrations of sodium (Na), ferrum (Fe), manganese (Mn), and molybdenum (Mo) were significantly increased in tea leaves, whereas the aluminum (Al) was decreased. These findings suggest that the ionic balance and metabolites are attributable to the development of F tolerance, providing new insight into tea plant adaptation to F stress.

Advances in studies on ion transporters involved in salt tolerance and breeding crop cultivars with high salt tolerance

Soil salinity is a global major abiotic stress threatening crop productivity. In salty conditions, plants may suffer from osmotic, ionic, and oxidative stresses, resulting in inhibition of growth and development. To deal with these stresses, plants have developed a series of tolerance mechanisms, including osmotic adjustment through accumulating compatible solutes in the cytoplasm, reactive oxygen species (ROS) scavenging through enhancing the activity of anti-oxidative enzymes, and Na+/K+ homeostasis regulation through controlling Na+ uptake and transportation. In this review, recent advances in studies of the mechanisms of salt tolerance in plants are described in relation to the ionome, transcriptome, proteome, and metabolome, and the main factor accounting for differences in salt tolerance among plant species or genotypes within a species is presented. We also discuss the application and roles of different breeding methodologies in developing salt-tolerant crop cultivars. In particular, we describe the advantages and perspectives of genome or gene editing in improving the salt tolerance of crops.

Salinity tolerance in barley during germination- homologs and potential genes

Salinity affects more than 6% of the world's total land area, causing massive losses in crop yield. Salinity inhibits plant growth and development through osmotic and ionic stresses; however, some plants exhibit adaptations through osmotic regulation, exclusion, and translocation of accumulated Na+ or Cl-. Currently, there are no practical, economically viable methods for managing salinity, so the best practice is to grow crops with improved tolerance. Germination is the stage in a plant's life cycle most adversely affected by salinity. Barley, the fourth most important cereal crop in the world, has outstanding salinity tolerance, relative to other cereal crops. Here, we review the genetics of salinity tolerance in barley during germination by summarizing reported quantitative trait loci (QTLs) and functional genes. The homologs of candidate genes for salinity tolerance in Arabidopsis, soybean, maize, wheat, and rice have been blasted and mapped on the barley reference genome. The genetic diversity of three reported functional gene families for salt tolerance during barley germination, namely dehydration-responsive element-binding (DREB) protein, somatic embryogenesis receptor-like kinase and aquaporin genes, is discussed. While all three gene families show great diversity in most plant species, the DREB gene family is more diverse in barley than in wheat and rice. Further to this review, a convenient method for screening for salinity tolerance at germination is needed, and the mechanisms of action of the genes involved in salt tolerance need to be identified, validated, and transferred to commercial cultivars for field production in saline soil.

Analysis of the Barley Malt Rootlet Proteome

Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.

Proteomic and physiological responses in mangrove Kandelia candel roots under short-term high-salinity stress

Kandelia candel is one of the mangrove species that are most resistant to environmental stress. As a typical nonsalt-secreting mangrove plant, K. candel is an ideal biological material to analyze the molecular mechanism of salt tolerance in woody plants. In this study, changes in protein abundance and expression profile in K. candel roots under high-salinity stress of 600 mmol L^-1 NaCl were analyzed using isobaric tags for relative and absolute quantification (iTRAQ) assay. Moreover, the physiological parameters associated with metabolic pathways in which the differentially abundant proteins (DAPs) are involved were determined. A total of 5577 proteins were identified by iTRAQ analysis of the K. candel root proteins, of which 227 were DAPs with a fold change ratio >1.2 or a fold change ratio <0.83 and a P-value <0.05. A total of 227 DAPs consisting of 110 up-regulated and 117 down-regulated proteins were identified. Our Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the DAPs were primarily involved in biological processes including carbohydrate and energy metabolisms, stress response and defense, cell wall structure, and secondary metabolism. The results of the physiological parameters showed that their profile changes were consistent with those of the proteome analysis. The results of the proteome and physiological parameters showed that K. candel roots could resist high-salinity stress by maintaining a normal Embden-Meyerhof-Parnas and tricarboxylic acid (EMP-TCA) pathway, increasing the activities of various antioxidant enzymes and antioxidant contents, stabilizing the cell wall structure, and accumulating secondary metabolites such as triterpenoids.

Root plasticity and Pi recycling within plants contribute to low-P tolerance in Tibetan wild barley

BACKGROUND

Barley is a low phosphorus (P) demand cereal crop. Tibetan wild barley, as a progenitor of cultivated barley, has revealed outstanding ability of tolerance to low-P stress. However, the underlying mechanisms of low-P adaption and the relevant genetic controlling are still unclear.

RESULTS

We identified low-P tolerant barley lines in a doubled-haploid (DH) population derived from an elite Tibetan wild barley accession and a high-yield cultivar. The tolerant lines revealed greater root plasticity in the terms of lateral root length, compared to low-P sensitive lines, in response to low-P stress. By integrating the QTLs associated with root length and root transcriptomic profiling, candidate genes encoding isoflavone reductase, nitrate reductase, nitrate transporter and transcriptional factor MYB were identified. The differentially expressed genes (DEGs) involved the growth of lateral root, Pi transport within cells as well as from roots to shoots contributed to the differences between low-P tolerant line L138 and low-P sensitive lines L73 in their ability of P acquisition and utilization.

CONCLUSIONS

The plasticity of root system is an important trait for barley to tolerate low-P stress. The low-P tolerance in the elite DH line derived from a cross of Tibetan wild barley and cultivated barley is characterized by enhanced growth of lateral root and Pi recycling within plants under low-P stress.

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

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

Metabolite profiling and gene expression of Na/K transporter analyses reveal mechanisms of the difference in salt tolerance between barley and rice

Barley (Hordeum vulgare) and rice (Oryza sativa) differ greatly in their salt tolerance, although both species belong to the Poaceae family. To understand the mechanisms in the difference of salt tolerance between the two species, the responses of ionome, metabolome and gene expression of Na and K transporters to the different salt treatments were analyzed using 4 barley and 4 rice genotypes differing in salt tolerance. In comparison with 4 rice genotypes, four barley genotypes showed better plant growth, lower shoot Na concentration and higher K concentration at the 9 day after salt treatments. There was a dramatic difference in absolute expression levels of SOS, HKT and NHX family genes between barley and rice, which might account for their difference in Na/K homeostasis and salt tolerance. Moreover, rice leaves accumulated excess Na under salt treatments, which caused serious damages to physiological metabolisms based on metabolomic analysis, but barley leaves had lower Na concentration and small changes in the most metabolites. These results provide useful insights into the molecular mechanism in the difference of salt tolerance between rice and barley.