Alfalfa MsCBL4 enhances calcium metabolism but not sodium transport in transgenic tobacco under salt and saline-alkali stress

Shifts in Microbial Community Structure and Co-occurrence Network along a Wide Soil Salinity Gradient

The response of microbiomes to salinity has been clarified in different geographic scales or ecosystems. However, how soil microbial community structure and interaction respond to salinity across wide salinity range and climatic region is still unclearly resolved. To address this issue, we examined the microbial community's composition in saline soils from two climatic regions (coastal wetland and arid desert). Our research confirms that soil salinity had a negative effect on soil nutrient content. Salinity decreased the relative abundance of bacteria, but increased archaea abundance, leading to the shifts from bacteria dominant community to archaea dominant community. Low-water medium-salinity soil (LWMS) had the most complex archaeal community network, whereas for bacteria, the most complex bacterial community network was observed in low-water high-salinity soils (LWHS). Key microbial taxa differed in three salinity gradients. Salinity, soil water content, pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors for the composition of archaeal and bacterial community. Salinity directly affected archaeal community, but indirectly influenced bacteria community through SOC; pH affected archaeal community indirectly through TN, but directly affected bacterial community. Our study suggests that soil salinity dramatically influences diversity, composition, and interactions within the microbial community.

Salinity affects microbial function genes related to nutrient cycling in arid regions

Introduction

Salinization damages soil system health and influences microbial communities structure and function. The response of microbial functions involved in the nutrient cycle to soil salinization is a valuable scientific question. However, our knowledge of the microbial metabolism functions in salinized soil and their response to salinity in arid desert environments is inadequate.

Methods

Here, we applied metagenomics technology to investigate the response of microbial carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling and the key genes to salinity, and discuss the effects of edaphic variables on microbial functions.

Results

We found that carbon fixation dominated the carbon cycle. Nitrogen fixation, denitrification, assimilatory nitrate reduction (ANRA), and nitrogen degradation were commonly identified as the most abundant processes in the nitrogen cycle. Organic phosphorus dissolution and phosphorus absorption/transport were the most enriched P metabolic functions, while sulfur metabolism was dominated by assimilatory sulfate reduction (ASR), organic sulfur transformation, and linkages between inorganic and organic sulfur transformation. Increasing salinity inhibited carbon degradation, nitrogen fixation, nitrogen degradation, anammox, ANRA, phosphorus absorption and transport, and the majority of processes in sulfur metabolism. However, some of the metabolic pathway and key genes showed a positive response to salinization, such as carbon fixation (facA, pccA, korAB), denitrification (narG, nirK, norBC, nosZ), ANRA (nasA, nirA), and organic phosphorus dissolution processes (pstABCS, phnCD, ugpAB). High salinity reduced the network complexity in the soil communities. Even so, the saline microbial community presented highly cooperative interactions. The soil water content had significantly correlations with C metabolic genes. The SOC, N, and P contents were significantly correlated with C, N, P, and S network complexity and functional genes. AP, NH4+, and NO3- directly promote carbon fixation, denitrification, nitrogen degradation, organic P solubilization and mineralization, P uptake and transport, ASR, and organic sulfur transformation processes.

Conclusion

Soil salinity in arid region inhibited multiple metabolic functions, but prompted the function of carbon fixation, denitrification, ANRA, and organic phosphorus dissolution. Soil salinity was the most important factor driving microbial functions, and nutrient availability also played important roles in regulating nutrient cycling.

MsSPL12 is a positive regulator in alfalfa (Medicago sativa L.) salt tolerance

KEY MESSAGE

Over expression of MsSPL12 improved alfalfa salt tolerance by reducing Na+ accumulation and increasing antioxidant enzyme activity and regulating down-stream gene expression. Improvement of salt tolerance is one of the major goals in alfalfa breeding. Here, we demonstrated that MsSPL12, an alfalfa transcription factor gene highly expressed in the stem cells, plays a positive role in alfalfa salt tolerance. MsSPL12 is localized in the nucleus and shows transcriptional activity in the presence of its C-terminus. To investigate MsSPL12 function in plant response to salt stress, we generated transgenic plants overexpressing either MsSPL12 or a chimeric MsSPL12-SRDX gene that represses the function of MsSPL12 by using the Chimeric REpressor gene-Silencing Technology (CRES-T), and observed that overexpression of MsSPL12 increased the salt tolerance of alfalfa transgenic plants associated with an increase in K+/Na+ ratio and relative water content (RWC) under salt stress treatment, but a reduction in electrolyte leakage (EL), reactive oxygen species (ROS), malondialdehyde (MDA), and proline (Pro) compared to wild type (WT) plants. However, transgenic plants overexpressing MsSPL12-SRDX showed an inhibited plant growth and a reduced salt tolerance. RNA-sequencing and quantitative real-time PCR analyses revealed that MsSPL12 affected the expression of plant abiotic resistance-related genes in multiple physiological pathways. The potential MsSPL12-mediated regulatory pathways based on the differentially expressed genes between the MsSPL12 overexpression transgenics and WT controls were predicted. In summary, our study proves that MsSPL12 is a positive regulator in alfalfa salt tolerance and can be used as a new candidate for manipulation to develop forage crops with enhanced salt tolerance.

PvARL1 Increases Biomass Yield and Enhances Alkaline Tolerance in Switchgrass (Panicum virgatum L.)

Switchgrass is an important bioenergy crop valued for its biomass yield and abiotic tolerance. Alkali stress is a major abiotic stress that significantly impedes plant growth and yield due to high salinity and pH; however, the response mechanism of switchgrass to alkali stress remains limited. Here, we characterized PvARL1, an ARF-like gene, which was up-regulated in both the shoot and root tissues under alkali stress conditions. Overexpression of PvARL1 not only improved alkali tolerance but also promoted biomass yield with more tiller and higher plant height in switchgrass. Moreover, PvARL1 overexpression lines displayed higher capacities in the maintenance of water content and photosynthetic stability compared with the controls under alkali treatments. A significant reduction in the ratio of electrolyte leakage, MDA content, and reactive oxygen species (ROS) showed that PvARL1 plays a positive role in protecting cell membrane integrity. In addition, PvARL1 also negatively affected the K+ efflux or uptake in roots to alleviate ion toxicity under alkali treatments. Overall, our results suggest that PvARL1 functions as a positive regulator in plant growth as well as in the plant response to alkali stress, which could be used to improve switchgrass biomass yield and alkali tolerance genetically.

Ion Changes and Signaling under Salt Stress in Wheat and Other Important Crops

High concentrations of sodium (Na+), chloride (Cl-), calcium (Ca2+), and sulphate (SO42-) are frequently found in saline soils. Crop plants cannot successfully develop and produce because salt stress impairs the uptake of Ca2+, potassium (K+), and water into plant cells. Different intracellular and extracellular ionic concentrations change with salinity, including those of Ca2+, K+, and protons. These cations serve as stress signaling molecules in addition to being essential for ionic homeostasis and nutrition. Maintaining an appropriate K+:Na+ ratio is one crucial plant mechanism for salt tolerance, which is a complicated trait. Another important mechanism is the ability for fast extrusion of Na+ from the cytosol. Ca2+ is established as a ubiquitous secondary messenger, which transmits various stress signals into metabolic alterations that cause adaptive responses. When plants are under stress, the cytosolic-free Ca2+ concentration can rise to 10 times or more from its resting level of 50-100 nanomolar. Reactive oxygen species (ROS) are linked to the Ca2+ alterations and are produced by stress. Depending on the type, frequency, and intensity of the stress, the cytosolic Ca2+ signals oscillate, are transient, or persist for a longer period and exhibit specific "signatures". Both the influx and efflux of Ca2+ affect the length and amplitude of the signal. According to several reports, under stress Ca2+ alterations can occur not only in the cytoplasm of the cell but also in the cell walls, nucleus, and other cell organelles and the Ca2+ waves propagate through the whole plant. Here, we will focus on how wheat and other important crops absorb Na+, K+, and Cl- when plants are under salt stress, as well as how Ca2+, K+, and pH cause intracellular signaling and homeostasis. Similar mechanisms in the model plant Arabidopsis will also be considered. Knowledge of these processes is important for understanding how plants react to salinity stress and for the development of tolerant crops.

MsWRKY33 increases alfalfa (Medicago sativa L.) salt stress tolerance through altering the ROS scavenger via activating MsERF5 transcription

Alfalfa (Medicago sativa L.) is considered to be the most important forage crop on a global scale. Nevertheless, soil salinity significantly decreases productivity, seriously threatening food security worldwide. One viable strategy is to explore salt stress-responsive factors and elucidate their underlying molecular mechanism, and utilize them in further alfalfa breeding. In the present study, we designated MsWRKY33 as a representative salt stress-responsive factor preferentially expressed in alfalfa roots and leaves. Subsequently, it was demonstrated that MsWRKY33 was localized in the cell nucleus, and functioned as a transcriptional activator of the W-box element. Transgenic alfalfa overexpressing MsWRKY33 displayed enhanced salt stress tolerance and antioxidant activities with no significant difference in other agronomic traits. Transcriptome profiling of MsWRKY33 transgenic alfalfa under control and salt treatment unveiled significantly altered expression of reactive oxygen species (ROS) scavenger genes in transgenic alfalfa. Subsequent examination revealed that MsWRKY33 binded to the promoter of MsERF5, activating its expression and consequently fine-tuning the ROS-scavenging enzyme activity. Furthermore, MsWRKY33 interacted with the functional fragment of MsCaMBP25, which participates in Ca2+ signaling transduction. Collectively, this research offers new insight into the molecular mechanism of alfalfa salt stress tolerance and highlights the potential utility of MsWRKY33 in alfalfa breeding.

Genome-wide identification of the myo-inositol oxygenase gene family in alfalfa (Medicago sativa L.) and expression analysis under abiotic stress

Myo-inositol oxygenase (MIOX), a pivotal enzyme in the myo-inositol oxygenation pathway, catalyzes the cleavage of myo-inositol to UDP-glucuronic acid and plays a major role in plant adaptation to abiotic stress factors. However, studies pertaining to the MIOX gene family in alfalfa (Medicago sativa L.) are lacking. Therefore, this study characterized ten MsMIOX genes in the alfalfa genome. These genes were divisible into two classes distributed over three chromosomes and produced 12 pairs of fragment repeats and one pair of tandem repeats. Physicochemical properties, subcellular location, protein structure, conserved motifs, and gene structure pertinent to these MsMIOX genes were analyzed. Construction of a phylogenetic tree revealed that similar gene structures and conserved motifs were present in the same MsMIOX groups. Analysis of cis-acting elements revealed the presence of stress- and hormone-induced expression elements in the promoter regions of the MsMIOX genes. qRT-PCR analysis revealed that MsMIOX genes could be induced by various abiotic stress factors, such as salt, saline-alkali, drought, and cold. Under such conditions, MIOX activity in alfalfa was significantly increased. Heterologous MsMIOX2 expression in yeast enhanced salt, saline-alkali, drought, and cold tolerance. Overexpression of MsMIOX2 in the hairy roots of alfalfa decreased O₂^- and H₂O₂ content and enhanced the abiotic stress tolerance. This study offers comprehensive perspectives on the functional features of the MsMIOX family and provides a candidate gene for improving the abiotic stress tolerance of alfalfa.

Advances and future research in ecological stoichiometry under saline-alkali stress

Saline-alkali stress is a serious abiotic factor which negatively impacts agricultural production and the ecological environment. Thus, improving the development of saline-alkali soil and reducing the effects of saline-alkali stress is a key issue for sustainable agricultural development and environmental protection. As such, it is unsurprising that researchers have lately focused on how to improve saline-alkali soil, increase the agricultural yield of saline-alkali land, and promote the adaptive growth of plants in saline-alkali soil. This paper reviews the latest research concerning nutrient content changes in saline-alkali soil, along with the associated changes in key nutrients in plants, to summarize which methods are most effective for improving the plant growth under saline-alkali stress. Finally, the prospects for alleviating saline-alkali stress and improving saline-alkali soil are put forward as a theoretical foundation for the stabilization of plant growth in saline-alkali soil, expansion of arable land area, crop yield improvement, and effective environmental protection.

IAA Plays an Important Role in Alkaline Stress Tolerance by Modulating Root Development and ROS Detoxifying Systems in Rice Plants

Auxin regulates plant growth and development, as well as helps plants to survive abiotic stresses, but the effects of auxin on the growth of alkaline-stressed rice and the underlying molecular and physiological mechanisms remain unknown. Through exogenous application of IAA/TIBA, this study explored the physiological and molecular mechanisms of alkaline stress tolerance enhancement using two rice genotypes. Alkaline stress was observed to damage the plant growth, while exogenous application of IAA mitigates the alkaline-stress-induce inhibition of plant growth. After application of exogenous IAA to alkaline-stressed rice, dry shoot biomass, foliar chlorophyll content, photosynthetic rate in the two rice genotypes increased by 12.6-15.6%, 11.7-40.3%, 51.4-106.6%, respectively. The adventitious root number, root surface area, total root length and dry root biomass in the two rice genotypes increased by 29.3-33.3%, 26.4-27.2%, 42.5-35.5% and 12.8-33.1%, respectively. The accumulation of H₂O₂, MAD were significantly decreased with the application of IAA. The activities of CAT, POD, and SOD in rice plants were significantly increased by exogenous application of IAA. The expression levels of genes controlling IAA biosynthesis and transport were significantly increased, while there were no significant effects on the gene expression that controlled IAA catabolism. These results showed that exogenous application of IAA could mitigate the alkaline-stress-induced inhibition of plant growth by regulating the reactive oxygen species scavenging system, root development and expression of gene involved in IAA biosynthesis, transport and catabolism. These results provide a new direction and empirical basis for improving crop alkaline tolerance with exogenous application of IAA.

Irrigation with Magnetized Water Alleviates the Harmful Effect of Saline-Alkaline Stress on Rice Seedlings

Saline–alkaline stress suppresses rice growth and threatens crop production. Despite substantial research on rice’s tolerance to saline–alkaline stress, fewer studies have examined the impact of magnetic water treatments on saline–alkaline-stressed rice plants. We explored the physiological and molecular mechanisms involved in saline–alkaline stress tolerance enhancement via irrigation with magnetized water using Nipponbare. The growth of Nipponbare plants was inhibited by saline–alkaline stress, but this inhibition was alleviated by irrigating the plants with magnetized water, as evidenced by greater plant height, biomass, chlorophyll content, photosynthetic rates, and root system in plants irrigated with magnetized water compared to those irrigated with non-magnetized water. Plants that were irrigated with magnetized water were able to acquire more total nitrogen. In addition, we proved that rice seedlings irrigated with magnetized water had a greater root NO₃⁻-nitrogen concentration and root NH₄⁺-nitrogen concentration than plants irrigated with non-magnetized water. These findings suggest that treatment with magnetized water could increase nitrogen uptake. To test this hypothesis, we analyzed the expression levels of genes involved in nitrogen acquisition. The expression levels of OsNRT1;1, OsNRT1;2, OsNRT2;1, OsAMT1;2, OsAMT2;1, OsAMT2;2, OsAMT2;3, OsAMT3;1, OsAMT3;2, and OsAMT3;3 were higher in plants exposed to magnetized water medium compared to those exposed to non-magnetized water media. We further demonstrated that treatment with magnetized water increases available nitrogen, NO₃⁻-nitrogen content, and NH₄⁺-nitrogen content in soil under saline–alkaline stress. Our results revealed that the increased resistance of rice seedlings to saline–alkaline stress may be attributable to a very effective nitrogen acquisition system enhanced by magnetized water.

Identification of Alkaline Salt Tolerance Genes in Brassica napus L. by Transcriptome Analysis

Soil salt alkalization is one major abiotic factor reducing the productivity of crops, including rapeseed, an indispensable oil crop and vegetable. The mechanism studies of alkali salt tolerance can help breed highly resistant varieties. In the current study, rapeseed (B. napus) line 2205 exhibited more tolerance to alkaline salt than line 1423 did. In line 2205, the lesser plasma membrane damage index, the accumulated osmotic solute, and higher antioxidant enzyme activities contributed to alkaline tolerance. A more integrated mesophyll-cell structure was revealed under alkali salt stress by ultrastructure observation in line 2205, which also implied a lesser injury. Transcriptome analysis showed that more genes responded to alkaline salt in line 2205. The expression of specific-response genes in line 1423 was lower than in line 2205. However, most of the specific-response genes in line 2205 had higher expression, which was mainly enriched in carbohydrate metabolism, photosynthetic processes, ROS regulating, and response to salt stress. It can be seen that the tolerance to alkaline salt is attributed to the high expression of some genes in these pathways. Based on these, twelve cross-differentially expressed genes were proposed as candidates. They provide clues for further analysis of the resistance mechanism of rapeseed.

Comparative Physiological and Transcriptome Profiles Uncover Salt Tolerance Mechanisms in Alfalfa

Salinity is a major limiting factor that affects crop production. Understanding of the mechanisms of plant salt tolerance is critical for improving crop yield on saline land. Alfalfa (Medicago sativa L.) is the most important forage crop, while its salt tolerance mechanisms are largely unknown. The physiological and transcriptomic responses in two contrasting salt tolerant cultivars to salinity stress were investigated in the present study. "Magnum Salt" showed higher salt tolerance than "Adrenalin," with higher relative germination rate, survival rate, biomass and K⁺/Na⁺ ratio after salt treatment. Activities of antioxidant enzymes SOD, CAT and GR, and proline concentrations were upregulated to higher levels in roots and shoots in Magnum Salt than in Adrenalin after salinity stress, except for no difference in GR activity in shoots, and lower levels of O₂ ^⋅- and H₂O₂ were accumulated in leaves. It was interesting to find that salinity caused a decrease in total unsaturated fatty acid in Adrenalin other than Magnum Salt, C18:2 was increased significantly after salinity in Magnum Salt, while it was unaltered in Adrenalin. High quality RNA sequencing (RNA-seq) data was obtained from samples of Magnum Salt and Adrenalin at different time points (0, 2, and 26 h). Generally, "phagosome," "TCA cycle" and "oxidative phosphorylation" pathways were inhibited by salinity stress. Upregulated DEGs in Magnum Salt were specifically enriched in "fatty acid metabolism," "MAPK signaling" and "hormone signal transduction" pathways. The DEGs involved in ionic homeostasis, reactive oxygen species (ROS) scavenging and fatty acid metabolism could partially explain the difference in salt tolerance between two cultivars. It is suggested that salt tolerance in alfalfa is associated with regulation of ionic homeostasis, antioxidative enzymes and fatty acid metabolism at both transcriptional and physiological level.

Metabolic differences of two constructive species in saline-alkali grassland in China

BACKGROUND

Salinization of soil is an urgent problem that restricts agroforestry production and environmental protection. Substantial accumulation of metal ions or highly alkaline soil alters plant metabolites and may even cause plant death. To explore the differences in the response strategies between Suaeda salsa (S. salsa) and Puccinellia tenuiflora (P. tenuiflora), two main constructive species that survive in saline-alkali soil, their metabolic differences were characterized.

RESULT

Metabolomics was conducted to study the role of metabolic differences between S. salsa and P. tenuiflora under saline-alkali stress. A total of 68 significantly different metabolites were identified by GC-MS, including 9 sugars, 13 amino acids, 8 alcohols, and 34 acids. A more detailed analysis indicated that P. tenuiflora utilizes sugars more effectively and may be saline-alkali tolerant via sugar consumption, while S. salsa utilizes mainly amino acids, alcohols, and acids to resist saline-alkali stress. Measurement of phenolic compounds showed that more C6C3C6-compounds accumulated in P. tenuiflora, while more C6C1-compounds, phenolic compounds that can be used as signalling molecules to defend against stress, accumulated in S. salsa.

CONCLUSIONS

Our observations suggest that S. salsa resists the toxicity of saline-alkali stress using aboveground organs and that P. tenuiflora eliminates this toxicity via roots. S. salsa has a stronger habitat transformation ability and can provide better habitat for other plants.

Potassium signaling in plant abiotic responses: Crosstalk with calcium and reactive oxygen species/reactive nitrogen species

Potassium ion (K⁺) has been regarded as an essential signaling in plant growth and development. K⁺ transporters and channels at transcription and protein levels have been made great progress. K⁺ can enhance plant abiotic stress resistance. Meanwhile, it is now clear that calcium (Ca²⁺), reactive oxygen species (ROS), and reactive nitrogen species (RNS) act as signaling molecules in plants. They regulate plant growth and development and mediate K⁺ transport. However, the interaction of K⁺ with these signaling molecules remains unclear. K⁺ may crosstalk with Ca²⁺ and ROS/RNS in abiotic stress responses in plants. Also, there are interactions among K⁺, Ca²⁺, and ROS/RNS signaling pathways in plant growth, development, and abiotic stress responses. They regulate ion homeostasis, antioxidant system, and stress resistance-related gene expression in plants. Future work needs to focus on the deeper understanding of molecular mechanism of crosstalk among K⁺, Ca²⁺, and ROS/RNS under abiotic stress.

Proteomic analysis reveals responsive mechanisms for saline-alkali stress in alfalfa

Saline-alkali stress is a major abiotic stress that limits plant growth, yield, and geographical distribution. Alfalfa is a perennial legume with the largest planting area in the world because of its high protein content, good palatability, and long utilization life. However, saline-alkali stress seriously affects alfalfa yield and quality. To better understand the saline-alkali stress response mechanisms of alfalfa, an isobaric tags proteomics method was used to compare and analyse alfalfa under saline-alkali stress for 0, 1, and 7 days, and 126 (1 vs. 0 days) and 1869 (7 vs. 0 days) differentially abundant proteins (DAPs) were found. Through integrative analysis with differentially expressed genes (DEGs), we found correlated DEGs-DAPs of RNA and protein with similar expression trends at the mRNA and protein levels; these were mainly involved in ABA and Ca²⁺ signal pathways, regulation of photosynthesis, ROS scavenging, secondary metabolism, and transcription factors (TFs) related to saline-alkali stress. Some genes not exhibiting such trends may have been regulated post-transcriptionally. Furthermore, through transgenic experiments, MsFTL was found to significantly improve the saline-alkali tolerance of plants. Overall, our findings provide important clues for understanding the molecular mechanisms underlying the response of alfalfa to saline-alkali stress.

Ionomic and Metabolomic Analyses Reveal Different Response Mechanisms to Saline-Alkali Stress Between Suaeda salsa Community and Puccinellia tenuiflora Community

Soil salinization imposes severe stress to plants, inhibits plant growth, and severely limits agricultural productivity and land utilization. The response of a single plant to saline-alkali stress has been well investigated. However, the plant community that usually works as a group to defend against saline-alkali stress was neglected. To determine the functions of plant community, in our current work, Suaeda salsa (S. salsa) community and Puccinellia tenuiflora (P. tenuiflora) community, two communities that are widely distributed in Hulun Buir Grassland in Northeastern China, were selected as research objects. Ionomic and metabolomic were applied to compare the differences between S. salsa community and P. tenuiflora community from the aspects of ion transport and phenolic compound accumulation, respectively. Ionomic studies demonstrated that many macroelements, including potassium (K) and calcium (Ca), were highly accumulated in S. salsa community whereas microelement manganese (Mn) was highly accumulated in P. tenuiflora community. In S. salsa community, transportation of K to aboveground parts of plants helps to maintain high K+ and low Na+ concentrations whereas the accumulation of Ca triggers the salt overly sensitive (SOS)-Na+ system to efflux Na+. In P. tenuiflora community, enrichment of Mn in roots elevates the level of Mn-superoxide dismutase (SOD) and increases the resistance to saline-alkali stress. Metabolomic studies revealed the high levels of C6C1-compounds and C6C3C6-compounds in S. salsa community and also the high levels of C6C3-compounds in P. tenuiflora community. C6C1-compounds function as signaling molecules to defend against stress and may stimulate the accumulation of C6C3C6-compounds. C6C3-compounds contribute to the elimination of free radicals and the maintenance of cell morphology. Collectively, our findings determine the abundance of phenolic compounds and various elements in S. salsa community and P. tenuiflora community in Hulun Buir Grassland and we explored different responses of S. salsa community and P. tenuiflora community to cope with saline-alkali stress. Understanding of plant response strategies from the perspective of community teamwork may provide a feasible and novel way to transform salinization land.

Ectopic expression of finger millet calmodulin confers drought and salinity tolerance in Arabidopsis thaliana

Overexpression of finger millet calmodulin imparts drought and salt tolerance in plants. Drought and salinity are major environmental stresses which affect crop productivity and therefore are major hindrance in feeding growing population world-wide. Calcium (Ca²⁺) signaling plays a crucial role during the plant's response to these stress stimuli. Calmodulin (CaM), a crucial Ca²⁺sensor, is involved in transducing the signal downstream in various physiological, developmental and stress responses by modulating a plethora of target proteins. The role of CaM has been well established in the model plant Arabidopsis thaliana for regulating various developmental processes, stress signaling and ion transport. In the current study, we investigate the CaM of Eleusine coracana (common name finger millet, known especially for its drought tolerance and superior Ca²⁺ content). In-silico analysis showed that Eleusine CaM (EcCaM) has greater similarity to rice CaM as compared to Arabidopsis CaM due to the presence of highly conserved four EF-hand domains. To decipher the in-planta function of EcCaM, we have adopted the gain-of-function approach by generating the 35S::EcCaM over-expression transgenic in Arabidopsis. Overexpression of EcCaM in Arabidopsis makes the plant tolerant to polyethylene glycol (PEG) induced drought and salt stress (NaCl) as demonstrated by post-germination based phenotypic assay, ion leakage, MDA and proline estimation, ROS detection under stressed and normal conditions. Moreover, EcCaM overexpression leads to hypersensitivity toward exogenously applied ABA at the seed germination stage. These findings reveal that EcCaM mediates tolerance to drought and salinity stress. Also, our results indicate that EcCaM is involved in modulating ABA signaling. Summarizing our results, we report for the first time that EcCaM is involved in modulating plants response to stress and this information can be used for the generation of future-ready crops that can tolerate a wide range of abiotic stresses.

De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

Background

Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.

Results

Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.

Conclusions

Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07368-w.

Genome-Wide Association Analysis Coupled With Transcriptome Analysis Reveals Candidate Genes Related to Salt Stress in Alfalfa (Medicago sativa L.)

Salt stress is the main abiotic factor affecting alfalfa yield and quality. However, knowledge of the genetic basis of the salt stress response in alfalfa is still limited. Here, a genome-wide association study (GWAS) involving 875,023 single-nucleotide polymorphisms (SNPs) was conducted on 220 alfalfa varieties under both normal and salt-stress conditions. Phenotypic analysis showed that breeding status and geographical origin play important roles in the alfalfa salt stress response. For germination ability under salt stress, a total of 15 significant SNPs explaining 9%-14% of the phenotypic variation were identified. For tolerance to salt stress in the seedling stage, a total of 18 significant SNPs explaining 12%-23% of the phenotypic variation were identified. Transcriptome analysis revealed 2,097 and 812 differentially expressed genes (DEGs) that were upregulated and 2,445 and 928 DEGs that were downregulated in the leaves and roots, respectively, under salt stress. Among these DEGs, many encoding transcription factors (TFs) were found, including MYB-, CBF-, NAC-, and bZIP-encoding genes. Combining the results of our GWAS analysis and transcriptome analysis, we identified a total of eight candidate genes (five candidate genes for tolerance to salt stress and three candidate genes for germination ability under salt stress). Two SNPs located within the upstream region of MsAUX28, which encodes an auxin response protein, were significantly associated with tolerance to salt stress. The two significant SNPs within the upstream region of MsAUX28 existed as three different haplotypes in this panel. Hap 1 (G/G, A/A) was under selection in the alfalfa domestication and improvement process.

Comparative transcriptome analysis of two rice genotypes differing in their tolerance to saline-alkaline stress

Saline-alkaline stress is an abiotic stress that suppresses rice plant growth and reduces yield. However, few studies have investigated the mechanism by which rice plants respond to saline-alkaline stress at a global transcriptional level. Dongdao-4 and Jigeng-88, which differ in their tolerance to saline-alkaline stress, were used to explore gene expression differences under saline-alkaline stress by RNA-seq technology. In seedlings of Dongdao-4 and Jigeng-88, 3523 and 4066 genes with differential levels of expression were detected, respectively. A total of 799 genes were upregulated in the shoots of both Dongdao-4 and Jigeng-88, while 411 genes were upregulated in the roots of both genotypes. Among the downregulated genes in Dongdao-4 and Jigeng-88, a total of 453 and 372 genes were found in shoots and roots, respectively. Gene ontology (GO) analysis showed that upregulated genes were enriched in several GO terms such as response to stress, response to jasmonic acid, organic acid metabolic process, nicotianamine biosynthetic process, and iron homeostasis. The downregulated genes were enriched in several GO terms, such as photosynthesis and response to reactive oxygen species. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that Dongdao-4 seedlings were specifically enriched in the biosynthesis of secondary metabolites such as diterpenoids and phenylpropanoids. The upregulated genes that were involved in secondary metabolite biosynthesis, amino acid biosynthesis, betalain biosynthesis, organic acid metabolic process, and iron homeostasis pathways may be central to saline-alkaline tolerance in both rice genotypes. In contrast, the genes involved in the diterpenoid and phenylpropanoid biosynthesis pathways may contribute to the greater tolerance to saline-alkaline stress in Dongdao-4 seedlings than in Jigeng-88. These results suggest that Dongdao-4 was equipped with a more efficient mechanism involved in multiple biological processes to adapt to saline-alkaline stress.