De novo transcriptome sequencing and analysis of salt-, alkali-, and drought-responsive genes in Sophora alopecuroides

Integration analysis of miRNA-mRNA pairs between two contrasting genotypes reveals the molecular mechanism of jujube (Ziziphus jujuba Mill.) response to high-temperature stress

With global warming, high temperature (HT) has become one of the most common abiotic stresses resulting in significant crop yield losses, especially for jujube (Ziziphus jujuba Mill.), an important temperate economic crop cultivated worldwide. This study aims to explore the coping mechanism of jujube to HT stress at the transcriptional and post-transcriptional levels, including identifying differentially expressed miRNAs and mRNAs as well as elucidating the critical pathways involved. High-throughput sequencing analyses of miRNA and mRNA were performed on jujube leaves, which were collected from "Fucumi" (heat-tolerant) and "Junzao" (heat-sensitive) cultivars subjected to HT stress (42 °C) for 0, 1, 3, 5, and 7 days, respectively. The results showed that 45 known miRNAs, 482 novel miRNAs, and 13,884 differentially expressed mRNAs (DEMs) were identified. Among them, integrated analysis of miRNA target genes prediction and mRNA-seq obtained 1306 differentially expressed miRNAs-mRNAs pairs, including 484, 769, and 865 DEMIs-DEMs pairs discovered in "Fucuimi", "Junzao" and two genotypes comparative groups, respectively. Furthermore, functional enrichment analysis of 1306 DEMs revealed that plant-pathogen interaction, starch and sucrose metabolism, spliceosome, and plant hormone signal transduction were crucial pathways in jujube leaves response to HT stress. The constructed miRNA-mRNA network, composed of 20 DEMIs and 33 DEMs, displayed significant differently expressions between these two genotypes. This study further proved the regulatory role of miRNAs in the response to HT stress in plants and will provide a theoretical foundation for the innovation and cultivation of heat-tolerant varieties.

Genome-Wide Identification of CHYR Gene Family in Sophora alopecuroides and Functional Analysis of SaCHYR4 in Response to Abiotic Stress

Sophora alopecuroides has important uses in medicine, wind breaking, and sand fixation. The CHY-zinc-finger and RING-finger (CHYR) proteins are crucial for plant growth, development, and environmental adaptation; however, genetic data regarding the CHYR family remain scarce. We aimed to investigate the CHYR gene family in S. alopecuroides and its response to abiotic stress, and identified 18 new SaCHYR genes from S. alopecuroides whole-genome data, categorized into 3 subclasses through a phylogenetic analysis. Gene structure, protein domains, and conserved motifs analyses revealed an exon-intron structure and conserved domain similarities. A chromosome localization analysis showed distribution across 12 chromosomes. A promoter analysis revealed abiotic stress-, light-, and hormone-responsive elements. An RNA-sequencing expression pattern analysis revealed positive responses of SaCHYR genes to salt, alkali, and drought stress. SaCHYR4 overexpression considerably enhanced alkali and drought tolerance in Arabidopsis thaliana. These findings shed light on SaCHYR's function and the resistance mechanisms of S. alopecuroides, presenting new genetic resources for crop resistance breeding.

Inroads into saline-alkaline stress response in plants: unravelling morphological, physiological, biochemical, and molecular mechanisms

MAIN CONCLUSION

This article discusses the complex network of ion transporters, genes, microRNAs, and transcription factors that regulate crop tolerance to saline-alkaline stress. The framework aids scientists produce stress-tolerant crops for smart agriculture. Salinity and alkalinity are frequently coexisting abiotic limitations that have emerged as archetypal mediators of low yield in many semi-arid and arid regions throughout the world. Saline-alkaline stress, which occurs in an environment with high concentrations of salts and a high pH, negatively impacts plant metabolism to a greater extent than either stress alone. Of late, saline stress has been the focus of the majority of investigations, and saline-alkaline mixed studies are largely lacking. Therefore, a thorough understanding and integration of how plants and crops rewire metabolic pathways to repair damage caused by saline-alkaline stress is of particular interest. This review discusses the multitude of resistance mechanisms that plants develop to cope with saline-alkaline stress, including morphological and physiological adaptations as well as molecular regulation. We examine the role of various ion transporters, transcription factors (TFs), differentially expressed genes (DEGs), microRNAs (miRNAs), or quantitative trait loci (QTLs) activated under saline-alkaline stress in achieving opportunistic modes of growth, development, and survival. The review provides a background for understanding the transport of micronutrients, specifically iron (Fe), in conditions of iron deficiency produced by high pH. Additionally, it discusses the role of calcium in enhancing stress tolerance. The review highlights that to encourage biomolecular architects to reconsider molecular responses as auxiliary for developing tolerant crops and raising crop production, it is essential to (a) close the major gaps in our understanding of saline-alkaline resistance genes, (b) identify and take into account crop-specific responses, and (c) target stress-tolerant genes to specific crops.

Transcriptome-Based Identification of the SaR2R3-MYB Gene Family in Sophora alopecuroides and Function Analysis of SaR2R3-MYB15 in Salt Stress Tolerance

As one of the most prominent gene families, R2R3-MYB transcription factors significantly regulate biochemical and physiological processes under salt stress. However, in Sophora alopecuroides, a perennial herb known for its exceptional saline alkali resistance, the comprehensive identification and characterization of SaR2R3-MYB genes and their potential functions in response to salt stress have yet to be determined. We investigated the expression profiles and biological functions of SaR2R3-MYB transcription factors in response to salt stress, utilizing a transcriptome-wide mining method. Our analysis identified 28 SaR2R3-MYB transcription factors, all sharing a highly conserved R2R3 domain, which were further divided into 28 subgroups through phylogenetic analysis. Some SaR2R3-MYB transcription factors showed induction under salt stress, with SaR2R3-MYB15 emerging as a potential regulator based on analysis of the protein-protein interaction network. Validation revealed the transcriptional activity and nuclear localization of SaR2R3-MYB15. Remarkably, overexpression of SaR2R3-MYB15 in transgenic plants could increase the activity of antioxidant enzymes and the accumulation of proline but decrease the content of malondialdehyde (MDA), compared with wild-type plants. Moreover, several salt stress-related genes showed higher expression levels in transgenic plants, implying their potential to enhance salt tolerance. Our findings shed light on the role of SaR2R3-MYB genes in salt tolerance in S. alopecuroides.

Analysis of Genes Associated with Feeding Preference and Detoxification in Various Developmental Stages of Aglais urticae

Herbivorous insects and host plants have developed a close and complex relationship over a long period of co-evolution. Some plants provide nutrients for insects, but plants' secondary metabolites also influence their growth and development. Urtica cannabina roots and leaves are poisonous, yet Aglais urticae larvae feed on them, so we aimed to clarify the mechanism enabling this interaction. At present, studies on the detoxification mechanism of the A. urticae are rare. In our study, first, we used the A. urticae larval odor selection behavior bioassay and choice feeding preference assay to analyze the feeding preferences of A. urticae on its host plant, U. cannabina. Next, we used transcriptome sequencing to obtain the unigenes annotated and classified by various databases, such as KEGG and GO. In this study, we found that U. cannabina could attract A. urticae larvae to feed via scent, and the feeding preference assay confirmed that larvae preferred U. cannabina leaves over three other plants: Cirsium japonicum, Cannabis sativa, and Arctium lappa. The activity of detoxifying enzymes GST and CarE changed in larvae that had consumed U. cannabina. Furthermore, through transcriptomic sequencing analysis, 77,624 unigenes were assembled from raw reads. The numbers of differentially expressed genes were calculated using pairwise comparisons of all life stages; the expression of detoxification enzyme genes was substantially higher in larvae than in the pupal and adult stages. Finally, we identified and summarized 34 genes associated with detoxification enzymes, such as UDP-glucose 4-epimerase gene, 5 Glutathione S-transferase genes, 4 Carboxylesterase genes, 4 Cytochrome P450 genes, 10 ATP-binding cassette genes, 4 Superoxide dismutase, and Peroxidase. Moreover, we identified 28 genes associated with the development of A. urticae. The qRT-PCR results were nearly consistent with the transcriptomic data, showing an increased expression level of four genes in larvae. Taken together, this study examines the correlation between A. urticae and host plants U. cannabina, uncovering a pronounced preference for A. urticae larvae toward host plants. Consistent with RNA-seq, we investigated the mechanism of A. urticae's interaction with host plants and identified detoxification-related genes. The present study provides theoretical support for studying insect adaptation mechanisms and biological control.

Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2

Abiotic stresses are a significant constraint to plant production globally. Identifying stress-related genes can aid in the development of stress-tolerant elite genotypes and facilitate trait and crop manipulation. The primary aim of this study was to conduct whole transcriptome analyses of the salt-tolerant faba bean genotype, Hassawi-2, under different durations of salt stress (6 h, 12 h, 24 h, 48 h, and 72 h) at the early vegetative stage, to better understand the molecular basis of salt tolerance. After de novo assembly, a total of 140,308 unigenes were obtained. The up-regulated differentially expressed genes (DEGs) were 2380, 2863, 3057, 3484, and 4820 at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. Meanwhile, 1974, 3436, 2371, 3502, and 5958 genes were downregulated at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. These DEGs encoded various regulatory and functional proteins, including kinases, plant hormone proteins, transcriptional factors (TFs) basic helix-loop-helix (bHLH), Myeloblastosis (MYB), and (WRKY), heat shock proteins (HSPs), late embryogenesis abundant (LEA) proteins, dehydrin, antioxidant enzymes, and aquaporin proteins. This suggests that the faba bean genome possesses an abundance of salinity resistance genes, which trigger different adaptive mechanisms under salt stress. Some selected DEGs validated the RNA sequencing results, thus confirming similar gene expression levels. This study represents the first transcriptome analysis of faba bean leaves subjected to salinity stress offering valuable insights into the mechanisms governing salt tolerance in faba bean during the vegetative stage. This comprehensive investigation enhances our understanding of precise gene regulatory mechanisms and holds promise for the development of novel salt-tolerant faba bean salt-tolerant cultivars.

Transcriptome-Wide Analysis of Core Transcription Factors Associated with Defense Responses in Autotetraploid versus Diploid Rice under Saline Stress and Recovery

Saline stress is a major abiotic stress that inhibits plant growth and yields worldwide. The plant transcription factor (TF) family plays an important role in converting abiotic stress signals into gene expression changes. In this study, a transcriptome-based comparative analysis was performed to investigate the global gene expression of all the TFs in diploid and autotetraploid rice during the early stage of NaCl stress and recovery period. The phenotypic data indicated that the tetraploid rice exhibited a superior salt-tolerant ability compared to the diploid rice. A total of 55 TF families were co-expressed in the tetraploid and diploid rice, and the cumulative number of TF-expressed genes was relatively higher in the diploid rice than in the tetraploid rice at all time points. Unlike the diploid rice, the overall gene expression levels of the tetraploid rice were comparable to the control during recovery. The number of differentially expressed TFs (DE-TFs) in the tetraploid rice decreased after recovery, whereas it increased to a large extent in the diploid rice. GO and KEGG pathway enrichment analysis of the DE-TFs discovered the early switching of the ABA-activated signaling pathway and specific circadian rhythm in the tetraploid rice. Combining the PPI network and heatmap analysis, some core DE-TFs were found that may have potential roles to play in tetraploid salt tolerance. This study will pave the way for elucidating the complex network regulatory mechanisms of salt tolerance in tetraploid rice.

Salt stress responses and alleviation strategies in legumes: a review of the current knowledge

Salinity is one of the most significant environmental factors limiting legumes development and productivity. Salt stress disturbs all developmental stages of legumes and affects their hormonal regulation, photosynthesis and biological nitrogen fixation, causing nutritional imbalance, plant growth inhibition and yield losses. At the molecular level, salt stress exposure involves large number of factors that are implicated in stress perception, transduction, and regulation of salt responsive genes' expression through the intervention of transcription factors. Along with the complex gene network, epigenetic regulation mediated by non-coding RNAs, and DNA methylation events are also involved in legumes' response to salinity. Different alleviation strategies can increase salt tolerance in legume plants. The most promising ones are Plant Growth Promoting Rhizobia, Arbuscular Mycorrhizal Fungi, seed and plant's priming. Genetic manipulation offers an effective approach for improving salt tolerance. In this review, we present a detailed overview of the adverse effect of salt stress on legumes and their molecular responses. We also provide an overview of various ameliorative strategies that have been implemented to mitigate/overcome the harmful effects of salt stress on legumes.

Sand Burial, Rather than Salinity or Drought, Is the Main Stress That Limits the Germination Ability of Sophora alopecuroides L. Seed in the Desert Steppe of Yanchi, Ningxia, China

Global change and environmental pollution have reawakened ecologists to the great threat of multi-stress interactions to different growth stages of plants. Sophora alopecuroides L., a dune plant, has been widely studied for its medicinal components and strong salinity tolerance. S. alopecuroides seeds, obtained from the desert steppe of Yanchi, Ningxia, China, were used to analyze the effects of sand burial, salinity, drought, and their interactions on seed germination (germination percentage, germination energy, and germination index). The results showed that sand burial and salinity stress had significant effects on the seed germination ability of S. alopecuroides, and drought stress had no significant effect, but the interaction of the three stresses had a significant effect. Under different drought-stress treatments, the interaction of no sand burial and a certain degree of salinity stress significantly improved the germination ability of S. alopecuroides, and the overall intensity of the effects of the three stresses showed that sand burial > salinity > drought. Considering the germination percentage, germination energy, and germination index of S. alopecuroides under various stress interactions, the treatment of no sand burial × 1% soil saline-alkali content × 18-20% soil water content was adopted to maximize the germination ability of S. alopecuroides. In the desert steppe area of Yanchi, Ningxia, sand burial stress was still the most limiting factor for seed germination of S. alopecuroides, and soil saline-alkali content should be increased moderately, and soil moisture should be ensured to obtain the best germination ability.

Exogenous Selenium Improves Physio-Biochemical and Performance of Drought-Stressed Phaseolus vulgaris Seeded in Saline Soil

Water and salt stresses are among the most important global problems that limit the growth and production of several crops. The current study aims at the possibility of mitigating the effect of deficit irrigation of common bean plants growing in saline lands by foliar spraying with selenium via the assessment of growth, productivity, physiological, and biochemical measurements. In our study, two field-based trials were conducted in 2017 and 2018 to examine the influence of three selenium (Se) concentrations (0 (Se0), 25 (Se25), and 50 mg L−1 (Se50)) on common bean plants grown under full irrigation (I100 = 100% of the crop evapotranspiration; ETc) and deficit irrigation (I80 = 80% of ETc, and I60 = 60% of ETc). Bean plants exposed to water stress led to a notable reduction in growth, yield, water productivity (WP), water status, SPAD value, and chlorophyll a fluorescence features (Fv/Fm and PI). However, foliar spraying of selenium at 25 or 50 mg L−1 on stressed bean plants attenuated the harmful effects of water stress. The findings suggest that foliage application of 25 or 50 mg L−1 selenium to common bean plants grown under I80 resulted in a higher membrane stability index, relative water content, SPAD chlorophyll index, and better efficiency of photosystem II (Fv/Fm, and PI). Water deficit at 20% increased the WP by 17%; however, supplementation of 25 or 50 mg L−1 selenium mediated further increases in WP up to 26%. Exogenous application of selenium (25 mg L−1 or 50 mg L−1) to water-stressed bean plants elevated the plant defense system component, given that it increased the free proline, ascorbic acid, and glutathione levels, as well as antioxidant enzymes (SOD, APX, GPX, and CAT). It was concluded that the application of higher levels (25 or/and 50 mg L−1) of Se improves plant water status as well as the growth and yield of common beans cultivated in saline soil.

Transcriptome analysis reveals defense-related genes and pathways during dodder (Cuscuta australis) parasitism on white clover (Trifolium repens)

Dodders (Cuscuta australis R. Br.) are holo-parasitic stem angiosperms with an extensive host range that have significant ecological and economic potential impact on the ecosystem and the agricultural system. However, how the host plant responds to this biotic stress remains mostly unexplored. To identify the defense-related genes and the pathways in white clover (Trifolium repens L.) induced by dodder parasitism, we performed a comparative transcriptome analysis of the leaf and root tissues from white clover with and without dodder infection by high throughput sequencing. We identified 1,329 and 3,271 differentially expressed genes (DEGs) in the leaf and root tissues, respectively. Functional enrichment analysis revealed that plant-pathogen interaction, plant hormone signal transduction, and phenylpropanoid biosynthesis pathways were significantly enriched. Eight WRKY, six AP2/ERF, four bHLH, three bZIP, three MYB, and three NAC transcription factors showed a close relationship with lignin synthesis-related genes, which defended white clover against dodder parasitism. Real-time quantitative PCR (RT-qPCR) for nine DEGs, further validated the data obtained from transcriptome sequencing. Our results provide new insights into understanding the complex regulatory network behind these parasite-host plant interactions.

Mechanisms of plant saline-alkaline tolerance

Saline-alkaline soil affects crop growth and development, thereby suppressing the yields. Human activities and climate changes are putting arable land under the threat of saline-alkalization. To feed a growing global population in limited arable land, it is of great urgence to breed saline-alkaline tolerant crops to cope with food security. Plant salt-tolerance mechanisms have already been explored for decades. However, to date, the molecular mechanisms underlying plants responses to saline-alkaline stress have remained largely elusive. Here, we summarize recent advances in plant response to saline-alkaline stress and propose some points deserving of further exploration.

Application of Sophora alopecuroides organic fertilizer changes the rhizosphere microbial community structure of melon plants and increases the fruit sugar content

BACKGROUND

Sophora alopecuroides L. is a leguminous plant commonly found in northwest China. In Xinjiang, the fresh herb of S. alopecuroides is often applied as a green fertilizer to the rhizosphere of melon (Cucumis melo) plants at the end of their flowering period, to improve the taste of the fruits. However, the effects of S. alopecuroides-based fertilizers on the microbial community structure of soil and crop-root systems are unclear. In order to study the sweetening mechanism of the S. alopecuroides organic fertilizer, three different varieties of melon were selected. The untreated plants were used as the control (CK) group, and the plants treated with S. alopecuroides-based organic fertilizer were selected as the treatment (T) group. The physical and chemical properties, enzyme activities and microbial community structure of the rhizosphere samples were also determined, and a correlation analysis with the fruit sweetness index was conducted.

RESULTS

Sugar content of group T was at least 40% higher than that of group CK. The increase in fruit sugar content positively correlated with the increase in the abundance of beneficial microorganisms, including Pseudomonas, Bacillus, Mycobacterium, Burkholderia, Streptomyces, Acinetobacter, Proteobacteria, Lysobacter, Actinomycetes, Penicillium and Aspergillus.

CONCLUSION

Sophora alopecuroides organic fertilizer could alter the composition and function of bacterial and fungal communities and promote the growth of beneficial bacteria in the melon plant rhizosphere. Further, it could increase the content of soluble solids and sugar in the fruits to achieve a sweetening effect. This fertilizer can be applied as a fruit sweetener in melon cultivation, improving the sugar content of the fruit and consequently the sweetness. © 2022 Society of Chemical Industry.

New Insight into Plant Saline-Alkali Tolerance Mechanisms and Application to Breeding

Saline-alkali stress is a widespread adversity that severely affects plant growth and productivity. Saline-alkaline soils are characterized by high salt content and high pH values, which simultaneously cause combined damage from osmotic stress, ionic toxicity, high pH and HCO₃^-/CO₃^2- stress. In recent years, many determinants of salt tolerance have been identified and their regulatory mechanisms are fairly well understood. However, the mechanism by which plants respond to comprehensive saline-alkali stress remains largely unknown. This review summarizes recent advances in the physiological, biochemical and molecular mechanisms of plants tolerance to salinity or salt- alkali stress. Focused on the progress made in elucidating the regulation mechanisms adopted by plants in response to saline-alkali stress and present some new views on the understanding of plants in the face of comprehensive stress. Plants generally promote saline-alkali tolerance by maintaining pH and Na⁺ homeostasis, while the plants responding to HCO₃^-/CO₃^2- stress are not exactly the same as high pH stress. We proposed that pH-tolerant or sensitive plants have evolved distinct mechanisms to adapt to saline-alkaline stress. Finally, we highlight the areas that require further research to reveal the new components of saline-alkali tolerance in plants and present the current and potential application of key determinants in breed improvement and molecular breeding.

Grapevine (Vitis vinifera) responses to salt stress and alkali stress: transcriptional and metabolic profiling

BACKGROUND

Soil salinization and alkalization are widespread environmental problems that limit grapevine (Vitis vinifera L.) growth and yield. However, little is known about the response of grapevine to alkali stress. This study investigated the differences in physiological characteristics, chloroplast structure, transcriptome, and metabolome in grapevine plants under salt stress and alkali stress.

RESULTS

We found that grapevine plants under salt stress and alkali stress showed leaf chlorosis, a decline in photosynthetic capacity, a decrease in chlorophyll content and Rubisco activity, an imbalance of Na⁺ and K⁺, and damaged chloroplast ultrastructure. Fv/Fm decreased under salt stress and alkali stress. NPQ increased under salt stress whereas decreased under alkali stress. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed the differentially expressed genes (DEGs) induced by salt stress and alkali stress were involved in different biological processes and have varied molecular functions. The expression of stress genes involved in the ABA and MAPK signaling pathways was markedly altered by salt stress and alkali stress. The genes encoding ion transporter (AKT1, HKT1, NHX1, NHX2, TPC1A, TPC1B) were up-regulated under salt stress and alkali stress. Down-regulation in the expression of numerous genes in the 'Porphyrin and chlorophyll metabolism', 'Photosynthesis-antenna proteins', and 'Photosynthesis' pathways were observed under alkali stress. Many genes in the 'Carbon fixation in photosynthetic organisms' pathway in salt stress and alkali stress were down-regulated. Metabolome showed that 431 and 378 differentially accumulated metabolites (DAMs) were identified in salt stress and alkali stress, respectively. L-Glutamic acid and 5-Aminolevulinate involved in chlorophyll synthesis decreased under salt stress and alkali stress. The abundance of 19 DAMs under salt stress related to photosynthesis decreased. The abundance of 16 organic acids in salt stress and 22 in alkali stress increased respectively.

CONCLUSIONS

Our findings suggested that alkali stress had more adverse effects on grapevine leaves, chloroplast structure, ion balance, and photosynthesis than salt stress. Transcriptional and metabolic profiling showed that there were significant differences in the effects of salt stress and alkali stress on the expression of key genes and the abundance of pivotal metabolites in grapevine plants.

Effects of drought and salt stress on seed germination of ephemeral plants in desert of northwest China

Seed germination is the most sensitive stage of plant life history. Studying its response to drought and salinity can analysis the response and adaptation characteristics of desert plants to the environment. In this experiment, the seeds of four common desert ephemeral plants in Xinjiang (Ixiolirion tataricum, Nepeta micrantha, Lepidium apetalum, and Plantago minuta) were used as materials. To study the germination characteristics of seeds under drought, we used salt stress, and coupled salt-drought stress under treatments and explored the germination recovery ability of rehydrated seeds after salt and drought stress treatments. The results showed that: (1) Under salt stress, the germination ability of four plant seeds was inhibited in different degrees. Overall, the degree of inhibition was proportional to the concentration of NaCl solution. (2) Drought stress slowed the seed germination process, and the greater the degree of stress, the more pronounced the slowdown; PEG treatment showed no significant effect on the germination of the four seeds at low concentrations and significant inhibition at medium and high concentrations. (3) The coupled salt-drought treatment significantly alleviated the stress effect of one factor and improved the germination characteristics of seeds. (4) Seeds that did not germinate under different concentrations of salt stress, drought stress, and coupled stresses rapidly recover germination when the stress was relieved or lifted. Ephemeral plants are sensitive to environmental changes, and this study aims to provide a reference basis for vegetation restoration and ecological rehabilitation in arid and semi-arid areas.

Transcriptome analysis of Tamarix ramosissima leaves in response to NaCl stress

Halophyte Tamarix ramosissima. Lcdcb (T. ramosissima) are known as the representative of Tamarix plants that are widely planted in salinized soil. However, molecular mechanisms towards salt tolerance and adaptation are largely rare. In this study, we carried out RNA-sequence and transcriptome analysis of T. ramosissima in response to NaCl stress, screened differentially expressed genes (DEGs) and further verified by qRT-PCR. Results showed that 105702 unigenes were spliced from the raw data of transcriptome sequencing, where 54238 unigenes were retrieved from KEGG, KOG, NR, and SwissProt. After 48 hours of NaCl treatment, the expression levels of 6374 genes were increased, and 5380 genes were decreased in leaves. After 168 hours, the expression levels of 3837 genes were up-regulated and 7808 genes were down-regulated. In particular, 8 transcription factors annotated to the KEGG Pathway were obtained, involving the WRKY and bZIP transcription family. In addition, KEGG pathway annotation showed that expression of 39 genes involved in ROS scavenging mechanisms were significantly changed, in which 21 genes were up-regulated and 18 genes were down-regulated after 48 hours as well as 15 genes were up-regulated and 24 genes were down-regulated after 168h. Simultaneously, the enzyme activities of SOD and POD were significantly enhanced under NaCl treatment, but the enzyme activity of CAT was not significantly enhanced. Moreover, WRKY, MYB and bZIP may participate in the process of salt resistance in T. ramosissima. This study provides gene resources and a theoretical basis for further molecular mechanisms of salt tolerance in T. ramosissima.

Identification of Potential Pathways of Morella cerifera Seedlings in Response to Alkali Stress via Transcriptomic Analysis

Alkali stress, a type of abiotic stress, severely inhibits plant growth. Only a few studies have investigated the mechanism underlying the transcriptional-level response of Morella cerifera to saline-alkali stress. Based on RNA-seq technology, gene expression differences in the fibrous roots of M. cerifera seedlings exposed to low- and high-concentration alkali stress (LAS and HAS, respectively) were investigated, and the corresponding 1312 and 1532 alkali stress-responsive genes were identified, respectively. According to gene set enrichment analysis, 65 gene sets were significantly enriched. Of these, 24 gene sets were shared by both treatment groups. LAS and HAS treatment groups exhibited 9 (all downregulated) and 32 (23 downregulated) unique gene sets, respectively. The differential gene sets mainly included those involved in trehalose biosynthesis and metabolism, phospholipid translocation, and lignin catabolism. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that M. cerifera seedlings were specifically enriched in stilbenoid, diarylheptanoid, and gingerol biosynthesis; phenylalanine, tyrosine, and tryptophan biosynthesis; and sesquiterpenoid and triterpenoid biosynthesis. Moreover, the related genes involved in hormone signaling pathways and transcription factors were determined through a localization analysis of core abiotic stress pathways. These genes and their molecular mechanisms will be the focus of future research.

Physiological Analysis and Transcriptome Sequencing Reveal the Effects of Salt Stress on Banana (Musa acuminata cv. BD) Leaf

The salinization of soil is a widespread environmental problem. Banana (Musa acuminata L.) is a salt-sensitive plant whose growth, development, and production are constrained by salt stresses. However, the tolerance mechanism of this salt-sensitive banana to salt stress is still unclear. This study aimed to investigate the influence of NaCl treatment on phenotypic, physiological, and transcriptome changes in bananas. We found that the content of root activity, MDA, Pro, soluble sugar, soluble protein, and antioxidant enzymes activity in salt-stress treatment were significantly higher than the control in bananas. Transcriptome sequencing result identified an overall of 3,378 differentially expressed genes (DEGs) in banana leaves, and the Kyoto Encyclopedia of Genes and Genomes analysis indicated that these DEGs were involved in phenylpropanoid biosynthesis process, ribosome process, starch and sucrose metabolism, amino sugar process, and plant hormone signal transduction process that had simultaneously changed their expression under salt stress, which indicated these DEGs may play a role in promoting BD banana growth under salt treatments. The genes which were enriched in the phenylpropanoid biosynthesis process, starch and sucrose metabolism process, amino sugar process, and plant hormone signal transduction process were specifically regulated to respond to the salt stress treatments. Here, totally 48 differentially expressed transcription factors (TFs), including WRKY, MYB, NAC, and bHLH, were annotated in BD banana under salt stress. In the phenylpropane biosynthesis pathway, all transcripts encoding key enzymes were found to be significantly up-regulated, indicating that the genes in these pathways may play a significant function in the response of BD banana to salt stress. In conclusion, this study provides new insights into the mechanism of banana tolerance to salt stress, which provides a potential application for the genetic improvement of banana with salt tolerance.

Physio-Morphological, Biochemical and Transcriptomic Analyses Provide Insights Into Drought Stress Responses in Mesona chinensis Benth

Drought stress affects the normal growth and development of Mesona chinensis Benth (MCB), which is an important medicinal and edible plant in China. To investigate the physiological and molecular mechanisms of drought resistance in MCB, different concentrations of polyethylene glycol 6000 (PEG6000) (0, 5, 10, and 15%) were used to simulate drought conditions in this study. Results showed that the growth of MCB was significantly limited under drought stress conditions. Drought stress induced the increases in the contents of Chla, Chlb, Chla + b, soluble protein, soluble sugar, and soluble pectin and the activities of superoxide dismutase (SOD), catalase (CAT), total antioxidant capacity (TAC), hydrogen peroxide (H2O2), and malondialdehyde (MDA). Transcriptome analysis revealed 3,494 differentially expressed genes (DEGs) (1,961 up-regulated and 1,533 down-regulated) between the control and 15% PEG6000 treatments. These DEGs were identified to be involved in the 10 metabolic pathways, including "plant hormone signal transduction," "brassinosteroid biosynthesis," "plant-pathogen interaction," "MAPK signaling pathway-plant," "starch and sucrose metabolism," "pentose and glucuronate interconversions," "phenylpropanoid biosynthesis," "galactose metabolism," "monoterpenoid biosynthesis," and "ribosome." In addition, transcription factors (TFs) analysis showed 8 out of 204 TFs, TRINITY_DN3232_c0_g1 [ABA-responsive element (ABRE)-binding transcription factor1, AREB1], TRINITY_DN4161_c0_g1 (auxin response factor, ARF), TRINITY_DN3183_c0_g2 (abscisic acid-insensitive 5-like protein, ABI5), TRINITY_DN28414_c0_g2 (ethylene-responsive transcription factor ERF1b, ERF1b), TRINITY_DN9557_c0_g1 (phytochrome-interacting factor, PIF3), TRINITY_DN11435_c1_g1, TRINITY_DN2608_c0_g1, and TRINITY_DN6742_c0_g1, were closely related to the "plant hormone signal transduction" pathway. Taken together, it was inferred that these pathways and TFs might play important roles in response to drought stress in MCB. The current study provided important information for MCB drought resistance breeding in the future.

TMT based proteomic profiling of Sophora alopecuroides leaves reveal flavonoid biosynthesis processes in response to salt stress

Salt stress is the major abiotic stress worldwide, adversely affecting crop yield and quality. Utilizing salt tolerance genes for the genetic breeding of crops is one of the most effective measures to withstand salinization. Sophora alopecuroides is a well-known saline-alkaline and drought-tolerant medicinal plant. Understanding the underlying molecular mechanism for Sophora alopecuroides salt tolerance is crucial to identifying the salt-tolerant genes. In this study, we performed tandem mass tag (TMT) based proteomic profiling of S. alopecuroides leaves under 150 mM NaCl induced salt stress condition for 3 d and 7 d. Data are available on ProteomeXchange (PXD027627). Furthermore, the proteomic findings were validated through parallel reaction monitoring (PRM). We observed that the expression levels of several transporter proteins related to the secondary messenger signaling pathway were altered under salt stress conditions induced for 3 d. However, the expression of the certain transferase, oxidoreductase, dehydrogenase, which are involved in the biosynthesis of flavonoids, alkaloids, phenylpropanoids, and amino acid metabolism, were mainly alerted after 7 d post-salt-stress induction. Several potential genes that might be involved in salt stress conditions were identified; however, it demands further investigation. Although salt stress affects the level of secondary metabolites, their correlation needs to be investigated further. SIGNIFICANCE: Salinization is the most severe abiotic adversity, which has had a significant negative effect on world food security over the time. Excavating salt-tolerant genes from halophytes or medicinal plants is one of the important measures to cope with salt stress. S. alopecuroides is a well-known medicinal plant with anti-tumor, anti-inflammatory, and antibacterial effects, anti-saline properties, and resistance to drought stress. Currently, only a few studies have explored the S. alopecuroides' gene function, and regulation and these studies are mostly related to the unpublished genome sequence information of S. alopecuroides. Recently, transcriptomics and metabolomics studies have been carried on the abiotic stress in S. alopecuroides roots. Multiple studies have shown that altered gene expression at the transcript level and altered metabolite levels do not correspond to the altered protein levels. In this study, TMT and PRM based proteomic analyses of S. alopecuroides leaves under salt stress condition induced using 150 mM NaCl for 3 d and 7 d was performed. These analyses elucidated the activation of different mechanisms in response to salt stress. A total of 434 differentially abundant proteins (DAPs) in salt stress conditions were identified and analyzed. For the first time, this study utilized proteomics technology to dig out plentiful underlying salt-tolerant genes from the medicinal plant, S. alopecuroides. We believe that this study will be of great significance to crop genetics and breeding.

Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

BACKGROUND

Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood.

RESULTS

To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs.

CONCLUSION

This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

Screening and identification of salt-tolerance genes in Sophora alopecuroides and functional verification of SaAQP

Overexpression of SaAQP can improve the salt tolerance of transgenic soybean hairy roots and A. thaliana. Salt stress severely affects crop yield and food security. There is a need to improve the salt tolerance of crops, but the discovery and utilization of salt-tolerance genes remains limited. Owing to its strong stress tolerance, Sophora alopecuroides is ideal for the identification of salt-tolerance genes. Therefore, we aimed to screen and identify the salt-tolerance genes in S. alopecuroides. With a yeast expression library of seedlings, salt-tolerant genes were screened using a salt-containing medium to simulate salt stress. By combining salt-treatment screening and transcriptome sequencing, 11 candidate genes related to salt tolerance were identified, including genes for peroxidase, inositol methyltransferase, aquaporin, cysteine synthase, pectinesterase, and WRKY. The expression dynamics of candidate genes were analyzed after salt treatment of S. alopecuroides, and salt tolerance was verified in yeast BY4743. The candidate genes participated in the salt-stress response in S. alopecuroides, and their overexpression significantly improved the salt tolerance of yeast. Salt tolerance mediated by SaAQP was further verified in soybean hairy roots and Arabidopsis thaliana, and it was found that SaAQP might enhance the salt tolerance of A. thaliana by participating in a reactive oxygen species scavenging mechanism. This result provides new genetic resources in plant breeding for salt resistance.

Analysis of Phytohormone Signal Transduction in Sophora alopecuroides under Salt Stress

Salt stress seriously restricts crop yield and quality, leading to an urgent need to understand its effects on plants and the mechanism of plant responses. Although phytohormones are crucial for plant responses to salt stress, the role of phytohormone signal transduction in the salt stress responses of stress-resistant species such as Sophora alopecuroides has not been reported. Herein, we combined transcriptome and metabolome analyses to evaluate expression changes of key genes and metabolites associated with plant hormone signal transduction in S. alopecuroides roots under salt stress for 0 h to 72 h. Auxin, cytokinin, brassinosteroid, and gibberellin signals were predominantly involved in regulating S. alopecuroides growth and recovery under salt stress. Ethylene and jasmonic acid signals may negatively regulate the response of S. alopecuroides to salt stress. Abscisic acid and salicylic acid are significantly upregulated under salt stress, and their signals may positively regulate the plant response to salt stress. Additionally, salicylic acid (SA) might regulate the balance between plant growth and resistance by preventing reduction in growth-promoting hormones and maintaining high levels of abscisic acid (ABA). This study provides insight into the mechanism of salt stress response in S. alopecuroides and the corresponding role of plant hormones, which is beneficial for crop resistance breeding.

Autophagy in Plant Abiotic Stress Management

Plants can be considered an open system. Throughout their life cycle, plants need to exchange material, energy and information with the outside world. To improve their survival and complete their life cycle, plants have developed sophisticated mechanisms to maintain cellular homeostasis during development and in response to environmental changes. Autophagy is an evolutionarily conserved self-degradative process that occurs ubiquitously in all eukaryotic cells and plays many physiological roles in maintaining cellular homeostasis. In recent years, an increasing number of studies have shown that autophagy can be induced not only by starvation but also as a cellular response to various abiotic stresses, including oxidative, salt, drought, cold and heat stresses. This review focuses mainly on the role of autophagy in plant abiotic stress management.

Combined Transcriptomic and Metabolomic Analysis Reveals the Role of Phenylpropanoid Biosynthesis Pathway in the Salt Tolerance Process of Sophora alopecuroides

Salt stress is the main abiotic stress that limits crop yield and agricultural development. Therefore, it is imperative to study the effects of salt stress on plants and the mechanisms through which plants respond to salt stress. In this study, we used transcriptomics and metabolomics to explore the effects of salt stress on Sophora alopecuroides. We found that salt stress incurred significant gene expression and metabolite changes at 0, 4, 24, 48, and 72 h. The integrated transcriptomic and metabolomic analysis revealed that the differentially expressed genes (DEGs) and differential metabolites (DMs) obtained in the phenylpropanoid biosynthesis pathway were significantly correlated under salt stress. Of these, 28 DEGs and seven DMs were involved in lignin synthesis and 23 DEGs and seven DMs were involved in flavonoid synthesis. Under salt stress, the expression of genes and metabolites related to lignin and flavonoid synthesis changed significantly. Lignin and flavonoids may participate in the removal of reactive oxygen species (ROS) in the root tissue of S. alopecuroides and reduced the damage caused under salt stress. Our research provides new ideas and genetic resources to study the mechanism of plant responses to salt stress and further improve the salt tolerance of plants.

Response Mechanisms of Plants Under Saline-Alkali Stress

As two coexisting abiotic stresses, salt stress and alkali stress have severely restricted the development of global agriculture. Clarifying the plant resistance mechanism and determining how to improve plant tolerance to salt stress and alkali stress have been popular research topics. At present, most related studies have focused mainly on salt stress, and salt-alkali mixed stress studies are relatively scarce. However, in nature, high concentrations of salt and high pH often occur simultaneously, and their synergistic effects can be more harmful to plant growth and development than the effects of either stress alone. Therefore, it is of great practical importance for the sustainable development of agriculture to study plant resistance mechanisms under saline-alkali mixed stress, screen new saline-alkali stress tolerance genes, and explore new plant salt-alkali tolerance strategies. Herein, we summarized how plants actively respond to saline-alkali stress through morphological adaptation, physiological adaptation and molecular regulation.