Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles

Understanding the salinity resilience and productivity of halophytes in saline environments

The escalating salinity levels in cultivable soil pose a significant threat to agricultural productivity and, consequently, human sustenance. This problem is being exacerbated by natural processes and human activities, coinciding with a period of rapid population growth. Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. Evolution has created many close halophyte relatives of our major glycophytic crops, such as Puccinellia tenuiflora (relative of barley and wheat), Oryza coarctata (relative of rice) and Glycine soja (relative of soybean). There are also some halophytes have been subjected to semi-domestication and are considered as minor crops, such as Chenopodium quinoa. In this paper, we examine the prevailing comprehension of robust salinity resilience in halophytes. We summarize the existing strategies and technologies that equip researchers with the means to enhance the salt tolerance capabilities of primary crops and investigate the genetic makeup of halophytes.

Low-cost and reliable substrate-based phenotyping platform for screening salt tolerance of cutting propagation-dependent grass, paspalum vaginatum

BACKGROUND

Salt tolerance in plants is defined as their ability to grow and complete their life cycle under saline conditions. Staple crops have limited salt tolerance, but forage grass can survive in large unexploited saline areas of costal or desert land. However, due to the restriction of self-incompatible fertilization in many grass species, vegetative propagation via stem cuttings is the dominant practice; this is incompatible with current methodologies of salt-tolerance phenotyping, which have been developed for germination-based seedling growth. Therefore, the performance of seedlings from cuttings under salt stress is still fuzzy. Moreover, the morphological traits involved in salt tolerance are still mostly unknown, especially under experimental conditions with varying levels of stress.

RESULTS

To estimate the salt tolerance of cutting propagation-dependent grasses, a reliable and low-cost workflow was established with multiple saline treatments, using Paspalum vaginatum as the material and substrate as medium, where cold stratification and selection of stem segments were the two variables used to control for experimental errors. Average leaf number (ALN) was designated as the best criterion for evaluating ion-accumulated salt tolerance. The reliability of ALN was revealed by the consistent results among four P. vaginatum genotypes, and three warm-season (pearl millet, sweet sorghum, and wild maize) and four cold-season (barley, oat, rye, and ryegrass) forage cultivars. Dynamic curves simulated by sigmoidal mathematical models were well-depicted for the calculation of the key parameter, Salt50. The reliability of the integrated platform was further validated by screening 48 additional recombinants, which were previously generated from a self-fertile mutant of P. vaginatum. The genotypes displaying extreme ALN-based Salt50 also exhibited variations in biomass and ion content, which not only confirmed the reliability of our phenotyping platform but also the representativeness of the aerial ALN trait for salt tolerance.

CONCLUSIONS

Our phenotyping platform is proved to be compatible with estimations in both germination-based and cutting propagation-dependent seedling tolerance under salt stresses. ALN and its derived parameters are prone to overcome the species barriers when comparing salt tolerance of different species together. The accuracy and reliability of the developed phenotyping platform is expected to benefit breeding programs in saline agriculture.

PHT1;5 Repressed by ANT Mediates Pi Acquisition and Distribution under Low Pi and Salinity in Salt Cress

Salinity and phosphate (Pi) starvation are the most common abiotic stresses that threaten crop productivity. Salt cress (Eutrema salsugineum) displays good tolerance to both salinity and Pi limitation. Previously, we found several Phosphate Transporter (PHT) genes in salt cress upregulated under salinity. Here, EsPHT1;5 induced by both low Pi (LP) and salinity was further characterized. Overexpression of EsPHT1;5 in salt cress enhanced plant tolerance to LP and salinity, while the knock-down lines exhibited growth retardation. The analysis of phosphorus (P) content and shoot/root ratio of total P in EsPHT1;5-overexpressing salt cress seedlings and the knock-down lines as well as arsenate uptake assays suggested the role of EsPHT1;5 in Pi acquisition and root-shoot translocation under Pi limitation. In addition, overexpression of EsPHT1;5 driven by the native promoter in salt cress enhanced Pi mobilization from rosettes to siliques upon a long-term salt treatment. Particularly, the promoter of EsPHT1;5 outperformed that of AtPHT1;5 in driving gene expression under salinity. We further identified a transcription factor EsANT, which negatively regulated EsPHT1;5 expression and plant tolerance to LP and salinity. Taken together, EsPHT1;5 plays an integral role in Pi acquisition and distribution in plant response to LP and salt stress. Further, EsANT may be involved in the cross-talk between Pi starvation and salinity signaling pathways. This work provides further insight into the mechanism underlying high P use efficiency in salt cress in its natural habitat, and evidence for a link between Pi and salt signaling.

Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses

ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.

S-nitrosylation of RABG3E positively regulates vesicle trafficking to promote salt tolerance

Nitric oxide (NO) is a key signaling molecule affecting the response of plants to salt stress; however, the underlying molecular mechanism is poorly understood. In this study, we conducted a phenotype analysis and found that the small GTPase RABG3E (RAB7) promotes salt tolerance in Arabidopsis thaliana. NO promotes the S-nitrosylation of RAB7 at Cys-171, which in turn helps maintain the ion balance in salt-stressed plants. Furthermore, the S-nitrosylation of RAB7 at Cys-171 enhances the enzyme's GTPase activity, thereby promoting vesicle trafficking and increasing its interaction with phosphatidylinositol phosphates-especially phosphatidylinositol-4-phosphate (PI4P). Exogenously applied PI4P increases vesicle trafficking and promotes salt tolerance depending on the S-nitrosylation of RAB7 at Cys-171. These findings illustrate a unique mechanism in salt tolerance, by which NO regulates vesicle trafficking and ion homeostasis through the S-nitrosylation of RAB7 and its interaction with PI4P.

Effective root responses to salinity stress include maintained cell expansion and carbon allocation

Acclimation of root growth is vital for plants to survive salt stress. Halophytes are great examples of plants that thrive even under severe salinity, but their salt tolerance mechanisms, especially those mediated by root responses, are still largely unknown. We compared root growth responses of the halophyte Schrenkiella parvula with its glycophytic relative species Arabidopsis thaliana under salt stress and performed transcriptomic analysis of S. parvula roots to identify possible gene regulatory networks underlying their physiological responses. Schrenkiella parvula roots do not avoid salt and experience less growth inhibition under salt stress. Salt-induced abscisic acid levels were higher in S. parvula roots compared with Arabidopsis. Root transcriptomic analysis of S. parvula revealed the induction of sugar transporters and genes regulating cell expansion and suberization under salt stress. ¹⁴ C-labeled carbon partitioning analyses showed that S. parvula continued allocating carbon to roots from shoots under salt stress while carbon barely allocated to Arabidopsis roots. Further physiological investigation revealed that S. parvula roots maintained root cell expansion and enhanced suberization under severe salt stress. In summary, roots of S. parvula deploy multiple physiological and developmental adjustments under salt stress to maintain growth, providing new avenues to improve salt tolerance of plants using root-specific strategies.

A high-quality chromosome-level Eutrema salsugineum genome, an extremophile plant model

BACKGROUND

Eutrema salsugineum (2n = 14), a halophyte in the family Brassicaceae, is an attractive model to study abiotic stress tolerance in plants. Two versions of E. salsugineum genomes that previously reported were based on relatively short reads; thus, the repetitive regions were difficult to characterize.

RESULTS

We report the sequencing and assembly of the E. salsugineum (Shandong accession) genome using long-read sequencing and chromosome conformation capture data. We generated Oxford Nanopore long reads at high depth (> 60X) of genome coverage with additional short reads for error correction. The new assembly has a total size of 295.5 Mb with 52.8% repetitive sequences, and the karyotype of E. salsugineum is consistent with the ancestral translocation Proto-Calepineae Karyotype structure in both order and orientation. Compared with previous assemblies, this assembly has higher contiguity, especially in the centromere region. Based on this new assembly, we predicted 25,399 protein-coding genes and identified the positively selected genes associated with salt and drought stress responses.

CONCLUSION

The new genome assembly will provide a valuable resource for future genomic studies and facilitate comparative genomic analysis with other plants.

SHORT-ROOT and SCARECROW homologs regulate patterning of diverse cell types within and between species

The roles of SHORT-ROOT (SHR) and SCARECROW (SCR) in ground tissue patterning and differentiation have been well established in the root of Arabidopsis thaliana. Recently, work in additional organs and species revealed the extensive functional diversification of these genes, including regulation of cortical divisions essential for nodule organogenesis in legume roots, bundle sheath specification in the Arabidopsis leaf, patterning of inner leaf cell layers in maize, and stomatal development in rice. The co-option of distinct functions and cell types is attributed to different mechanisms, including paralog retention, spatiotemporal changes in gene expression, and novel protein functions. Elaborating our knowledge of the SHR-SCR module further unravels the developmental regulation that controls diverse forms and functions within and between species.

Overexpression of an aquaporin gene EsPIP1;4 enhances abiotic stress tolerance and promotes flowering in Arabidopsis thaliana

Aquaporins are water channel proteins that play an essential role in plant growth and development. Despite extensive functional characterization of aquaporins in model plants such as Arabidopsis, their contributions to abiotic stress tolerance in non-model plants are still poorly understood. As a close relative of Arabidopsis thaliana, Eutrema salsugineum is an excellent model for studying salt tolerance. Here, we identified and functionally characterized EsPIP1;4, a gene encoding a plasma membrane intrinsic protein (PIP) aquaporin in E. salsugineum. Overexpression of EsPIP1;4 in Arabidopsis improved seed germination and root growth of transgenic plants under abiotic stress, which was accompanied by an increase in proline accumulation, reduction in MDA, and decrease in the rate of ion leakage. Under abiotic stress, transgenic plants overexpressing EsPIP1;4 also showed increased antioxidant enzyme activity, and enhanced K⁺/Na⁺ ratio compared to control plants. Furthermore, overexpression of EsPIP1;4 promoted flowering by regulating genes in multiple flowering pathways. Together, our results demonstrated that an aquaporin from E. salsugineum improves abiotic stress tolerance and promotes flowering.

Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment

Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.

KLU/CYP78A5, a Cytochrome P450 Monooxygenase Identified via Fox Hunting, Contributes to Cuticle Biosynthesis and Improves Various Abiotic Stress Tolerances

Acquired osmotolerance after salt stress is widespread among Arabidopsis thaliana (Arabidopsis) accessions. Most salt-tolerant accessions exhibit acquired osmotolerance, whereas Col-0 does not. To identify genes that can confer acquired osmotolerance to Col-0 plants, we performed full-length cDNA overexpression (FOX) hunting using full-length cDNAs of halophyte Eutrema salsugineum, a close relative of Arabidopsis. We identified EsCYP78A5 as a gene that can confer acquired osmotolerance to Col-0 wild-type (WT) plants. EsCYP78A5 encodes a cytochrome P450 monooxygenase and the Arabidopsis ortholog is known as KLU. We also demonstrated that transgenic Col-0 plants overexpressing AtKLU (AtKLUox) exhibited acquired osmotolerance. Interestingly, KLU overexpression improved not only acquired osmotolerance but also osmo-shock, salt-shock, oxidative, and heat-stress tolerances. Under normal conditions, the AtKLUox plants showed growth retardation with shiny green leaves. The AtKLUox plants also accumulated higher anthocyanin levels and developed denser cuticular wax than WT plants. Compared to WT plants, the AtKLUox plants accumulated significantly higher levels of cutin monomers and very-long-chain fatty acids, which play an important role in the development of cuticular wax and membrane lipids. Endoplasmic reticulum (ER) stress induced by osmotic or heat stress was reduced in AtKLUox plants compared to WT plants. These findings suggest that KLU is involved in the cuticle biosynthesis, accumulation of cuticular wax, and reduction of ER stress induced by abiotic stresses, leading to the observed abiotic stress tolerances.

Dissecting the Molecular Regulation of Natural Variation in Growth and Senescence of Two Eutrema salsugineum Ecotypes

Salt cress (Eutrema salsugineum, aka Thellungiella salsuginea) is an extremophile and a close relative of Arabidopsis thaliana. To understand the mechanism of selection of complex traits under natural variation, we analyzed the physiological and proteomic differences between Shandong (SD) and Xinjiang (XJ) ecotypes. The SD ecotype has dark green leaves, short and flat leaves, and more conspicuous taproots, and the XJ ecotype had greater biomass and showed clear signs of senescence or leaf shedding with age. After 2-DE separation and ESI-MS/MS identification, between 25 and 28 differentially expressed protein spots were identified in shoots and roots, respectively. The proteins identified in shoots are mainly involved in cellular metabolic processes, stress responses, responses to abiotic stimuli, and aging responses, while those identified in roots are mainly involved in small-molecule metabolic processes, oxidation-reduction processes, and responses to abiotic stimuli. Our data revealed the evolutionary differences at the protein level between these two ecotypes. Namely, in the evolution of salt tolerance, the SD ecotype highly expressed some stress-related proteins to structurally adapt to the high salt environment in the Yellow River Delta, whereas the XJ ecotype utilizes the specialized energy metabolism to support this evolution of the short-lived xerophytes in the Xinjiang region.

Divergence in the ABA gene regulatory network underlies differential growth control

The phytohormone abscisic acid (ABA) is a central regulator of acclimation to environmental stress; however, its contribution to differences in stress tolerance between species is unclear. To establish a comparative framework for understanding how stress hormone signalling pathways diverge across species, we studied the growth response of four Brassicaceae species to ABA treatment and generated transcriptomic and DNA affinity purification and sequencing datasets to construct a cross-species gene regulatory network (GRN) for ABA. Comparison of genes bound directly by ABA-responsive element binding factors suggests that cis-factors are most important for determining the target loci represented in the ABA GRN of a particular species. Using this GRN, we reveal how rewiring of growth hormone subnetworks contributes to stark differences in the response to ABA in the extremophyte Schrenkiella parvula. Our study provides a model for understanding how divergence in gene regulation can lead to species-specific physiological outcomes in response to hormonal cues.

Eutrema EsMYB90 Gene Improves Growth and Antioxidant Capacity of Transgenic Wheat Under Salinity Stress

The ectopic expression of the EsMYB90 transcription factor gene from halophytic Eutrema salsugineum has been reported to enhance the level of anthocyanin and other flavonoid metabolites in transgenic tobacco. In this study, the wheat JW1 overexpressing EsMYB90 showed longer roots and higher fresh weight than that in wild type (WT) under salt stress. In addition, the transgenic wheat plants displayed significantly higher peroxidase (POD) and glutathione S-transferase (GST) activity, as well as markedly lower malondialdehyde (MDA) content than that of the WT during salt stress conditions. The analysis of histochemical staining and H₂O₂ level indicated that the accumulation of reactive oxygen species (ROS) was significantly lower in the roots of transgenic wheat plants compared to the WT under salt stress. Transcriptome analysis revealed that the EsMYB90 gene affected the expression of considerable amounts of stress-related genes that were involved in phenylpropanoid biosynthesis and antioxidant activity in transgenic plants subjected to NaCl treatment. Importantly, the significantly upregulated expression genes in transgenic wheat under salt stress were mainly associated with the antioxidative enzymes POD and GST encoding genes compared with the WT. Furthermore, EsMYB90 is suggested to bind with the MYB-binding elements of pTaANS2 and pTaDFR1 by dual luciferase assay, to activate the transcription of TaANS2 and TaDFR1 genes that are encoding key enzymes of anthocyanin biosynthesis in transgenic wheat plants. All the results indicated that, under salt stress, the EsMYB90 gene plays a crucial role in preventing wheat seedlings from oxidative stress damage via enhancing the accumulation of non-enzymatic flavonoids and activities of antioxidative enzymes, which suggested that EsMYB90 is an ideal candidate gene for the genetic engineering of crops.

Constitutive and Adaptive Traits of Environmental Stress Tolerance in the Threatened Halophyte Limonium angustebracteatum Erben (Plumbaginaceae)

Limonium angustebracteatum is a halophyte endemic to the E and SE Iberian Peninsula with interest in conservation. Salt glands represent an important adaptive trait in recretohalophytes like this and other Limonium species, as they allow the excretion of excess salts, reducing the concentration of toxic ions in foliar tissues. This study included the analysis of the salt gland structure, composed of 12 cells, 4 secretory and 8 accessory. Several anatomical, physiological and biochemical responses to stress were also analysed in adult plants subjected to one month of water stress, complete lack of irrigation, and salt stress, by watering with aqueous solutions of 200, 400, 600 and 800 mM NaCl. Plant growth was inhibited by the severe water deficit and, to a lesser extent, by high NaCl concentrations. A variation in the anatomical structure of the leaves was detected under conditions of salt and water stress; plants from the salt stress treatment showed salt glands sunken between epidermal cells, bordered by very large epidermal cells, whereas in those from the water stress treatment, the epidermal cells were heterogeneous in shape and size. In both, the palisade structure of the leaves was altered. Salt excretion is usually accompanied by the accumulation of salts in the foliar tissue. This was also found in L. angustebracteatum, in which the concentration of all ions analysed was higher in the leaves than in the roots. The increase of K⁺ in the roots of plants subjected to water stress was also remarkable. The multivariate analysis indicated differences in water and salt stress responses, such as the accumulation of Na and Cl, or proline, but K⁺ homeostasis played a relevant role in the mechanism of tolerance to both stressful conditions.

Mechanism of high affinity potassium transporter (HKT) towards improved crop productivity in saline agricultural lands

Glycophytic plants are susceptible to salinity and their growth is hampered in more than 40 mM of salt. Salinity not only affects crop yield but also limits available land for farming by decreasing its fertility. Presence of distinct traits in response to environmental conditions might result in evolutionary adaptations. A better understanding of salinity tolerance through a comprehensive study of how Na⁺ is transported will help in the development of plants with improved salinity tolerance and might lead to increased yield of crops growing in strenuous environment. Ion transporters play pivotal role in salt homeostasis and maintain low cytotoxic effect in the cell. High-affinity potassium transporters are the critical class of integral membrane proteins found in plants. It mainly functions to remove excess Na⁺ from the transpiration stream to prevent sodium toxicity in the salt-sensitive shoot and leaf tissues. However, there are large number of HKT proteins expressed in plants, and it is possible that these members perform in a wide range of functions. Understanding their mechanism and functions will aid in further manipulation and genetic transformation of different crops. This review focuses on current knowledge of ion selectivity and molecular mechanisms controlling HKT gene expression. The current review highlights the mechanism of different HKT transporters from different plant sources and how this knowledge could prove as a valuable tool to improve crop productivity.

Ecological and evolutionary diversification of sulphated polysaccharides in diverse photosynthetic lineages: A review

Sulphated polysaccharides (SPs) are carbohydrate macromolecules with sulphate esters that are found among marine algae, seagrasses, mangroves and some terrestrial plants. The sulphate concentration in the ocean (28 mM) since ancient time could have driven the production of SPs in marine algae. SPs have a gelatinous property that can protect marine algae against desiccation and salinity stress. Agar and carrageenan are red algal SPs that are widely used as gelling agents in the food and pharmaceutical industries. The information on the SPs from freshwater and land plants are limited. In this review, we reviewed the taxonomic distribution and composition of SPs in different photosynthetic lineages, and explored the association of SP production in these diversified photosynthetic organisms with evolution history and environmental stresses. We also reviewed the genes/proteins involved in SP biosynthesis. Insights into SP biosynthetic machinery may shed light on the evolution that accompanied adaptation to life on earth.

Genetic background and cis-organization regulate ALDH7B4 gene expression in Eutrema salsugineum: a promoter analysis case study

ALDH7B4 promoter analysis in A. thaliana and E. salsugineum reveals that both genetic background and promoter architecture contribute to gene expression in response to stress in different species. Many genes are differentially regulated in a comparison of salinity-sensitive and salinity-tolerant plant species. The aldehyde dehydrogenase 7B4 (ALDH7B4) gene is turgor-responsive in A. thaliana and encodes a highly conserved detoxification enzyme in plants. This study compared the ALDH7B4 gene in A. thaliana (salinity-sensitive) and in the salinity-tolerant close relative Eutrema salsugineum. EsALDH7B4 in E. salsugineum is the ortholog of AtALDH7B4 and the expression is also salinity, drought, and wound responsive. However, E. salsugineum requires higher salinity stress to induce the EsALDH7B4 transcriptional response. The GUS expression driven either by the promoter AtALDH7B4 or EsALDH7B4 was induced under 300 mM NaCl treatment in A. thaliana while 600 mM NaCl treatment was required in E. salsugineum, suggesting that the genetic background plays a crucial role in regulation of gene expression. Promoter sequences of ALDH7B4 are less conserved than the protein coding region. A series of EsALDH7B4 promoter deletion fragments were fused to the GUS reporter gene and promoter activity was determined in A. thaliana. The promoter region that contains two conserved ACGT-containing motifs was identified to be essential for stress induction. Furthermore, a 38 bp "TC" rich motif in the EsALDH7B4 promoter, absent from the AtALDH7B4 promoter, negatively affects EsALDH7B4 expression. A MYB-like transcription factor was identified to bind the "TC" motif and to repress the EsALDH7B4 promoter activity. This study reveals that genetic background and cis-acting elements coordinately regulate gene expression.

Cuticular lipids and associated gene expression analysis under NaCl stress in Thellungiella salsuginea

Cuticular lipids, including wax and cutin, protect plants against external environmental stress. The relationship between the cuticle properties and salt tolerance is not clear. In this article, photosynthetic and physiological characteristics related to water use and cuticle permeability were assessed in the leaves of Thellungiella salsuginea under NaCl stress. The chemical composition of wax and cutin monomers, and the expression of cuticle-associated genes were also analyzed. The results showed that the net photosynthetic rate and stomatal conductance in the leaves of T. salsuginea decreased, and the water use efficiency increased with increasing NaCl concentration. Salt stress caused a significant increase in total wax, but total cutin monomers only increased under high salt. Transcriptome sequencing and lipid metabolism pathway analysis were performed on rosette leaves of T. salsuginea after 24 h of NaCl treatment. We analyzed the expression of 42 genes involved in cuticle lipid metabolism, and found that most of them exhibited higher expression levels at 0.15 mol L^-1 NaCl, but lower expression levels at 0.3 mol L^-1 NaCl. The expression of 12 of these genes was further detected by qRT-PCR after 1 week of NaCl treatment: most of them were upregulated both under low and high NaCl stress. Hence, we speculate that the cuticle acts as an adaptive trait in T. salsuginea in salty environments.

Transcriptome Profiling of the Salt Stress Response in the Leaves and Roots of Halophytic Eutrema salsugineum

Eutrema salsugineum can grow in natural harsh environments; however, the underlying mechanisms for salt tolerance of Eutrema need to be further understood. Herein, the transcriptome profiling of Eutrema leaves and roots exposed to 300 mM NaCl is investigated, and the result emphasized the role of genes involved in lignin biosynthesis, autophagy, peroxisome, and sugar metabolism upon salt stress. Furthermore, the expression of the lignin biosynthesis and autophagy-related genes, as well as 16 random selected genes, was validated by qRT-PCR. Notably, the transcript abundance of a large number of lignin biosynthesis genes such as CCoAOMT, C4H, CCR, CAD, POD, and C3′H in leaves was markedly elevated by salt shock. And the examined lignin content in leaves and roots demonstrated salt stress led to lignin accumulation, which indicated the enhanced lignin level could be an important mechanism for Eutrema responding to salt stress. Additionally, the differentially expressed genes (DEGs) assigned in the autophagy pathway including Vac8, Atg8, and Atg4, as well as DEGs enriched in the peroxisome pathway such as EsPEX7, EsCAT, and EsSOD2, were markedly induced in leaves and/or roots. In sugar metabolism pathways, the transcript levels of most DEGs associated with the synthesis of sucrose, trehalose, raffinose, and xylose were significantly enhanced. Furthermore, the expression of various stress-related transcription factor genes including WRKY, AP2/ERF-ERF, NAC, bZIP, MYB, C2H2, and HSF was strikingly improved. Collectively, the increased expression of biosynthesis genes of lignin and soluble sugars, as well as the genes in the autophagy and peroxisome pathways, suggested that Eutrema encountering salt shock possibly possess a higher capacity to adjust osmotically and facilitate water transport and scavenge reactive oxidative species and oxidative proteins to cope with the salt environment. Thus, this study provides a new insight for exploring the salt tolerance mechanism of halophytic Eutrema and discovering new gene targets for the genetic improvement of crops.

Thylakoid proteome variation of Eutrema salsugineum in response to drought and salinity combined stress

It is well known that plant responses to stress involve different events occurring at different places of the cell/leaf and at different time scales in relation with the plant development. In fact, the organelles proteomes include a wide range of proteins that could include a wide range of proteins showing a considerable change in cellular functions and metabolism process. On this basis, a comparative proteomics analysis and fluorescence induction measurements were performed to investigate the photosynthetic performance and the relative thylakoid proteome variation in Eutrema salsugineum cultivated under salt stress (200 mM NaCl), water deficit stress (PEG) and combined treatment (PEG + NaCl) as a hyperosmotic stress. The obtained results showed a significant decrease of plant growth under drought stress conditions, with the appearance of some toxicity symptoms, especially in plants subjected to combined treatment. Application of salt or water stress alone showed no apparent change in the chlorophyll a fluorescence transients, primary photochemistry (fluorescence kinetics of the O-J phase), the PQ pool state (J-I phase changes), (Fv/Fm) and (Fk/Fj) ratios. However, a considerable decrease of all these parameters was observed under severe osmotic stress (PEG + NaCl). The thylakoid proteome analysis revealed 58 proteins showing a significant variation in their abundance between treatments (up or down regulation). The combined treatment (PEG + NaCl) induced a decrease in the expression of the whole PSII core subunit (D1, D2, CP43, CP47, PsbE and PsbH), whereas the OEC subunits proteins remained constant. An increase in the amount of PsaD, PsaE, PsaF, PsaH, PsaK and PsaN was detected under drought stress (PEG5%). No significant change in the accumulation of Cyt b6 and Cyt f was observed. Some regulated proteins involved in cellular redox homeostasis were detected (glutamine synthetase, phosphoglycerate kinase, transketolase), and showed a significant decrease under the combined treatment. Some oxidative stress related proteins were significantly up-regulated under salt or drought stress and could play a crucial role in the PSI photoprotection and the control of ROS production level.

Root Patterning: Tuning SHORT ROOT Function Creates Diversity in Form

Roots have a fundamental role in plant growth and adaptation to different environments. Diversity in root morphology and architecture enables plants to acquire water and nutrients in contrasting substrate conditions, resist biotic and abiotic stress, and develop symbiotic associations. At its most fundamental level, morphology is determined by discrete changes in tissue patterning. Differences in the number and arrangement of the cell layers in the root can change tissue structure, as well as root length and girth, affecting important productivity traits. Therefore, understanding the molecular mechanisms controlling variation in developmental patterning is an important goal in biology. The ground tissue (GT) system is an ideal model to study the genetic basis of morphological diversity because it displays great interspecific variability in cell layer number. In addition, the genetic circuit controlling GT patterning in Arabidopsis thaliana has been well described, although little is known about species with more complex root anatomies. In this review, we will describe the Arabidopsis model for root radial patterning and present recent progress in elucidating the genetic circuitry controlling GT patterning in monocots and the legume Medicago truncatula (Mt), species that develop roots with more complex anatomies and multilayered cortex.

Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum

Eutrema salsugineum has long been used as the model for examining salt and other abiotic stress in plants. In addition to the forward genetics approaches widely used in the lab, natural variations undoubtedly will provide a rich genetic resource for studying molecular mechanisms underlying the stress tolerance and local adaptation of this species. We used 90 resequencing whole genomes of natural populations of this species across its Asian and North American distributions to detect the selection signals for genes involved in salt and other stresses at the species-range level and local distribution. We detected selection signals for genes involved in salt and other abiotic tolerance at the species level. In addition, several cold-induced and defense genes showed selection signals due to local adaptation in North America-NE Russia or northern China, respectively. These variations and findings provide valuable resources for further deciphering genetic mechanisms underlying the stress tolerance and local adaptations of this model species.

Copy number analyses of DNA repair genes reveal the role of poly(ADP-ribose) polymerase (PARP) in tree longevity

Long-lived organisms are exposed to the risk of accumulating mutations due to DNA damage. Previous studies in animals have revealed the positive relationship between the copy number of DNA repair genes and longevity. However, the role of DNA repair in the lifespan of plants remains poorly understood. Using the recent accumulation of the complete genome sequences of diverse plant species, we performed systematic comparative analyses of the copy number variations of DNA repair genes in 61 plant species with different lifespans. Among 121 DNA repair gene families, PARP gene family was identified as a unique gene that exhibits significant expansion in trees compared to annual and perennial herbs. Among three paralogs of plant PARPs, PARP1 showed a close association with growth rate. PARPs catalyze poly(ADP-ribosyl)ation and play pivotal roles in DNA repair and antipathogen defense. Our study suggests the conserved role of PARPs in longevity between plants and animals.

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Comparing the copy number variations of DNA repair genes in diverse plant species

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PARP gene family showed higher copy number in trees compared to herbs

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There was negative correlation between copy number of PARP1 and growth rate in trees

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Increased copy number of PARP would be evolutionary favored in plant longevity

Molecular cloning and characterization of high-affinity potassium transporter (AlHKT2;1) gene promoter from halophyte Aeluropus lagopoides

HKT subfamily II functions as Na⁺- K⁺ co-transporter and prevents plants from salinity stress. A 760 bp promoter region of AlHKT2;1 was isolated, sequenced and cloned. The full length promoter D1, has many cis-regulatory elements like MYB, MBS, W box, ABRE etc. involved in abiotic stress responses. D1 and subsequent 5' deletions were cloned into pCAMBIA1301 and studied for its efficacy in stress conditions in heterologous system. Blue colour staining was observed in flower petals, anther lobe, and dehiscence slit of anther in T₀ plants. The T₁ seedlings showed staining in leaf veins, shoot vasculature and root except root tip. T₁ seedlings were subjected to NaCl, KCl, NaCl + KCl and ABA stresses. GUS activity was quantified by 4-methylumbelliferyl glucuronide (4-MUG) assay under control and stress conditions. The smallest deletion- D4 also showed GUS expression but highest activity was observed in D2 as compared to full length promoter and other deletions. The electrophoretic mobility shift assay using stress-induced protein with different promoter deletions revealed more prominent binding in D2. These results suggest that AlHKT2;1 promoter is involved in abiotic stress response and deletion D2 might be sufficient to drive the stress-inducible expression of various genes involved in providing stress tolerance in plants.

Halophytes and other molecular strategies for the generation of salt-tolerant crops

The current increase in salinity can intensify the disparity between potential and actual crop yields, thus affecting economies and food security. One of the mitigating alternatives is plant breeding via biotechnology, where advances achieved so far are significant. Considering certain aspects when developing studies related to plant breeding can determine the success and accuracy of experimental design. Besides this strategy, halophytes with intrinsic and efficient abilities against salinity can be used as models for improving the response of crops to salinity stress. As crops are mostly glycophytes, it is crucial to point out the molecular differences between these two groups of plants, which may be the key to guiding and optimizing the transformation of glycophytes with halophytic tolerance genes. Therefore, this can broaden perspectives in the trajectory of research towards the cultivation, commercialization, and consumption of salt-tolerant crops on a large scale.

HKT sodium and potassium transporters in Arabidopsis thaliana and related halophyte species

High salinity induces osmotic stress and often leads to sodium ion-specific toxicity, with inhibitory effects on physiological, biochemical and developmental pathways. To cope with increased Na⁺ in soil water, plants restrict influx, compartmentalize ions into vacuoles, export excess Na⁺ from the cell, and distribute ions between the aerial and root organs. In this review, we discuss our current understanding of how high-affinity K⁺ transporters (HKT) contribute to salinity tolerance, focusing on HKT1-like family members primarily involved in long-distance transport, and in the recent research in the model plant Arabidopsis and its halophytic counterparts of the Eutrema genus. Functional characterization of the salt overly sensitive (SOS) pathway and HKT1-type transporters in these species indicate that they utilize similar approaches to deal with salinity, regardless of their tolerance.

Two subgroups of receptor-like kinases promote early compatible pollen responses in the Arabidopsis thaliana pistil

In flowering plants, cell-cell communication between the compatible pollen grain/growing pollen tube and the pistil is an essential component for successful sexual reproduction. In Arabidopsis thaliana, the later stages of this dialogue are mediated by several peptide ligands and receptors that guide pollen tubes to the ovules for the release of sperm cells. Despite a detailed understanding of these processes, a key gap remains regarding the nature of the regulators that function at the earlier stages which are essential steps leading to fertilization. Here, we report on new functions for A. thaliana Receptor-Like Kinase (RLK) genes belonging to the LRR-II and LRR-VIII-2 RLK subgroups in the female reproductive tract to regulate compatible pollen hydration and the early stages of pollen tube growth. Mutant pistils for the A. thaliana RKF1 gene cluster were observed to support reduced wild-type pollen hydration and, when combined with the SERK1 and SERK3/BAK1 mutations, reduced pollen tube travel distances occurred. As these mutant pistils displayed a wild-type morphology, we propose that the observed altered compatible pollen responses result from an impaired pollen-pistil dialogue at these early stages.

Cytokinetic and anatomical analysis of Thellungiella botschantzevii meristem cells in high concentrations of NaCl and Na2SO4

The study of cytokinetic and anatomical properties of the extramophile plant Thellungiella botschantzevii (German) at high concentrations of NaCl and Na2SO4 and without them (control) allowed to identify structural and functional transformations at the cellular level and evaluate the effect of salinity. Cytophotometric method showed the accumulation of cells in the root meristem in G1 and S stages, which indicated the adaptation of Thellungiella botschantzevii to high concentrations of NaCl and Na2SO4. A high level of ploidy (up to 16C) and the maximum number of polyploid cells at the level of 4C and 8C gave the plant stability. Anatomical characteristics of Thellungiella botschantzevii root and leaf were obtained on semi-thin and ultra-thin sections, and accumulation of lipid and protein inclusions in the root cell was determined. The data obtained indicate that Thellungiella botschantzevii is a unique model for various kinds of research, including genetic research, and can help to develop proposals for increasing resistance in crops.

Overexpression of a Eutrema salsugineum phosphate transporter gene EsPHT1;4 enhances tolerance to low phosphorus stress in soybean

OBJECTIVE

To enhance Pi absorption and utilization efficiency of soybean, a member of PHT1 gene family was isolated and characterized from E. salsugineum, which was a homologous gene of AtPHT1;4 and consequently designated as EsPHT1;4.

RESULTS

Quantitative real-time PCR (qRT-PCR) analysis showed that the transcript level of EsPHT1;4 significantly increased both in roots and leaves of E. salsugineum under Pi deficient conditions. Furthermore, EsPHT1;4 was transferred to soybean cultivar "YD22" using an Agrobacterium-mediated cotyledonary-node transformation method. Overexpression of EsPHT1;4 in soybean not only promoted the increase of plant biomass and yield of transgenic plants upon low P stress, but also increased the accumulation and transportation of Pi from roots to leaves in the transgenic soybean lines.

CONCLUSION

EsPHT1;4 was critical for controlling the accumulation and translocation of Pi in plants, and can be subsequently used as an effective foreign gene for the improvement of P use efficiency of crops by genetic manipulation.

Abiotic stress signalling in extremophile land plants

Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.

Plant science's next top models

BACKGROUND

Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models.

SCOPE

Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers.

CONCLUSIONS

Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.

Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

Background

The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has become an important objective for crop improvement. Some wild crop relatives have adapted to extreme osmotic stresses and can provide valuable insights into traits and genetic signatures that can guide efforts to improve crop tolerance to water deficits. Eutrema salsugineum, a close relative of many cruciferous crops, is a halophytic plant and extremophyte model for abiotic stress research.

Results

Using comparative transcriptomics, we show that two E. salsugineum ecotypes display significantly different transcriptional responses towards a two-stage drought treatment. Even before visibly wilting, water deficit led to the differential expression of almost 1,100 genes for an ecotype from the semi-arid, sub-arctic Yukon, Canada, but only 63 genes for an ecotype from the semi-tropical, monsoonal, Shandong, China. After recovery and a second drought treatment, about 5,000 differentially expressed genes were detected in Shandong plants versus 1,900 genes in Yukon plants. Only 13 genes displayed similar drought-responsive patterns for both ecotypes. We detected 1,007 long non-protein coding RNAs (lncRNAs), 8% were only expressed in stress-treated plants, a surprising outcome given the documented association between lncRNA expression and stress. Co-expression network analysis of the transcriptomes identified eight gene clusters where at least half of the genes in each cluster were differentially expressed. While many gene clusters were correlated to drought treatments, only a single cluster significantly correlated to drought exposure in both ecotypes.

Conclusion

Extensive, ecotype-specific transcriptional reprogramming with drought was unexpected given that both ecotypes are adapted to saline habitats providing persistent exposure to osmotic stress. This ecotype-specific response would have escaped notice had we used a single exposure to water deficit. Finally, the apparent capacity to improve tolerance and growth after a drought episode represents an important adaptive trait for a plant that thrives under semi-arid Yukon conditions, and may be similarly advantageous for crop species experiencing stresses attributed to climate change.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

How to choose your research organism

Despite August Krogh's famous admonition that a 'convenient' organism exists for every biological problem, we argue that appeals to 'convenience' are not sufficient to capture reasoning about organism choice. Instead, we offer a detailed analysis based on empirical data and philosophical arguments for a working set of twenty criteria that interact with each other in the highly contextualized judgements that biologists make about organism choice. We propose to think of these decisions as a form of 'differential analysis' where researchers weigh multiple criteria for organismal choice against each other, and often utilize multidimensional refinement processes to finalize their choices. The specific details of any one case make it difficult to draw generalizations or to abstract away from specific research situations. However, this analysis of criteria for organismal choice and how these are related in practice allows us to reflect more generally on what makes a particular organism useful or 'good.'

Modulation of Energy Metabolism Is Important for Low-Oxygen Stress Adaptation in Brassicaceae Species

Low-oxygen stress, mainly caused by soil flooding, is a serious abiotic stress affecting crop productivity worldwide. To understand the mechanisms of low-oxygen stress responses and adaptation of plants, we characterized and compared low-oxygen responses in six species with different accessions of the Brassicaceae family. Based on the growth and survival responses to submergence or low-oxygen condition, these accessions could be divided into three groups: (i) Highly tolerant species (Rorippa islandica and Arabis stelleri); (ii) moderately tolerant species (Arabidopsis thaliana [esk-1, Ler, Ws and Col-0 ecotype]); and (iii) intolerant species (Thlaspi arvense, Thellungiella salsuginea [Shandong and Yukon ecotype], and Thellungiella parvula). Gene expression profiling using Operon Arabidopsis microarray was carried out with RNA from roots of A. thaliana (Col-0), A. stelleri, R. islandica, and T. salsuginea (Shandong) treated with low-oxygen stress (0.1% O2/99.9% N2) for 0, 1, 3, 8, 24, and 72 h. We performed a comparative analysis of the gene expression profiles using the gene set enrichment analysis (GSEA) method. Our comparative analysis suggested that under low-oxygen stress each species distinctively reconfigures the energy metabolic pathways including sucrose-starch metabolism, glycolysis, fermentation and nitrogen metabolism, tricarboxylic acid flow, and fatty acid degradation via beta oxidation and glyoxylate cycle. In A. thaliana, a moderately tolerant species, the dynamical reconfiguration of energy metabolisms occurred in the early time points of low-oxygen treatment, but the energy reconfiguration in the late time points was not as dynamic as in the early time points. Highly tolerant A. stelleri appeared to have high photosynthesis capacity that could produce more O2 and in turn additional ATP energy to cope with energy depletion caused by low-oxygen stress. R. islandica seemed to retain some ATP energy produced by anaerobic energy metabolism during a prolonged period of low-oxygen conditions. Intolerant T. salsuginea did not show significant changes in the expression of genes involved in anaerobic energy metabolisms. These results indicate that plants developed different energy metabolisms to cope with the energy crisis caused by low-oxygen stress.

The relationship between cuticular lipids and associated gene expression in above ground organs of Thellungiella salsugineum (Pall.) Al-Shehbaz & Warwick

The cuticle plays a critical role as barrier between plant and environment. Here, cuticular wax morphology, cuticular wax and cutin monomer composition, and expression of associated genes in five above ground organs were examined in model extremophyte Thellungiella salsugineum. Alkanes, ketones, and 2-alcohols were the predominant wax constitutes in rosette leaves, inflorescence stem leaves, stems, and siliques, whereas alkanes and acids were the predominant cuticular lipids in whole flowers. Unsubstituted acids were the most abundant cutin monomers in vegetative organs, especially C18:2 dioic acids, which reached the highest levels in stems. Hydroxy fatty acids were the predominant cutin monomers in flowers, especially 16-OH C16:0 and diOH C16:0. High-throughput RNA-Seq analysis using the Hiseq4000 platform was performed on these five above organs of T. salsugineum, and the differentially expressed lipid-associated genes and their associated metabolic pathways were identified. Expression of genes associated in previous reports to cuticle production, including those having roles in cuticle lipid biosynthesis, transport, and regulation were examined. The association of cuticle lipid composition and gene expression within different organs of T. salsugineum, and potential relationships between T. salsugineum's extreme cuticle and its adaptation to extreme environments is discussed.

Chemical and Transcriptomic Analysis of Cuticle Lipids under Cold Stress in Thellungiella salsuginea

Plant cuticle lipids form outer protective layers to resist environmental stresses; however, the relationship between cuticle properties and cold tolerance is unclear. Here, the extremophyte Thellungiella salsuginea was stressed under cold conditions (4 °C) and the cuticle of rosette leaves was examined in terms of epicuticular wax crystal morphology, chemical composition, and cuticle-associated gene expression. The results show that cold induced formation of distinct lamellas within the cuticle ultrastructure. Cold stress caused 14.58% and 12.04% increases in the amount of total waxes and cutin monomer per unit of leaf area, respectively, probably associated with the increase in total fatty acids. The transcriptomic analysis was performed on rosette leaves of Thellungiella exposed to cold for 24 h. We analyzed the expression of 72 genes putatively involved in cuticle lipid metabolism, some of which were validated by qRT-PCR (quantitative reverse transcription PCR) after both 24 h and one week of cold exposure. Most cuticle-associated genes exhibited higher expression levels under cold conditions, and some key genes increased more dramatically over the one week than after just 24 h, which could be associated with increased amounts of some cuticle components. These results demonstrate that the cuticle provides some aspects of cold adaptation in T. salsuginea.

Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)

Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237-323 amino acids, with a theoretical molecular weight (MW) of 24.31-31.80 kDa and an isoelectric point (pI) value of 4.73-10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger's position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.

Global transcriptome analysis provides new insights in Thellungiella salsuginea stress response

Thellungiella salsuginea is highly tolerant to abiotic stress, while its a close relative Arabidopsis thaliana is sensitive to stress. This characteristic makes T. salsuginea an excellent model for uncovering the mechanisms of abiotic stress tolerance. Abscisic acid (ABA) plays essential roles in plant abiotic and biotic stress tolerance. To test the changes in gene expression of T. salsuginea under ABA treatment, in this study, the transcriptomes of T. salsuginea roots and leaves were compared in response to exogenously application of ABA. The results showed that ABA treatment caused different expression of 2,200 and 3,305 genes in leaves and roots, respectively, compared with the untreated control. In particular, genes encoding transcription factors such as WRKY, MYB, NAC, GATA, ethylene-responsive factors (ERFs), heat stress transcription factors, basic helix-loop-helix, PLATZ and B3 domain-containing family members were enriched. In addition, 49 and 114 differentially expressed genes were identified as ABA-regulated genes, separately in leaves and roots, respectively, which were related to biotic and abiotic stresses. The expression levels of some genes were validated by qRT-PCR. Different responses of genes to ABA treatment were discovered in T. salsuginea and A. thaliana. This transcriptome analysis expands our understanding of the role of ABA in stress tolerance in T. salsuginea. Our study provides a wealth of information for improving stress tolerance in crop plants.

Comparative expression analysis of heavy metal ATPase subfamily genes between Cd-tolerant and Cd-sensitive turnip landraces

The heavy metal ATPase (HMA) subfamily is mainly involved in heavy metal (HM) tolerance and transport in plants, but an understanding of the definite roles and mechanisms of most HMA members are still limited. In the present study, we identified 14 candidate HMA genes named BrrHMA1-BrrHMA8 from the turnip genome and analyzed the phylogeny, gene structure, chromosome distribution, and conserved domains and motifs of HMAs in turnip (Brassica rapa var. rapa). According to our phylogenetic tree, the BrrHMAs are divided into a Zn/Cd/Co/Pb subclass and Cu/Ag subclass. The BrrHMA members show similar structural characteristics within subclasses. To explore the roles of BrrHMAs in turnip, we compared the gene sequences and expression patterns of the BrrHMA genes between a Cd-tolerant landrace and a Cd-sensitive landrace. Most BrrHMA genes showed similar spatial expression patterns in both Cd-tolerant and Cd-sensitive turnip landraces; some BrrHMA genes, however, were differentially expressed in specific tissue in Cd-tolerant and Cd-sensitive turnip. Specifically, BrrHMA genes in the Zn/Cd/Co/Pb subclass shared the same coding sequence but were differentially expressed in Cd-tolerant and Cd-sensitive turnip landraces under Cd stress. Our findings suggest that the stable expression and up-regulated expression of BrrHMA Zn/Cd/Co/Pb subclass genes under Cd stress may contribute to the higher Cd tolerance of turnip landraces.

Drought resistance is mediated by divergent strategies in closely related Brassicaceae

Droughts cause severe crop losses worldwide and climate change is projected to increase their prevalence in the future. Similar to the situation for many crops, the reference plant Arabidopsis thaliana (Ath) is considered drought-sensitive, whereas, as we demonstrate, its close relatives Arabidopsis lyrata (Aly) and Eutrema salsugineum (Esa) are drought-resistant. To understand the molecular basis for this plasticity we conducted a deep phenotypic, biochemical and transcriptomic comparison using developmentally matched plants. We demonstrate that Aly responds most sensitively to decreasing water availability with early growth reduction, metabolic adaptations and signaling network rewiring. By contrast, Esa is in a constantly prepared mode as evidenced by high basal proline levels, ABA signaling transcripts and late growth responses. The stress-sensitive Ath responds later than Aly and earlier than Esa, although its responses tend to be more extreme. All species detect water scarcity with similar sensitivity; response differences are encoded in downstream signaling and response networks. Moreover, several signaling genes expressed at higher basal levels in both Aly and Esa have been shown to increase water-use efficiency and drought resistance when overexpressed in Ath. Our data demonstrate contrasting strategies of closely related Brassicaceae to achieve drought resistance.

Metabolomics in Plant Stress Physiology

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

Landscape of gene transposition-duplication within the Brassicaceae family

We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition-duplication (tr-d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. These were derived from older tr-d events and had a higher chance of being expressed. We also found an enrichment of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3 that relate to their adaptive evolution. CLfinder-OrthNet provides a flexible toolkit to compare gene order, visualize evolutionary paths among orthologues as networks, and identify gene loci that share an evolutionary history.

Linking Duplication of a Calcium Sensor to Salt Tolerance in Eutrema salsugineum

The SALT-OVERLY-SENSITIVE (SOS) pathway in Arabidopsis (Arabidopsis thaliana) functions to prevent the toxic accumulation of sodium in the cytosol when plants are grown in salt-affected soils. In this pathway, the CALCINEURIN B-LIKE10 (AtCBL10) calcium sensor interacts with the AtSOS2 kinase to activate the AtSOS1 plasma membrane sodium/proton exchanger. CBL10 has been duplicated in Eutrema (Eutrema salsugineum), a salt-tolerant relative of Arabidopsis. Because Eutrema maintains growth in salt-affected soils that kill most crop plants, the duplication of CBL10 provides a unique opportunity to functionally test the outcome of gene duplication and its link to plant salt tolerance. In Eutrema, individual down-regulation of the duplicated CBL10 genes (EsCBL10a and EsCBL10b) decreased growth in the presence of salt and, in combination, led to an even greater decrease, suggesting that both genes function in response to salt and have distinct functions. Cross-species complementation assays demonstrated that EsCBL10b has an enhanced ability to activate the SOS pathway while EsCBL10a has a function not performed by AtCBL10 or EsCBL10b Chimeric EsCBL10a/EsCBL10b proteins revealed that the specific functions of the EsCBL10 proteins resulted from changes in the amino terminus. The duplication of CBL10 increased calcium-mediated signaling capacity in Eutrema and conferred increased salt tolerance to salt-sensitive Arabidopsis.

Role and Functional Differences of HKT1-Type Transporters in Plants under Salt Stress

Abiotic stresses generally cause a series of morphological, biochemical and molecular changes that unfavorably affect plant growth and productivity. Among these stresses, soil salinity is a major threat that can seriously impair crop yield. To cope with the effects of high salinity on plants, it is important to understand the mechanisms that plants use to deal with it, including those activated in response to disturbed Na⁺ and K⁺ homeostasis at cellular and molecular levels. HKT1-type transporters are key determinants of Na⁺ and K⁺ homeostasis under salt stress and they contribute to reduce Na⁺-specific toxicity in plants. In this review, we provide a brief overview of the function of HKT1-type transporters and their importance in different plant species under salt stress. Comparison between HKT1 homologs in different plant species will shed light on different approaches plants may use to cope with salinity.

Crassulacean Acid Metabolism Abiotic Stress-Responsive Transcription Factors: a Potential Genetic Engineering Approach for Improving Crop Tolerance to Abiotic Stress

This perspective paper explores the utilization of abiotic stress-responsive transcription factors (TFs) from crassulacean acid metabolism (CAM) plants to improve abiotic stress tolerance in crop plants. CAM is a specialized type of photosynthetic adaptation that enhances water-use efficiency (WUE) by shifting CO2 uptake to all or part of the nighttime when evaporative water losses are minimal. Recent studies have shown that TF-based genetic engineering could be a useful approach for improving plant abiotic stress tolerance because of the role of TFs as master regulators of clusters of stress-responsive genes. Here, we explore the use of abiotic stress-responsive TFs from CAM plants to improve abiotic stress tolerance and WUE in crops by controlling the expression of gene cohorts that mediate drought-responsive adaptations. Recent research has revealed several TF families including AP2/ERF, MYB, WRKY, NAC, NF-Y, and bZIP that might regulate water-deficit stress responses and CAM in the inducible CAM plant Mesembryanthemum crystallinum under water-deficit stress-induced CAM and in the obligate CAM plant Kalanchoe fedtschenkoi. Overexpression of genes from these families in Arabidopsis thaliana can improve abiotic stress tolerance in A. thaliana in some instances. Therefore, we propose that TF-based genetic engineering with a small number of CAM abiotic stress-responsive TFs will be a promising strategy for improving abiotic stress tolerance and WUE in crop plants in a projected hotter and drier landscape in the 21st-century and beyond.

Friend or Foe? Chloride Patterning in Halophytes

In this opinion article, we challenge the traditional view that breeding for reduced Cl^- uptake would benefit plant salinity tolerance. A negative correlation between shoot Cl^- concentration and plant biomass does not hold for halophytes - naturally salt tolerant species. We argue that, under physiologically relevant conditions, Cl^- uptake requires plants to invest metabolic energy, and that the poor selectivity of Cl^--transporting proteins may explain the reported negative correlation between Cl^- accumulation and crop salinity tolerance. We propose a new paradigm: salinity tolerance could be achieved by improving the selectivity of some of the broadly selective anion-transporting proteins (e.g., for NO₃^->Cl^-), alongside tight control of Cl^- uptake, rather than targeting traits mediating its efflux from the root.