Development of a cDNA microarray to identify gene expression of Puccinellia tenuiflora under saline-alkali stress

Adaptive Strategy of the Perennial Halophyte Grass Puccinellia tenuiflora to Long-Term Salinity Stress

Salinity stress influences plants throughout their entire life cycle. However, little is known about the response of plants to long-term salinity stress (LSS). In this study, Puccinellia tenuiflora, a perennial halophyte grass, was exposed to 300 mM NaCl for two years (completely randomized experiment design with three biological replicates). We measured the photosynthetic parameters and plant hormones and employed a widely targeted metabolomics approach to quantify metabolites. Our results revealed that LSS induced significant metabolic changes in P. tenuiflora, inhibiting the accumulation of 11 organic acids in the leaves and 24 organic acids in the roots and enhancing the accumulation of 15 flavonoids in the leaves and 11 phenolamides in the roots. The elevated accumulation of the flavonoids and phenolamides increased the ability of P. tenuiflora to scavenge reactive oxygen species. A comparative analysis with short-term salinity stress revealed that the specific responses to long-term salinity stress (LSS) included enhanced flavonoid accumulation and reduced amino acid accumulation, which contributed to the adaptation of P. tenuiflora to LSS. LSS upregulated the levels of abscisic acid in the leaves and ACC (a direct precursor of ethylene) in the roots, while it downregulated the levels of cytokinins and jasmonic acids in both the organs. These tolerance-associated changes in plant hormones would be expected to reprogram the energy allocation among growth, pathogen defense, and salinity stress response. We propose that abscisic acid, ethylene, cytokinins, and jasmonic acids may interact with each other to construct a salinity stress response network during the adaptation of P. tenuiflora to LSS, which mediates salinity stress response and significant metabolic changes. Our results provided novel insights into the plant hormone-regulated metabolic response of the plants under LSS, which can enhance our understanding of plant salinity tolerance.

Progress of Research on the Physiology and Molecular Regulation of Sorghum Growth under Salt Stress by Gibberellin

Plant growth often encounters diverse abiotic stresses. As a global resource-based ecological problem, salinity is widely distributed and one of the major abiotic stresses affecting crop yields worldwide. Sorghum, a cereal crop with medium salt tolerance and great value for the development and utilization of salted soils, is an important source of food, brewing, energy, and forage production. However, in soils with high salt concentrations, sorghum experiences low emergence and suppressed metabolism. It has been demonstrated that the effects of salt stress on germination and seedling growth can be effectively mitigated to a certain extent by the exogenous amendment of hormonal gibberellin (GA). At present, most of the studies on sorghum salt tolerance at home and abroad focus on morphological and physiological levels, including the transcriptome analysis of the exogenous hormone on sorghum salt stress tolerance, the salt tolerance metabolism pathway, and the mining of key salt tolerance regulation genes. The high-throughput sequencing technology is increasingly widely used in the study of crop resistance, which is of great significance to the study of plant resistance gene excavation and mechanism. In this study, we aimed to review the effects of the exogenous hormone GA on leaf morphological traits of sorghum seedlings and further analyze the physiological response of sorghum seedling leaves and the regulation of sorghum growth and development. This review not only focuses on the role of GA but also explores the signal transduction pathways of GA and the performance of their responsive genes under salt stress, thus helping to further clarify the mechanism of regulating growth and production under salt stress. This will serve as a reference for the molecular discovery of key genes related to salt stress and the development of new sorghum varieties.

Effects of Exogenous Melatonin on Root Physiology, Transcriptome and Metabolome of Cotton Seedlings under Salt Stress

Root systems are the key organs through which plants absorb water and nutrients and perceive the soil environment and thus are easily damaged by salt stress. Melatonin can alleviate stress-induced damage to roots. The present study investigated the effects of exogenous melatonin on the root physiology, transcriptome and metabolome of cotton seedlings under salt stress. Salt stress was observed to damage the cell structure and disorder the physiological system of cotton seedling roots. After subjecting melatonin-soaked seeds to salt stress, the activities of SOD, CAT and POD in cotton seedling roots increased by 10–25%, 50–60% and 50–60%, respectively. The accumulation of H₂O₂ and MDA were significantly decreased by 30–60% and 30–50%, respectively. The contents of soluble sugar, soluble protein and K⁺ increased by 15–30%, 15–30% and 20–50%, respectively, while the Na⁺ content was significantly reduced. Melatonin also increased auxin (by 20–40%), brassinosteroids (by 5–40%) and gibberellin (by 5–35%) and promoted melatonin content and root activity. Exogenous melatonin maintained the integrity of root cells and increased the number of organelles. Transcriptomic and metabolomic results showed that exogenous melatonin could mitigate the salt-stress-induced inhibition of plant root development by regulating the reactive oxygen species scavenging system; ABC transporter synthesis; plant hormone signal transduction, endogenous melatonin gene expression; and the expression of the transcription factors MYB, TGA and WRKY33. These results provide a new direction and empirical basis for improving crop salt tolerance with melatonin.

Extensive secretion of phenolic acids and fatty acids facilitates rhizosphere pH regulation in halophyte Puccinellia tenuiflora under alkali stress

Puccinellia tenuiflora is a forage grass with high nutritional value that is an extreme alkali-tolerant halophyte: it can survive at pH 10-11. Root secretion is perceived as a major plant alkali tolerance mechanism. In the present study, we applied a widely targeted metabolomic approach to identify and quantify the root exudates of P. tenuiflora under alkali stress. We also surveyed the transcriptional and metabolic profiling of P. tenuiflora roots under salt (96-mM Na⁺ , pH 6.8) and alkali (96-mM Na⁺ , pH 9.6) stresses to reveal the biological processes mediating root secretion. In P. tenuiflora plants, 493 root exudates were detected under control conditions, 544 root exudates under salt stress conditions, and 607 root exudates under alkali stress conditions. Salt-stressed plants and alkali-stressed plants shared 64 root exudates, and 60 root exudates were unique to alkali-stressed plants. The secretion rate of 56 phenolic acids, 43 fatty acids, and 9 organic acids was faster in alkali-stressed roots than in control and salt-stressed roots. In P. tenuiflora roots, alkali stress enhanced the accumulation of 23 phenolic acids, five organic acids, and only one fatty acid. In addition, transcriptomic analysis revealed that alkali stress upregulated glycolysis and phenylpropanoid biosynthesis pathways in P. tenuiflora roots. Taken together, extensive secretion of phenolic acids and fatty acids promotes rhizosphere pH regulation of P. tenuiflora under alkali stress, which contributes to its strong alkali tolerance. The root secretion of P. tenuiflora upon alkali stress is highly organized. Enhanced glycolysis, phenylpropanoid biosynthesis, and organic acid synthesis in the roots provide more reducing power and carbon source for the root secretion process of alkali-stressed P. tenuiflora.

Genome-wide DNA methylation analysis and biochemical responses provide insights into the initial domestication of halophyte Puccinellia tenuiflora

Puccinellia tenuiflora was domesticated for two years by growing it under non-saline conditions, providing epigenetic and biochemical insights into the initial domestication of extreme halophytes. Some halophytes have economic value as crop species. The domestication of halophytes may offer hope in solving the problem of soil salinization. We domesticated a wild halophyte, Puccinellia tenuiflora, for two years by growing it under non-saline conditions in a greenhouse and used re-sequencing, genome-wide DNA methylation, biochemical, and transcriptome analyses to uncover the mechanisms underlying alterations in the halophyte's tolerance to saline following domestication. Our results showed that non-saline domestication altered the methylation status for a number of genes and transposable elements, resulting in a much higher frequency of hypomethylation than hypermethylation. These modifications to DNA methylation were observed in many critical salinity-tolerance genes, particularly their promoter regions or transcriptional start sites. Twenty-nine potassium channel genes were hypomethylated and three were hypermethylated, suggesting that the DNA methylation status of potassium channel genes was influenced by domestication. The accelerated uptake of potassium is a major salinity tolerance characteristic of P. tenuiflora. We propose that modifications to the DNA methylation of potassium channel genes may be associated with the development of salinity tolerance in this species. By assessing whether non-saline domestication could change the salinity tolerance of P. tenuiflora, we demonstrated that non-saline domesticated plants are less tolerant to saline, which may be attributable to altered sucrose metabolism. DNA methylation and transposable elements may, therefore, be integrated into an environment-sensitive molecular engine that promotes the rapid domestication of P. tenuiflora to enable its use as a crop plant.

Comparative Genomics and Transcriptomics of the Extreme Halophyte Puccinellia tenuiflora Provides Insights Into Salinity Tolerance Differentiation Between Halophytes and Glycophytes

Halophytes and glycophytes exhibit clear differences in their tolerance to high levels of salinity. The genetic mechanisms underlying this differentiation, however, remain unclear. To unveil these mechanisms, we surveyed the evolution of salinity-tolerant gene families through comparative genomic analyses between the model halophyte Puccinellia tenuiflora and glycophytic Gramineae plants, and compared their transcriptional and physiological responses to salinity stress. Under salinity stress, the K⁺ concentration in the root was slightly enhanced in P. tenuiflora, but it was greatly reduced in the glycophytic Gramineae plants, which provided a physiological explanation for differences in salinity tolerance between P. tenuiflora and these glycophytes. Interestingly, several K⁺ uptake gene families from P. tenuiflora experienced family expansion and positive selection during evolutionary history. This gene family expansion and the elevated expression of K⁺ uptake genes accelerated K⁺ accumulation and decreased Na⁺ toxicity in P. tenuiflora roots under salinity stress. Positively selected P. tenuiflora K⁺ uptake genes may have evolved new functions that contributed to development of P. tenuiflora salinity tolerance. In addition, the expansion of the gene families involved in pentose phosphate pathway, sucrose biosynthesis, and flavonoid biosynthesis assisted the adaptation of P. tenuiflora to survival under high salinity conditions.

Genome of extreme halophyte Puccinellia tenuiflora

Background

Puccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals. This halophyte has enormous values for improving our understanding of salinity tolerance mechanisms. The genetic information of P. tenuiflora also is a potential resource that can be used for improving the salinity tolerance of cereals.

Results

Here, we sequenced and assembled the P. tenuiflora genome (2n = 14) through the combined strategy of Illumina, PacBio, and 10× genomic technique. We generated 43.2× PacBio long reads, 123.87× 10× genomic reads, and 312.6× Illumina reads. Finally, we assembled 2638 scaffolds with a total size of 1.107 Gb, contig N50 of 117 kb, and scaffold N50 of 950 kb. We predicted 39,725 protein-coding genes, and identified 692 tRNAs, 68 rRNAs, 702 snRNAs, 1376 microRNAs, and 691 Mb transposable elements.

Conclusions

We deposited the genome sequence in NCBI and the Genome Warehouse in National Genomics Data Center. Our work may improve current understanding of plant salinity tolerance, and provides extensive genetic resources necessary for improving the salinity and drought tolerance of cereals.

Transcriptome profiling of Puccinellia tenuiflora during seed germination under a long-term saline-alkali stress

BACKGROUND

Puccinellia tenuiflora is the most saline-alkali tolerant plant in the Songnen Plain, one of the three largest soda saline-alkali lands worldwide. Here, we investigated the physicochemical properties of saline-alkali soils from the Songnen Plain and sequenced the transcriptomes of germinated P. tenuiflora seedlings under long-term treatment (from seed soaking) with saline-alkali soil extracts.

RESULTS

We found that the soils from Songnen Plain were reasonably rich in salts and alkali; moreover, the soils were severely deficient in nitrogen [N], phosphorus [P], potassium [K] and several other mineral elements. This finding demonstrated that P. tenuiflora can survive from not only high saline-alkali stress but also a lack of essential mineral elements. To explore the saline-alkali tolerance mechanism, transcriptional analyses of P. tenuiflora plants treated with water extracts from the saline-alkali soils was performed. Interestingly, unigenes involved in the uptake of N, P, K and the micronutrients were found to be significantly upregulated, which indicated the existence of an efficient nutrition-uptake system in P. tenuiflora. Compared with P. tenuiflora, the rice Oryza sativa was hypersensitive to saline-alkali stress. The results obtained using a noninvasive microtest techniques confirmed that the uptake of NO3- and NH4+ and the regulatory flux of Na+ and H+ were significantly higher in the roots of P. tenuiflora than in those of O. sativa. In the corresponding physiological experiments, the application of additional nutrition elements significantly eliminated the sensitive symptoms of rice to saline-alkali soil extracts.

CONCLUSIONS

Our results imply that the survival of P. tenuiflora in saline-alkali soils is due to a combination of at least two regulatory mechanisms and the high nutrient uptake capacity of P. tenuiflora plays a pivotal role in its adaptation to those stress. Taken together, our results highlight the role of nutrition uptake in saline-alkali stress tolerance in plants.

Dynamic responses of Haloxylon ammodendron to various degrees of simulated drought stress

Haloxylon ammodendron, a C4 perennial, succulent and xero-halophytic shrub, is highly resistant to harsh environments, therefore, exploring the stress resistance mechanism will be beneficial for the use of xerophytes to prevent desertification. To determine osmotic adjustment (OA) and antioxidase functions under simulated drought stress, 8-week-old seedlings were treated with sorbitol solutions to maintain osmotic potentials (Ψs) at a control and -0.5 and -1.0 MPa. Under -0.5 MPa osmotic stress, H. ammodendron stably maintained the water content of assimilating branches, a result that was not significantly different from the result of the control group. Moreover, the Ψs decreased significantly, which helped plants absorb water efficiently from the environment, as H. ammodendron accumulated massive osmotic regulators in its assimilating branches to adjust shoot Ψs. Specifically, the contribution of Na⁺ to shoot Ψs was up to 45%, and Na⁺ became the main osmotic regulator of OA. During the treatments, the content and contribution of K⁺ remained stable. However, the total contribution of three organic osmotic regulators (free proline, betaine and soluble sugar) was only 20%, and betaine was the main organic osmotic regulator, accounting for approximately 15% of the 20% contribution. Moreover, H. ammodendron seedlings presented strong antioxidases, especially when there was a high activity level of superoxide dismutase, and with an increase in treatment time and degree of osmotic stress, the activity of peroxidase and catalase increased significantly. Substantial accumulation of osmotic adjustment substances was an important strategy for H. ammodendron to cope with simulated drought stress, in particular, H. ammodendron absorbed much Na⁺ and transported Na⁺ into the assimilating branch for OA. The scavenging of reactive oxygen species by antioxidases was another adaptation strategy for H. ammodendron to adapt to simulated drought stress.

GsSLAH3, a Glycine soja slow type anion channel homolog, positively modulates plant bicarbonate stress tolerance

Alkaline stress is a major form of abiotic stress that severely inhibits plant growth and development, thus restricting crop productivity. However, little is known about how plants respond to alkali. In this study, a slow-type anion channel homolog 3 gene, GsSLAH3, was isolated and functionally characterized. Bioinformatics analysis showed that the GsSLAH3 protein contains 10 transmembrane helices. Consistently, GsSLAH3 was found to locate on plasma membrane by transient expression in onion epidermal cells. In wild soybeans, GsSLAH3 expression was induced by NaHCO₃ treatment, suggesting its involvement in plant response to alkaline stress. Ectopic expression of GsSLAH3 in yeast increased sensitivity to alkali treatment. Dramatically, overexpression of GsSLAH3 in Arabidopsis thaliana enhanced alkaline tolerance during the germination, seedling and adult stages. More interestingly, we found that transgenic lines also improved plant tolerance to KHCO₃ rather than high pH treatment. A nitrate content analysis of Arabidopsis shoots showed that GsSLAH3 overexpressing lines accumulated more NO₃^- than wild-type. In summary, our data suggest that GsSLAH3 is a positive alkali responsive gene that increases bicarbonate resistance specifically.

Transcriptomic analysis of boron hyperaccumulation mechanisms in Puccinellia distans

Puccinellia distans, common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were treated for three weeks with normal (0.5 mg L^-1) and elevated (500 mg L^-1) boron levels in hydroponic solution. Expressed sequence tags (ESTs) derived from shoot tissue were analyzed by RNA sequencing to identify genes up and down-regulated under boron stress. In this way, 3312 differentially expressed transcripts were detected, 67.7% of which were up-regulated and 32.3% of which were down-regulated in boron-treated plants. To partially confirm the RNA sequencing results, 32 randomly selected transcripts were analyzed for their expression levels in boron-treated plants. The results agreed with the expected direction of change (up or down-regulation). A total of 1652 transcripts had homologs in A. thaliana and/or O. sativa and mapped to 1107 different proteins. Functional annotation of these proteins indicated that the boron tolerance and hyperaccumulation mechanisms of P. distans involve many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.

Genome-wide analysis and expression profiling of PP2C clade D under saline and alkali stresses in wild soybean and Arabidopsis

Protein phosphatase 2Cs (PP2Cs) belong to the largest protein phosphatase family in plants. Some members have been described as being negative modulators of plant growth and development, as well as responses to hormones and environmental stimuli. However, little is known about the members of PP2C clade D, which may be involved in the regulation of signaling pathways, especially in response to saline and alkali stresses. Here, we identified 13 PP2C orthologs from the wild soybean (Glycine soja) genome. We examined the sequence characteristics, chromosome locations and duplications, gene structures, and promoter cis-elements of the PP2C clade D genes in Arabidopsis and wild soybean. Our results showed that GsPP2C clade D (GsAPD) genes exhibit more gene duplications than AtPP2C clade D genes. Plant hormone and abiotic stress-responsive elements were identified in the promoter regions of most PP2C genes. Moreover, we investigated their expression patterns in roots, stems, and leaves. Quantitative real-time PCR analyses revealed that the expression levels of representative GsPP2C and AtPP2C clade D genes were significantly influenced by alkali and salt stresses, suggesting that these genes might be associated with or directly involved in the relevant stress signaling pathways. Our results established a foundation for further functional characterization of PP2C clade D genes in the future.

Na2CO3-responsive mechanisms in halophyte Puccinellia tenuiflora roots revealed by physiological and proteomic analyses

Soil alkalization severely affects crop growth and agricultural productivity. Alkali salts impose ionic, osmotic, and high pH stresses on plants. The alkali tolerance molecular mechanism in roots from halophyte Puccinellia tenuiflora is still unclear. Here, the changes associated with Na₂CO₃ tolerance in P. tenuiflora roots were assessed using physiological and iTRAQ-based quantitative proteomic analyses. We set up the first protein dataset in P. tenuiflora roots containing 2,671 non-redundant proteins. Our results showed that Na₂CO₃ slightly inhibited root growth, caused ROS accumulation, cell membrane damage, and ion imbalance, as well as reduction of transport and protein synthesis/turnover. The Na₂CO₃-responsive patterns of 72 proteins highlighted specific signaling and metabolic pathways in roots. Ca²⁺ signaling was activated to transmit alkali stress signals as inferred by the accumulation of calcium-binding proteins. Additionally, the activities of peroxidase and glutathione peroxidase, and the peroxiredoxin abundance were increased for ROS scavenging. Furthermore, ion toxicity was relieved through Na⁺ influx restriction and compartmentalization, and osmotic homeostasis reestablishment due to glycine betaine accumulation. Importantly, two transcription factors were increased for regulating specific alkali-responsive gene expression. Carbohydrate metabolism-related enzymes were increased for providing energy and carbon skeletons for cellular metabolism. All these provide new insights into alkali-tolerant mechanisms in roots.

A novel Glycine soja homeodomain-leucine zipper (HD-Zip) I gene, Gshdz4, positively regulates bicarbonate tolerance and responds to osmotic stress in Arabidopsis

BACKGROUND

Wild soybean (Glycine soja) is a highly adaptive plant species which can grow well in saline-alkaline soils. In soybean genome, there exist about 140 HD-Zip (Homeodomain-leucine Zipper) genes. HD-Zip transcription factor family is one of the largest plant specific superfamilies and plays important roles in response to abiotic stresses. Although HD-Zip transcription factors have been broadly reported to be involved in plant resistance to abiotic stresses like salt and drought, their roles in response to bicarbonate stress is largely unknown.

RESULTS

From our previous transcriptome profile analysis of wild soybean treated by 50 mM NaHCO3, we identified an HD-Zip gene (Gshdz4) which showed high response to the alkaline stress. Our result of qRT-PCR showed that the expression of Gshdz4 was induced by alkaline stress (NaHCO3) in both leaves and roots of wild soybean. Overexpression of Gshdz4 in Arabidopsis resulted in enhanced tolerance to NaHCO3 and KHCO3 during the process of plant growth and development. However, the growths of transgenic and WT plants were not significantly different on the medium with high pH adjusted by KOH, implicating Gshdz4 is only responsible for resisting HCO3 (-) but not high pH. The transgenic plants had less MDA contents but higher POD activities and chlorophyll contents than the WT plants. Moreover, the transcript levels of stress-related genes, such as NADP-ME, H (+) -Ppase, RD29B and KIN1 were increased with greater extent in the transgenic plants than the wild plants. On the contrary, Gshdz4 overexpression lines were much sensitive to osmotic stress at seed germination and stocking stages compared to the wild plants.

CONCLUSIONS

We revealed that the important and special roles of Gshdz4 in enhancing bicarbonate tolerance and responding to osmotic stress. It is the first time to elucidate these novel functions of HD-ZIP transcription factors. All the evidences broaden our understanding of functions of HD-Zip family and provide clues for uncovering the mechanisms of high tolerance of wild soybean to saline-alkaline stresses.

Chilling-responsive mechanisms in halophyte Puccinellia tenuiflora seedlings revealed from proteomics analysis

Alkali grass (Puccinellia tenuiflora), a monocotyledonous perennial halophyte species, is a good pasture with great nutritional value for livestocks. It can thrive under low temperature in the saline-alkali soil of Songnen plain in northeastern China. In the present study, the chilling-responsive mechanism in P. tenuiflora leaves was investigated using physiological and proteomic approaches. After treatment of 10°C for 10 and 20days, photosynthesis, biomass, contents of osmolytes and antioxidants, and activities of reactive oxygen species scavenging enzymes were analyzed in leaves of 20-day-old seedlings. Besides, 89 chilling-responsive proteins were revealed from proteomic analysis. All the results highlighted that the growth of seedlings was inhibited due to chilling-decreased enzymes in photosynthesis, carbohydrate metabolism, and energy supplying. The accumulation of osmolytes (i.e., proline, soluble sugar, and glycine betaine) and enhancement of ascorbate-glutathione cycle and glutathione peroxidase/glutathione S-transferase pathway in leaves could minimize oxidative damage of membrane and other molecules under the chilling conditions. In addition, protein synthesis and turnover in cytoplasm and chloroplast were altered to cope with the chilling stress. This study provides valuable information for understanding the chilling-responsive and cross-tolerant mechanisms in monocotyledonous halophyte plant species.

Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress

Soil alkalinity is an important environmental problem limiting agricultural productivity. Wild soybean (Glycine soja) shows strong alkaline stress tolerance, so it is an ideal plant candidate for studying the molecular mechanisms of alkaline tolerance and identifying alkaline stress-responsive genes. However, limited information is available about G. soja responses to alkaline stress on a genomic scale. Therefore, in the present study, we used RNA sequencing to compare transcript profiles of G. soja root responses to sodium bicarbonate (NaHCO3) at six time points, and a total of 68,138,478 pairs of clean reads were obtained using the Illumina GAIIX. Expression patterns of 46,404 G. soja genes were profiled in all six samples based on RNA-seq data using Cufflinks software. Then, t12 transcription factors from MYB, WRKY, NAC, bZIP, C2H2, HB, and TIFY families and 12 oxidation reduction related genes were chosen and verified to be induced in response to alkaline stress by using quantitative real-time polymerase chain reaction (qRT-PCR). The GO functional annotation analysis showed that besides "transcriptional regulation" and "oxidation reduction," these genes were involved in a variety of processes, such as "binding" and "response to stress." This is the first comprehensive transcriptome profiling analysis of wild soybean root under alkaline stress by RNA sequencing. Our results highlight changes in the gene expression patterns and identify a set of genes induced by NaHCO3 stress. These findings provide a base for the global analyses of G. soja alkaline stress tolerance mechanisms.

Transcriptional responses of a bicarbonate-tolerant monocot, Puccinellia tenuiflora, and a related bicarbonate-sensitive species, Poa annua, to NaHCO3 stress

Puccinellia tenuiflora is an alkaline salt-tolerant monocot found in saline-alkali soil in China. To identify the genes which are determining the higher tolerance of P. tenuiflora compared to bicarbonate sensitive species, we examined the responses of P. tenuiflora and a related bicarbonate-sensitive Poeae plant, Poa annua, to two days of 20 mM NaHCO₃ stress by RNA-seq analysis. We obtained 28 and 38 million reads for P. tenuiflora and P. annua, respectively. For each species, the reads of both unstressed and stressed samples were combined for de novo assembly of contigs. We obtained 77,329 contigs for P. tenuiflora and 115,335 contigs for P.annua. NaHCO₃ stress resulted in greater than two-fold absolute expression value changes in 157 of the P. tenuiflora contigs and 1090 of P. annua contigs. Homologs of the genes involved in Fe acquisition, which are important for the survival of plants under alkaline stress, were up-regulated in P. tenuiflora and down-regulated in P. annua. The smaller number of the genes differentially regulated in P. tenuiflora suggests that the genes regulating bicarbonate tolerance are constitutively expressed in P. tenuiflora.

Discovery and characterization of two novel salt-tolerance genes in Puccinellia tenuiflora

Puccinellia tenuiflora is a monocotyledonous halophyte that is able to survive in extreme saline soil environments at an alkaline pH range of 9-10. In this study, we transformed full-length cDNAs of P. tenuiflora into Saccharomyces cerevisiae by using the full-length cDNA over-expressing gene-hunting system to identify novel salt-tolerance genes. In all, 32 yeast clones overexpressing P. tenuiflora cDNA were obtained by screening under NaCl stress conditions; of these, 31 clones showed stronger tolerance to NaCl and were amplified using polymerase chain reaction (PCR) and sequenced. Four novel genes encoding proteins with unknown function were identified; these genes had no homology with genes from higher plants. Of the four isolated genes, two that encoded proteins with two transmembrane domains showed the strongest resistance to 1.3 M NaCl. RT-PCR and northern blot analysis of P. tenuiflora cultured cells confirmed the endogenous NaCl-induced expression of the two proteins. Both of the proteins conferred better tolerance in yeasts to high salt, alkaline and osmotic conditions, some heavy metals and H2O2 stress. Thus, we inferred that the two novel proteins might alleviate oxidative and other stresses in P. tenuiflora.

Abiotic stress response in yeast and metal-binding ability of a type 2 metallothionein-like protein (PutMT2) from Puccinellia tenuiflora

Metallothioneins are low-molecular weight and cysteine-rich metal-binding proteins that play predominant cellular roles in the scavenging of reactive oxygen species and in mediating metal metabolism. To evaluate the role of a type-2 metallothionein-like gene from Puccinellia tenuiflora (PutMT2), the gene was over-expressed in yeast, and growth was assessed under a variety of abiotic stress conditions including peroxide (H2O2), salinity (NaCl and NaHCO3), and metal stress. PutMT2 overexpression in yeast improved the tolerance of cells to H2O2, NaCl, NaHCO3, Zn(2+), Fe(2+), Fe(3+), Cd(2+), Cr(6+), and Ag(+), but increased the sensitivity of cells to Mn(2+), Co(2+), Cu(2+), and Ni(2+) compared with control cells. PutMT2 was then expressed in Escherichia coli BL21as a glutathione S-transferase (GST) fusion protein (GST-PutMT2), and the metal-binding ability of GST-PutMT2 was analyzed and compared with GST alone using inductively coupled plasma atomic emission spectroscopy. Results showed that PutMT2 could bind to Cr, Cd, Co, Ag, Ba, Pb, Mn, Zn, Fe, Cu, P, Al, and Mg, but not Ni and As. There was no evidence to suggest that PutMT2 exhibited a specific or selective binding tendency to any individual metal ion. PutMT2 protein bound to Zn, Na, and Cu in vivo, perhaps with the highest affinity for Cu. Taken together, our results suggest that PutMT2 protein could play an important role in improving metal tolerance by metal binding in yeast. However, additional studies are required to confirm these results and to clarify the function of PutMT2 in transgenic plants.

Response to long-term NaHCO3-derived alkalinity in model Lotus japonicus Ecotypes Gifu B-129 and Miyakojima MG-20: transcriptomic profiling and physiological characterization

The current knowledge regarding transcriptomic changes induced by alkalinity on plants is scarce and limited to studies where plants were subjected to the alkaline salt for periods not longer than 48 h, so there is no information available regarding the regulation of genes involved in the generation of a new homeostatic cellular condition after long-term alkaline stress. Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. Gifu B-129 and MG-20 also differed in their regulation of genes that could play important roles in the generation of a new Fe/Zn homeostatic cellular condition, synthesis of plant compounds involved in stress response, protein-degradation, damage repair and root senescence, as well as in glycolysis, gluconeogenesis and TCA. In addition, there were differences between both ecotypes in the expression patterns of putative transcription factors that could determine distinct arrangements of flavonoid and isoflavonoid compounds. Our results provided a set of selected, differentially expressed genes deserving further investigation and suggested that the L. japonicus ecotypes could constitute a useful model to search for common and distinct tolerance mechanisms to long-term alkaline stress response in plants.

Combined effects of carbonate alkalinity and pH on survival, growth and haemocyte parameters of the Venus clam Cyclina sinensis

Carbonate alkalinity (CA) and pH are considered to be two important stress factors that determine the response of aquatic animals to sudden transfers into saline-alkaline water. To evaluate the potential for aquaculture production of Venus clams (Cyclina sinensis) farmed in saline-alkaline water, the combined effects of CA (2.5 (control), 10.0, 20.0 and 40.0 meq/l) and pH (8.0 (control), 8.5, 9.0 and 9.5) on survival rate was monitored every day for 10 days. Length gain rate (LGR) and weight gain rate (WGR) were also monitored for two months, and total haemocyte count (THC), phagocytic rate (PR) and haemocyte mortality (HM) were measured for 3, 6, 12 and 24 days under the same water temperature (20 °C) and salinity (15‰) conditions. The results showed that survival rates in treatments of CA ≤ 20.0, combined with pH ≤ 9.0, were 100%. LGR and WGR in treatments of CA 2.5 & pH 8.0 (control), CA 2.5 & pH 8.5 and CA 10.0 & pH 8.0 exhibited the largest values (P > 0.05), while in other treatments, they showed a decreasing trend with an increase in either CA or pH or both (P < 0.05). Similarly, for THC, PR and HM, no significant differences were observed among the fast growth treatments during the entire experimental period (P > 0.05), however, in other treatments, they presented significant differences, especially on day 3 and 6 (P < 0.05), most notably with increases in CA or pH, but returned to control levels on day 12. In conclusion, in this study, a strong interaction between CA and pH was observed. Additionally, it was ascertained that the Venus clam C. sinensis can withstand the stress of CA 20.0 combined pH 9.0, although individuals grows slowly and may take approximately 12 days to recover to the unstressed condition.

Physiological and molecular features of Puccinellia tenuiflora tolerating salt and alkaline-salt stress

Saline-alkali soil seriously threatens agriculture productivity; therefore, understanding the mechanism of plant tolerance to alkaline-salt stress has become a major challenge. Halophytic Puccinellia tenuiflora can tolerate salt and alkaline-salt stress, and is thus an ideal plant for studying this tolerance mechanism. In this study, we examined the salt and alkaline-salt stress tolerance of P. tenuiflora, and analyzed gene expression profiles under these stresses. Physiological experiments revealed that P. tenuiflora can grow normally with maximum stress under 600 mmol/L NaCl and 150 mmol/L Na2 CO3 (pH 11.0) for 6 d. We identified 4,982 unigenes closely homologous to rice and barley. Furthermore, 1,105 genes showed differentially expressed profiles under salt and alkaline-salt treatments. Differentially expressed genes were overrepresented in functions of photosynthesis, oxidation reduction, signal transduction, and transcription regulation. Almost all genes downregulated under salt and alkaline-salt stress were related to cell structure, photosynthesis, and protein synthesis. Comparing with salt stress, alkaline-salt stress triggered more differentially expressed genes and significantly upregulated genes related to H(+) transport and citric acid synthesis. These data indicate common and diverse features of salt and alkaline-salt stress tolerance, and give novel insights into the molecular and physiological mechanisms of plant salt and alkaline-salt tolerance.

Comparative proteomic analysis of Puccinellia tenuiflora leaves under Na2CO3 stress

Soil salt-alkalinization is a widespread environmental stress that limits crop growth and agricultural productivity. The influence of soil alkalization caused by Na₂CO₃ on plants is more severe than that of soil salinization. Plants have evolved some unique mechanisms to cope with alkali stress; however, the plant alkaline-responsive signaling and molecular pathways are still unknown. In the present study, Na₂CO₃ responsive characteristics in leaves from 50-day-old seedlings of halophyte Puccinellia tenuiflora were investigated using physiological and proteomic approaches. Comparative proteomics revealed 43 differentially expressed proteins in P. tenuiflora leaves in response to Na₂CO₃ treatment for seven days. These proteins were mainly involved in photosynthesis, stress and defense, carbohydrate/energy metabolism, protein metabolism, signaling, membrane and transport. By integrating the changes of photosynthesis, ion contents, and stress-related enzyme activities, some unique Na₂CO₃ responsive mechanisms have been discovered in P. tenuiflora. This study provides new molecular information toward improving the alkali tolerance of cereals.

Molecular cloning and characterization of plasma membrane- and vacuolar-type Na⁺/H⁺ antiporters of an alkaline-salt-tolerant monocot, Puccinellia tenuiflora

A better understanding of salt tolerance in plants might lead to the genetic engineering of crops that can grow in saline soils. Here we cloned and characterized plasma membrane and vacuolar Na⁺/H⁺ antiporters of a monocotyledonous alkaline-tolerant halophyte, Puccinellia tenuiflora. The predicted amino acid sequence of the transporters were very similar to those of orthologs in monocotyledonous crops. Expression analysis showed that (1) NHA was more strongly induced by NaCl in the roots of P. tenuiflora while in rice it was rather induced in the shoots, suggesting that the role of NHA in salt excretion from the roots partly accounts for the difference in the tolerance of the two species, and that (2) NHXs were specifically induced by NaHCO₃ but not by NaCl in the roots of both species, suggesting that vacuolar-type Na⁺/H⁺ antiporters play roles in pH regulation under alkaline salt conditions. Overexpression of the antiporters resulted in increased tolerance of shoots to NaCl and roots to NaHCO₃. Overexpression lines exhibited a lower Na⁺ content and a higher K⁺ content in shoots under NaCl treatments, leading to a higher Na⁺/H⁺ ratio.

Physiological and proteomic analysis of salinity tolerance in Puccinellia tenuiflora

Soil salinity poses a serious threat to agriculture productivity throughout the world. Studying mechanisms of salinity tolerance in halophytic plants will provide valuable information for engineering plants for enhanced salt tolerance. Monocotyledonous Puccinellia tenuiflora is a halophytic species that widely distributed in the saline-alkali soil of the Songnen plain in northeastern China. Here we investigate the molecular mechanisms underlying moderate salt tolerance of P. tenuiflora using a combined physiological and proteomic approach. The changes in biomass, inorganic ion content, osmolytes, photosynthesis, defense-related enzyme activities, and metabolites in the course of salt treatment were analyzed in the leaves. Comparative proteomic analysis revealed 107 identities (representing 93 unique proteins) differentially expressed in P. tenuiflora leaves under saline conditions. These proteins were mainly involved in photosynthesis, stress and defense, carbohydrate and energy metabolism, protein metabolism, signaling, membrane, and transport. Our results showed that reduction of photosynthesis under salt treatment was attributed to the down-regulation of the light-harvesting complex (LHC) and Calvin cycle enzymes. Selective uptake of inorganic ions, high K(+)/Na(+) ratio, Ca(2+) concentration changes, and an accumulation of osmolytes contributed to ion balance and osmotic adjustment in leaf cells. Importantly, P. tenuiflora plants developed diverse reactive oxygen species (ROS) scavenging mechanisms in their leaves to cope with moderate salinity, including enhancement of the photorespiration pathway and thermal dissipation, synthesis of the low-molecular-weight antioxidant α-tocopherol, and an accumulation of compatible solutes. This study provides important information toward improving salt tolerance of cereals.

Analysis of transcriptional and upstream regulatory sequence activity of two environmental stress-inducible genes, NBS-Str1 and BLEC-Str8, of rice

Two abiotic stress-inducible upstream regulatory sequences (URSs) from rice have been identified and functionally characterized in rice. NBS-Str1 and BLEC-Str8 genes have been identified, by analysing the transcriptome data of cold, salt and desiccation stress-treated 7-day-old rice (Oryza sativa L. var. IR64) seedling, to be preferentially responsive to desiccation and salt stress, respectively. NBS-Str1 and BLEC-Str8 genes code for putative NBS (nucleotide binding site)-LRR (leucine rich repeat) and β-lectin domain protein, respectively. NBS-Str1 URS is induced in root tissue, preferentially in vascular bundle, during 3 and 24 h of desiccation stress condition in transgenic 7-day-old rice seedling. In mature transgenic plants, this URS shows induction in root and shoot tissue under desiccation stress as well as under prolonged (1 and 2 day) salt stress. BLEC-Str8 URS shows basal activity under un-stressed condition, however, it is inducible under salt stress condition in both root and leaf tissues in young seedling and mature plants. Activity of BLEC-Str8 URS has been found to be vascular tissue preferential, however, under salt stress condition its activity is also found in the mesophyll tissue. NBS-Str1 and BLEC-Str8 URSs are inducible by heavy metal, copper and manganese. Interestingly, both the URSs have been found to be non responsive to ABA treatment, implying them to be part of ABA-independent abiotic stress response pathway. These URSs could prove useful for expressing a transgene in a stress responsive manner for development of stress tolerant transgenic systems.

Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors

Transcriptome of Glycine soja leaf tissue during a detailed time course formed a foundation for examining transcriptional processes during NaHCO(3) stress treatment. Of a total of 2,310 detected differentially expressed genes, 1,664 genes were upregulated and 1,704 genes were downregulated at various time points. The number of stress-regulated genes increased dramatically after a 6-h stress treatment. GO category gene enrichment analysis revealed that most of the differentially expressed genes were involved in cell structure, protein synthesis, energy, and secondary metabolism. Another enrichment test revealed that the response of G. soja to NaHCO(3) highlights specific transcription factors, such as the C2C2-CO-like, MYB-related, WRKY, GARP-G2-like, and ZIM families. Co-expressed genes were clustered into ten classes (P < 0.001). Intriguingly, one cluster of 188 genes displayed a unique expression pattern that increases at an early stage (0.5 and 3 h), followed by a decrease from 6 to 12 h. This group was enriched in regulation of transcription components, including AP2-EREBP, bHLH, MYB/MYB-related, C2C2-CO-like, C2C2-DOF, C2C2, C3H, and GARP-G2-like transcription factors. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified 19 conserved motifs, potential binding sites for transcription factors. The appearance of ABA-responsive elements in the upstream of co-expression genes reveals that ABA-mediated signaling participates in the signal transduction in alkaline response.

Functional characterization of a plasma membrane Na+/H+ antiporter from alkali grass (Puccinellia tenuiflora)

We have cloned a Na(+)/H(+) antiporter gene (GenBank accession no EF440291, PtNHA1) from Puccinellia tenuiflora (so-called alkali grass in Chinese) roots under NaCl salt stress. Its cDNA is 3775 bp and contains a 3414 bp open reading frame. The amino acid sequences of PtNHA1 show high identities with a putative plasma membrane Na(+)/H(+) antiporter from wheat. PtNHA1 was predicted to contain 11 hypothetical transmembrane domains in the N-terminal part and to localize in the plasma membrane. Genomic DNA gel blot analysis shows that PtNHA1 is a single-copy gene in the alkali grass genome. PtNHA1 is highly expressed in leaves, roots and shoots by RNA gel blot analysis. Furthermore, PtNHA1 gene expression of alkali grass was clearly up-regulated by NaCl salt stress. Overexpression of PtNHA1 in Arabidopsis resulted in enhanced tolerance of transgenic plants to NaCl stress. The ion contents analysis shows that, compared with the wild-type (WT), less Na(+) and more K(+) were accumulated in transgenic plants under NaCl stress. The results indicate that PtNHA1 play an important role in NaCl salt stress. Additionally, compared with the WT, total activities of ascorbate peroxidase (APX) and catalase (CAT), two key reactive oxygen species (ROS) detoxifying enzymes were high in transgenic plants under salt stress, respectively. The transcript levels of two APX genes (Apx1, s/mApx) and two CAT genes (Cat1, Cat2) in transgenic plants were higher than those in WT. This suggests that overexpression of PtNHA1 results in enhanced ROS-scavenging enzymes of transgenic plants under NaCl salt stress.

Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment

BACKGROUND

Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of saline-alkaline stress transcriptome is mostly focused on saline (NaCl) stress and only limited information on alkaline (NaHCO3) stress is available.

RESULTS

Using Affymetrix Soybean GeneChip, we conducted transcriptional profiling on Glycine soja roots subjected to 50 mmol/L NaHCO3 treatment. In a total of 7088 probe sets, 3307 were up-regulated and 5720 were down-regulated at various time points. The number of significantly stress regulated genes increased dramatically after 3 h stress treatment and peaked at 6 h. GO enrichment test revealed that most of the differentially expressed genes were involved in signal transduction, energy, transcription, secondary metabolism, transporter, disease and defence response. We also detected 11 microRNAs regulated by NaHCO3 stress.

CONCLUSIONS

This is the first comprehensive wild soybean root transcriptome analysis under alkaline stress. These analyses have identified an inventory of genes with altered expression regulated by alkaline stress. The data extend the current understanding of wild soybean alkali stress response by providing a set of robustly selected, differentially expressed genes for further investigation.

Puccinellia tenuiflora maintains a low Na+ level under salinity by limiting unidirectional Na+ influx resulting in a high selectivity for K+ over Na+

Puccinellia tenuiflora is a useful monocotyledonous halophyte that might be used for improving salt tolerance of cereals. This current work has shown that P. tenuiflora has stronger selectivity for K+ over Na+ allowing it to maintain significantly lower tissue Na+ and higher K+ concentration than that of wheat under short- or long-term NaCl treatments. To assess the relative contribution of Na+ efflux and influx to net Na+ accumulation, unidirectional 22Na+ fluxes in roots were carried out. It was firstly found that unidirectional 22Na+ influx into root of P. tenuiflora was significantly lower (by 31-37%) than in wheat under 100 and 150 mM NaCl. P. tenuiflora had lower unidirectional Na+ efflux than wheat; the ratio of efflux to influx was similar between the two species. Leaf secretion of P. tenuiflora was also estimated, and found the loss of Na+ content from leaves to account for only 0.0006% of the whole plant Na+ content over 33 d of NaCl treatments. Therefore, it is proposed that neither unidirectional Na+ efflux of roots nor salt secretion by leaves, but restricting unidirectional Na+ influx into roots with a strong selectivity for K+ over Na+ seems likely to contribute to the salt tolerance of P. tenuiflora.

Characterization of two plasma membrane protein 3 genes (PutPMP3) from the alkali grass, Puccinellia tenuiflora, and functional comparison of the rice homologues, OsLti6a/b from rice

Two full-length cDNAs, PutPMP3-1 and PutPMP3-2, encoding PMP3 family proteins were isolated from Puccinellia tenuiflora, a monocotyledonous halophyte. Expression of both genes was induced by low temperature, salt stress, dehydration, ABA, and NaHCO(3). Transcripts of PutPMP3-2 were more strongly induced by these stresses relative to those of PutPMP3-1, particularly under low temperature and dehydration conditions. Expression of PutPMP3-1 and PutPMP3-2 in yeast mutants lacking the PMP3 gene can functionally complement the membrane hyperpolarization and salt sensitivity phenotypes resulting from PMP3 deletion. To compare the functions of PutPMP3-1 and PutPMP3-2, the orthologous genes in rice (OsLti6a and OsLti6b) were isolated. Both OsLti6a and OsLti6b could functionally complement the loss of PMP3 in yeast. PutPMP3-2 and OsLti6a were more effective in reversing membrane hyperpolarization than PutPMP3-1 and OsLti6b. However, the four yeast transformants each showed similar levels of salt tolerance. These results imply that these PMP3 family members don't function identically under different stress tolerance conditions.