Understanding molecular mechanism of higher plant plasticity under abiotic stress

Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat

Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies have identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.

Whole-Transcriptome Profiling and Functional Prediction of Long Non-Coding RNAs Associated with Cold Tolerance in Japonica Rice Varieties

Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures has not been reported. Therefore, in this study, antioxidant physiological indices were combined with whole-transcriptome data through weighted correlation network analysis, which found that the gene modules had the highest correlation with the key antioxidant enzymes superoxide dismutase and peroxidase. The hub genes of the superoxide dismutase-related module included the UDP-glucosyltransferase family protein, sesquiterpene synthase and indole-3-glycerophosphatase gene. The hub genes of the peroxidase-related module included the WRKY transcription factor, abscisic acid signal transduction pathway-related gene plasma membrane hydrogen-ATPase and receptor-like kinase. Therefore, we selected the modular hub genes and significantly enriched the metabolic pathway genes to construct the key competitive endogenous RNA networks, resulting in three competitive endogenous RNA networks of seven long non-coding RNAs regulating three co-expressed messenger RNAs via four microRNAs. Finally, the negative regulatory function of the WRKY transcription factor OsWRKY61 was determined via subcellular localization and validation of the physiological indices in the mutant.

Physiochemical Responses and Ecological Adaptations of Peach to Low-Temperature Stress: Assessing the Cold Resistance of Local Peach Varieties from Gansu, China

In recent years, extreme weather events have become increasingly frequent, and low winter temperatures have had a significant impact on peach cultivation. The selection of cold-resistant peach varieties is an effective solution to mitigate freezing damage. To comprehensively and accurately evaluate the cold resistance of peaches and screen for high cold resistance among Gansu local resources, nine different types of peach were selected as test resources to assess physiological, biochemical, and anatomical indices. Subsequently, 28 peach germplasms were evaluated using relevant indices. The semi-lethal temperature (LT50) was calculated by fitting the change curve of the electrolyte leakage index (ELI) with the Logistic equation; this can be used as an important index for identifying and evaluating the cold resistance of peach trees. The LT50 values ranged from -28.22 °C to -17.22 °C among the 28 tested resources; Dingjiaba Liguang Tao exhibited the lowest LT50 value at -28.22 °C, indicating its high level of cold resistance. The LT50 was positively correlated with the ELI and malondialdehyde (MDA) content with correlation coefficients of 0.894 and 0.863, respectively, while it was negatively correlated with the soluble sugar (SS), soluble protein (SP), and free proline (Pro) contents with correlation coefficients of -0.894, -0.721, and -0.863, respectively. The thicknesses of the xylem, cork layer, cork layer ratio (CLR) and thickness/cortex thickness (X/C) showed negative correlations (-0.694, -0.741, -0.822, -0.814, respectively). Finally, the membership function method was used to evaluate cold resistance based on the ELI, MDA, Pro, SP, SS, CLR, and xylem thickness/cortex thickness (X/C) indices. The average membership degree among all tested resources ranged from 0.17 to 0.61. Dingjiaba Liguang Tao emerged prominently in terms of high-cold-resistance (HR) membership value (0.61).

Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae)

High levels of phenotypic plasticity are thought to be inherently costly in stable or extreme environments, but enhanced plasticity may evolve as a response to new environments and foster novel phenotypes. Heliosperma pusillum forms glabrous alpine and pubescent montane ecotypes that diverged recurrently and polytopically (parallel evolution) and can serve as evolutionary replicates. The specific alpine and montane localities are characterized by distinct temperature conditions, available moisture, and light. Noteworthy, the ecotypes show a home-site fitness advantage in reciprocal transplantations. To disentangle the relative contribution of constitutive versus plastic gene expression to altitudinal divergence, we analyze the transcriptomic profiles of two parallely evolved ecotype pairs, grown in reciprocal transplantations at native altitudinal sites. In this incipient stage of divergence, only a minor proportion of genes appear constitutively differentially expressed between the ecotypes in both pairs, regardless of the growing environment. Both derived, montane populations bear comparatively higher plasticity of gene expression than the alpine populations. Genes that change expression plastically or constitutively underlie similar ecologically relevant pathways, related to response to drought and trichome formation. Other relevant processes, such as photosynthesis, rely mainly on plastic changes. The enhanced plasticity consistently observed in the montane ecotype likely evolved as a response to the newly colonized, drier, and warmer niche. We report a striking parallelism of directional changes in gene expression plasticity. Thus, plasticity appears to be a key mechanism shaping the initial stages of phenotypic evolution, likely fostering adaptation to novel environments.

Synthetic developmental biology: molecular tools to re-design plant shoots and roots

Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would probably benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with a suite of gene regulation tools (e.g. cell type-specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.

Genome-wide analysis of HSF family and overexpression of PsnHSF21 confers salt tolerance in Populus simonii × P. nigra

Heat shock transcription factor (HSF) is an important TF that performs a dominant role in plant growth, development, and stress response network. In this study, we identified a total of 30 HSF members from poplar, which are unevenly distributed on 17 chromosomes. The poplar HSF family can be divided into three subfamilies, and the members of the same subfamily share relatively conserved domains and motifs. HSF family members are acidic and hydrophilic proteins that are located in the nucleus and mainly carry out gene expansion through segmental replication. In addition, they have rich collinearity across plant species. Based on RNA-Seq analysis, we explored the expression pattern of PtHSFs under salt stress. Subsequently, we cloned the significantly upregulated PtHSF21 gene and transformed it into Populus simonii × P. nigra. Under salt stress, the transgenic poplar overexpressing PtHSF21 had a better growth state and higher reactive oxygen scavenging ability. A yeast one-hybrid experiment indicated PtHSF21 could improve salt tolerance by specifically binding to the anti-stress cis-acting element HSE. This study comprehensively profiled the fundamental information of poplar HSF family members and their responses to salt stress and specifically verified the biological function of PtHSF21, which provides clues for understanding the molecular mechanism of poplar HSF members in response to salt stress.

Genome-Wide Identification and Characterization of Heat Shock Protein 20 Genes in Maize

Maize is an important cereal crop worldwide and is sensitive to abiotic stresses in fluctuant environments that seriously affect its growth, yield, and quality. The small heat shock protein (HSP20) plays a crucial role in protecting plants from abiotic stress. However, little is known about HSP20 in maize (ZmHSP20). In this study, 44 ZmHSP20s were identified, which were unequally distributed over 10 chromosomes, and 6 pairs of ZmHSP20s were tandemly presented. The gene structure of ZmHSP20s was highly conserved, with 95% (42) of the genes having no more than one intron. The analysis of the cis-element in ZmHSP20s promoter demonstrated large amounts of elements related to hormonal and abiotic stress responses, including abscisic acid (ABA), high temperature, and hypoxia. The ZmHSP20s protein had more than two conserved motifs that were predictably localized in the cytoplasm, nucleus, endoplasmic reticulum, peroxisome, mitochondria, and plasma. Phylogenetic analysis using HSP20s in Arabidopsis, rice, maize, and Solanum tuberosum indicated that ZmHSP20s were classified into 11 categories, of which each category had unique subcellular localization. Approximately 80% (35) of ZmHSP20 were upregulated under heat stress at the maize seedling stage, whereas the opposite expression profiling of 10 genes under 37 and 48 °C was detected. A total of 20 genes were randomly selected to investigate their expression under treatments of ABA, gibberellin (GA), ethylene, low temperature, drought, and waterlogging, and the results displayed that more than half of these genes were downregulated while ZmHSP20-3, ZmHSP20-7, ZmHSP20-24, and ZmHSP20-44 were upregulated under 1 h treatment of ethylene. A yeast-one-hybrid experiment was conducted to analyze the binding of four heat stress transcription factors (ZmHSFs) with eight of the ZmHSP20s promoter sequences, in which ZmHSF3, ZmHSF13, and ZmHSF17 can bind to most of these selected ZmHSP20s promoters. Our results provided a valuable resource for studying HSP20s function and offering candidates for genetic improvement under abiotic stress.

Combined nature and human selections reshaped peach fruit metabolome

Background

Plant metabolites reshaped by nature and human beings are crucial for both their lives and human health. However, which metabolites respond most strongly to selection pressure at different evolutionary stages and what roles they undertake on perennial fruit crops such as peach remain unclear.

Results

Here, we report 18,052 significant locus-trait associations, 12,691 expression-metabolite correlations, and 294,676 expression quantitative trait loci (eQTLs) for peach. Our results indicate that amino acids accumulated in landraces may be involved in the environmental adaptation of peaches by responding to low temperature and drought. Moreover, the contents of flavonoids, the major nutrients in fruits, have kept decreasing accompanied by the reduced bitter flavor during both domestication and improvement stages. However, citric acid, under the selection of breeders’ and consumers’ preference for flavor, shows significantly different levels between eastern and western varieties. This correlates with differences in activity against cancer cells in vitro in fruit from these two regions. Based on the identified key genes regulating flavonoid and acid contents, we propose that more precise and targeted breeding technologies should be designed to improve peach varieties with rich functional contents because of the linkage of genes related to bitterness and acid taste, antioxidant and potential anti-cancer activity that are all located at the top of chromosome 5.

Conclusions

This study provides powerful data for future improvement of peach flavor, nutrition, and resistance in future and expands our understanding of the effects of natural and artificial selection on metabolites.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02719-6.

Low-temperature stress affects reactive oxygen species, osmotic adjustment substances, and antioxidants in rice (Oryza sativa L.) at the reproductive stage

The sensitivity of rice to low-temperature stress (LTS), especially at the reproductive stage, is a primary factor of rice yield fluctuation in cold cultivate region. Here, the changes of reactive oxygen species (ROS), osmotic adjustment substances, and antioxidants in different tissues were analyzed during rice growing under low temperatures (LT) at the reproductive stage. Results showed that LTS increases the levels of proline (Pro), soluble protein (SP), glutathione (GSH), superoxidase (SOD), and ascorbate peroxidase (APX) in LJ25 (LTS-resistant) and LJ11 (LTS-sensitive). The activities of catalase (CAT) and peroxidase (POD) were significantly increased in LJ25 but decreased in LJ11 under LTS, while an opposite trend in ROS and malondialdehyde (MDA) was observed in both varieties. Moreover, most physicochemical properties were higher in flag leaves and panicles compared with those in leaf sheaths. The expression patterns of OsCOIN, OsCATC, OsMAP1, OsPOX1, and OsAPX were the same with phenotypic changes in Pro and the enzymes encoded by them, confirming the accuracy of the physicochemical analysis. Therefore, only CAT and POD increased more in LJ25, suggesting they could be the key factors used for LT-tolerant breeding of rice in cold regions.

Transcriptional and physiological data revealed cold tolerance in a photo-thermo sensitive genic male sterile line Yu17S

BACKGROUND

Rice is highly sensitive to chilling stress during the seedling stage. However, the adaptable photo-thermo sensitive genic male sterile (PTGMS) rice line, Yu17S, exhibits tolerance to low temperatures. Currently, the molecular characteristics of Yu17S are unclear.

RESULTS

To evaluate the molecular mechanisms behind cold responses in rice seedlings, a comparative transcriptome analysis was performed in Yu17S during seedling development under normal temperature and low temperature conditions. In total, 9317 differentially expressed genes were detected. Gene ontology and pathway analyses revealed that these genes were involved mostly in photosynthesis, carotenoid biosynthesis, carbohydrate metabolism and plant hormone signal transduction. An integrated analysis of specific pathways combined with physiological data indicated that rice seedlings improved the performance of photosystem II when exposed to cold conditions. Genes involved in starch degradation and sucrose metabolism were activated in rice plants exposed to cold stress treatments, which was accompanied by the accumulation of soluble sugar, trehalose, raffinose and galactinol. Furthermore, chilling stress induced the expression of phytoene desaturase, 15-cis-ζ-carotene isomerase, ζ-carotene desaturase, carotenoid isomerase and β-carotene hydroxylase; this was coupled with the activation of carotenoid synthase activity and increases in abscisic acid (ABA) levels in rice seedlings.

CONCLUSIONS

Our results suggest that Yu17S exhibited better tolerance to cold stress with the activation of carotenoid synthase activity and increasing of ABA levels, and as well as the expression of photosynthesis-related genes under cold condition in rice seedlings.

NILs of Cold Tolerant Japonica Cultivar Exhibited New QTLs for Mineral Elements in Rice

Chilling stress at booting stage can cause floret deterioration and sterility by limiting the supply of food chain and the accumulation of essential mineral elements resulting in reduction of yield and grain quality attributes in rice. Genomic selection of chilling tolerant rice with reference to the accumulation of mineral elements will have great potential to cope with malnutrition and food security in times of climate change. Therefore, a study was conducted to explore the genomic determinants of cold tolerance and mineral elements content in near-isogenic lines (NILs) of japonica rice subjected to chilling stress at flowering stage. Detailed morphological analysis followed by quantitative analysis of 17 mineral elements revealed that the content of phosphorus (P, 3,253 mg/kg) and potassium (K, 2,485 mg/kg) were highest while strontium (Sr, 0.26 mg/kg) and boron (B, 0.34 mg/kg) were lowest among the mineral elements. The correlation analysis revealed extremely positive correlation of phosphorus (P) and copper (Cu) with most of the cold tolerance traits. Among all the effective ear and the second leaf length correlation was significant with half of the mineral elements. As a result of comparative analysis, some QTLs (qBRCC-1, qBRCIC-2, qBRZC-6, qBRCHC-6, qBRMC-6, qBRCIC-6a, qBRCIC-6b, qBRCHC-6, and qBRMC-6) identified for calcium (Ca), zinc (Zn), chromium (Cr) and magnesium (Mg) on chromosome number 1, 2, and 6 while, a novel QTL (qBCPC-1) was identified on chromosome number 1 for P element only. These findings provided bases for the identification of candidate genes involved in mineral accumulation and cold tolerance in rice at booting stage.

Transcriptome analysis of Curcuma wenyujin from Haikou and Wenzhou, and a comparison of the main constituents and related genes of Rhizoma Curcumae

For more than a thousand years, Rhizoma Curcumae (known as E zhu), a Chinese herbal medicine, has been used to eradicate blood stasis and relieve aches. The plant Curcuma wenyujin, which is grown primarily in Wenzhou, China, is considered the best source of Rhizoma Curcumae. In this study, we sought to ascertain differences in transcript profiles of C. wenyujin grown in traditional (Wenzhou) and recently established (Haikou) production areas based on Illumina and RNA (RNA-seq) sequencing. We also examined differences in the main components of the volatile oil terpene; curcumin, polysaccharide, and starch constituents and related genes in the corresponding pathways, in C. wenyujin cultivated in the two production areas. We accordingly found that the essential oil (2.05%), curcumin (1.46%), and polysaccharide (8.90%) content in Wenzhou rhizomes was higher than that in the rhizomes of plants from Haikou (1.60%, 0.91%, and 6.15%, respectively). In contrast, the starch content of Wenzhou rhizomes (17.0%) was lower than that of Haikou rhizomes (23.8%). Furthermore, we detected significant differences in the oil components of Haikou and Wenzhou rhizomes, with curzerene (32.34%), curdione (21.35%), and germacrene B (9.39%) being the primary components of the essential oil derived from Wenzhou rhizomes, and curzerene (20.13%), curdione (14.73%), and cineole (9.76%) being the main constituents in Haikou rhizomes. Transcriptome and qPCR analyses revealed considerable differences in gene expression between Wenzhou and Haikou rhizomes. The expression of terpene, curcumin, and polysaccharide pathway-related genes in Wenzhou rhizomes was significantly up-regulated, whereas the expression of starch-associated genes was significantly down-regulated, compared with those in Haikou rhizomes. Difference in the content of terpene, curcumin, polysaccharides, and starch in rhizomes from the two production areas could be explained in terms of differences in expression of the related genes.

Quaternary Ammonium Salts of Iminofullerenes: Fabrication and Effect on Seed Germination

In this study, novel water-soluble quaternary ammonium salts of iminofullerenes (IFQA) were synthesized by nitrene chemistry in combination with quaternization and identified as [C₆₀(NCH₂CH₂NH₃⁺·CF₃COO^-)₄·10H₂O]_n by various spectroscopies. Maize and Arabidopsis seeds were used to test the bioactivity of IFQA in seed germination. Compared with the control, maize seed exposure to 50 mg/L IFQA (normal: 73.1% vs 58.7%; drought: 66.7% vs 50.0% at the second day) and Arabidopsis seed exposure to 20 mg/L IFQA (normal: 77.5% vs 58.8%; drought: 63.3% vs 36.7% at the second day) had higher germination rates and quicker germination. The results of two-dimensional gel electrophoresis combined with mass spectroscopy showed that the abundance of 21 proteins in embryo proteome of maize seeds was significantly changed (>1.5 fold). The downregulated six storage proteins and upregulated four proteins induced by IFQA for energy production and sugar metabolism indicated a faster metabolic activity of maize seed germination. The upregulated eight stress-related proteins and antioxidant enzymes suggested that the role of IFQA was to activate the metabolic processes in seed germination and also increase seed stress response. The results provide important information to understand the mechanism of seed germination enhancement by carbon nanomaterials.

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic networks, which also undergo changes in the process of evolution. The study of the network structure and evolution may highlight mechanisms of plants adaptation to adverse conditions, as well as their response to stresses and help in discovery and functional characterization of the stress-related genes. We performed an analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) at the network level using a phylostratigraphic approach. Our results show that a substantial fraction of genes associated with various types of abiotic stress is of ancient origin and evolves under strong purifying selection. The interaction networks of genes associated with stress response have a modular structure with a regulatory component being one of the largest for five of seven stress types. We demonstrated a positive relationship between the number of interactions of gene in the stress gene network and its age. Moreover, genes of the same age tend to be connected in stress gene networks. We also demonstrated that old stress-related genes usually participate in the response for various types of stress and are involved in numerous biological processes unrelated to stress. Our results demonstrate that the stress response genes represent the ancient and one of the fundamental molecular systems in plants.

Drought-induced change in yield capacity of ten wheat cultivars in relation to their vegetative characteristics at heading stage

Ten wheat (Triticum aestivum L.) cultivars were tested in a semi-field experiment for drought response in terms of their flag leaf vigor, whole shoot growth and ultimate yield capacity. At booting stage, 25% of field capacity was held for 3 weeks, then the plants were normally irrigated. Based on split plot analysis of the pooled data, the order in which the source of variation could affect the estimated traits was watering level, then cultivar and finally the combination of both. At p ≤ 0.05, significant positive linear correlation was recorded between the drought-induced change in grain total carbohydrate content and leaf total carbohydrate content, between biological yield and each of water use efficiency for biomass and evapotranspiration efficiency as well as between economic yield and each of leaf catalase activity, water use efficiency for grain and hundred kernel mass. On contrary, significant negative correlation was recorded between the drought-induced change in shoot evapotranspiration rate and each of leaf proline content and shoot water content. Based on the drought-induced change in the estimated vegetative and yield traits, cluster analysis could sequester the concerned cultivars into drought-tolerant, moderate and sensitive ones; with Sids 13 being the most drought-tolerant cultivar as well as Shandaweel 1 and Giza 168 as the most drought-sensitive ones.

Response of Phenylpropanoid Pathway and the Role of Polyphenols in Plants under Abiotic Stress

Phenolic compounds are an important class of plant secondary metabolites which play crucial physiological roles throughout the plant life cycle. Phenolics are produced under optimal and suboptimal conditions in plants and play key roles in developmental processes like cell division, hormonal regulation, photosynthetic activity, nutrient mineralization, and reproduction. Plants exhibit increased synthesis of polyphenols such as phenolic acids and flavonoids under abiotic stress conditions, which help the plant to cope with environmental constraints. Phenylpropanoid biosynthetic pathway is activated under abiotic stress conditions (drought, heavy metal, salinity, high/low temperature, and ultraviolet radiations) resulting in accumulation of various phenolic compounds which, among other roles, have the potential to scavenge harmful reactive oxygen species. Deepening the research focuses on the phenolic responses to abiotic stress is of great interest for the scientific community. In the present article, we discuss the biochemical and molecular mechanisms related to the activation of phenylpropanoid metabolism and we describe phenolic-mediated stress tolerance in plants. An attempt has been made to provide updated and brand-new information about the response of phenolics under a challenging environment.

Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices

Background

The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasting response is caused by gene-by-environment interactions (GxE). Understanding GxE interactions is particularly important in agronomy, since selected breeds and varieties may have divergent phenotypes according to their growing environment. Industrial microbes such as Saccharomyces cerevisiae are also faced with a large range of fermentation conditions that affect their technological properties. Finding the molecular determinism of such variations is a critical task for better understanding the genetic bases of phenotypic plasticity and can also be helpful in order to improve breeding methods.

Results

In this study we implemented a QTL mapping program using two independent cross (~ 100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to whole genome sequencing approaches, both crosses were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the environmental conditions. Molecular dissection of a major QTL demonstrated that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits.

Conclusions

The detection of QTLs and their interactions with environment emphasizes the complexity of yeast industrial traits. The validation of the interaction of SSU1 allelic variants with the nature of the fermented juice increases knowledge about the impact of the sulfite pump during fermentation. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5145-4) contains supplementary material, which is available to authorized users.

Biogas digestate – benefits and risks for soil fertility and crop quality – an evaluation of grain maize response

The agricultural usability of biogas digestate solids (BDS) as a soil amendment depends upon its impact on soil fertility and the content of minerals in the edible part of the grown crop. This hypothesis was verified in a series of field experiments with maize conducted between 2014 and 2016 at Brody, Poland. The two-factorial experiment consisted of the DBS application method (broadcast and row) and its rate: 0, 0.8, 1.6, 3.2 t ha–1. The post-harvest analysis of soil fertility showed that BDS can, at least partly, replace mineral fertilizers. The supply of N-NO3 to maize as a growth driving factor was significantly limited by a shortage of iron, potassium and, to some extent, magnesium. As recorded in 2016, the shortage of available Fe resulted in a low/pool of N-NO3, thus significantly decreasing the yield of grain. The shortage of K supply to grain created a pathway for the accumulation of other elements, including heavy metals. The disadvantage of the N-NO3 pool increase, due to the DBS application, was concomitant with the enhanced intake of cadmium and lead, which consequently exceeded their permissible concentration limits in grain. These unfavorable results of biogas digestate impact on the quality of maize grain can be ameliorated by incorporating zinc into the biogas type of soil amendment and keeping a sufficiently high level of available potassium and iron. The shortage of K can be partly overcome by a better sodium supply, however, its accumulation in grain results in an enhanced accumulation of cadmium and lead.

Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought

Metabolomes, as chemical phenotypes of organisms, are likely not only shaped by the environment but also by common ancestry. If this is the case, we expect that closely related species of pines will tend to reach similar metabolomic solutions to the same environmental stressors. We examined the metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada (southern Iberian Peninsula), in summer and winter and exposed to folivory by the pine processionary moth. The overall metabolomes differed between the subspecies but both tended to respond more similarly to folivory. The metabolomes of the subspecies were more dissimilar in summer than in winter, and iberica trees had higher concentrations of metabolites directly related to drought stress. Our results are consistent with the notion that certain plant metabolic responses associated with folivory have been phylogenetically conserved. The larger divergence between subspecies metabolomes in summer is likely due to the warmer and drier conditions that the northern iberica subspecies experience in Sierra Nevada. Our results provide crucial insights into how iberica populations would respond to the predicted conditions of climate change under an increased defoliation in the Mediterranean Basin.

Understanding and engineering plant form

A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.

Static magnetic field treatment of seeds improves carbon and nitrogen metabolism under salinity stress in soybean

The effectiveness of magnetopriming was assessed for alleviation of salt-induced adverse effects on soybean growth. Soybean seeds were pre-treated with static magnetic field (SMF) of 200 mT for 1 h to evaluate the effect of magnetopriming on growth, carbon and nitrogen metabolism, and yield of soybean plants under different salinity levels (0, 25, and 50 mM NaCl). The adverse effect of NaCl-induced salt stress was found on growth, yield, and various physiological attributes of soybeans. Results indicate that SMF pre-treatment significantly increased plant growth attributes, number of root nodules, nodules, fresh weight, biomass accumulation, and photosynthetic performance under both non-saline and saline conditions as compared to untreated seeds. Polyphasic chlorophyll a fluorescence (OJIP) transients from magnetically treated plants gave a higher fluorescence yield at J-I-P phase. Nitrate reductase activity, PIABS , photosynthetic pigments, and net rate of photosynthesis were also higher in plants that emerged from SMF pre-treated seeds as compared to untreated seeds. Leghemoglobin content and hemechrome content in root nodules were also increased by SMF pre-treatment. Thus pre-sowing exposure of seeds to SMF enhanced carbon and nitrogen metabolism and improved the yield of soybeans in terms of number of pods, number of seeds, and seed weight under saline as well as non-saline conditions. Consequently, SMF pre-treatment effectively mitigated adverse effects of NaCl on soybeans. It indicates that magnetopriming of dry soybean seeds can be effectively used as a pre-sowing treatment for alleviating salinity stress. Bioelectromagnetics. 37:455-470, 2016. © 2016 Wiley Periodicals, Inc.

Increased resistance to a generalist herbivore in a salinity-stressed non-halophytic plant

Plants often grow under the combined stress of several factors. Salinity and herbivory, separately, can severely hinder plant growth and reproduction, but the combined effects of both factors are still not clearly understood. Salinity is known to reduce plant tissue nitrogen content and growth rates. Since herbivores prefer tissues with high N content, and biochemical pathways leading to resistance are commonly elicited by salt-stress, we hypothesized that plants growing in saline conditions would have enhanced resistance against herbivores. The non-halophyte, Brassica juncea, and the generalist herbivore Trichoplusia ni were used to test the prediction that plants subjected to salinity stress would be both more resistant and more tolerant to herbivory than those growing without salt stress. Plants were grown under different NaCl levels, and either exposed to herbivores and followed by removal of half of their leaves, or left intact. Plants were left to grow and reproduce until senescence. Tissue quality was assessed, seeds were counted and biomass of different organs measured. Plants exposed to salinity grew less, had reduced tissue nitrogen, protein and chlorophyll content, although proline levels increased. Specific leaf area, leaf water content, transpiration and root:shoot ratio remained unaffected. Plants growing under saline condition had greater constitutive resistance than unstressed plants. However, induced resistance and tolerance were not affected by salinity. These results support the hypothesis that plants growing under salt-stress are better defended against herbivores, although in B. juncea this may be mostly through resistance, and less through tolerance.

Metabolic response of maize plants to multi-factorial abiotic stresses

Clarification of the metabolic mechanisms underlying multi-stress responses in plants will allow further optimisation of crop breeding and cultivation to obtain high yields in an increasingly variable environment. Using NMR metabolomic techniques, we examined the metabolic responses of maize plants grown under different conditions: soil drought, soil salinity, heat and multiple concurrent stresses. A detailed time-course metabolic profile was also performed on maize plants sampled 1, 3 and 7 days after initiation of soil drought and heat stress. The metabolic profile of maize plants subjected to soil drought was more similar to plants exposed to salt stress than to heat-stressed plants. Drought-stressed maize plants subjected to salt or heat stress showed distinct integrated metabolic profiles compared with those exposed to either stressor individually. These differences show the considerable metabolic plasticity of maize in response to different growth conditions. Moreover, glucose, fructose, malate, citrate, proline, alanine, aspartate, asparagine, threonine and one unknown compound fluctuated obviously between maize plants grown in controlled growth cabinet and a natural regime. These changes were associated with the TCA cycle and core nitrogen metabolism, and could be related to their multiple functions during plant growth. The evident stress-induced trajectory of metabolic changes in maize indicated that the primary metabolic responses to soil drought, heat and combined drought and heat stresses occurred in a time-dependent manner. Plasticity at the metabolic level may allow maize plants to acclimatise their metabolic ranges in response to changing environmental conditions.

Identification of Arabidopsis candidate genes in response to biotic and abiotic stresses using comparative microarrays

Plants have evolved with intricate mechanisms to cope with multiple environmental stresses. To adapt with biotic and abiotic stresses, plant responses involve changes at the cellular and molecular levels. The current study was designed to investigate the effects of combinations of different environmental stresses on the transcriptome level of Arabidopsis genome using public microarray databases. We investigated the role of cyclopentenones in mediating plant responses to environmental stress through TGA (TGACG motif-binding factor) transcription factor, independently from jasmonic acid. Candidate genes were identified by comparing plants inoculated with Botrytis cinerea or treated with heat, salt or osmotic stress with non-inoculated or non-treated tissues. About 2.5% heat-, 19% salinity- and 41% osmotic stress-induced genes were commonly upregulated by B. cinerea-treatment; and 7.6%, 19% and 48% of genes were commonly downregulated by B. cinerea-treatment, respectively. Our results indicate that plant responses to biotic and abiotic stresses are mediated by several common regulatory genes. Comparisons between transcriptome data from Arabidopsis stressed-plants support our hypothesis that some molecular and biological processes involved in biotic and abiotic stress response are conserved. Thirteen of the common regulated genes to abiotic and biotic stresses were studied in detail to determine their role in plant resistance to B. cinerea. Moreover, a T-DNA insertion mutant of the Responsive to Dehydration gene (rd20), encoding for a member of the caleosin (lipid surface protein) family, showed an enhanced sensitivity to B. cinerea infection and drought. Overall, the overlapping of plant responses to abiotic and biotic stresses, coupled with the sensitivity of the rd20 mutant, may provide new interesting programs for increased plant resistance to multiple environmental stresses, and ultimately increases its chances to survive. Future research directions towards a better dissection of the potential crosstalk between B. cinerea, abiotic stress, and oxylipin signaling are of our particular interest.

Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses

Background

Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear.

Results

Here, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses.

Conclusions

The comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1398-3) contains supplementary material, which is available to authorized users.

Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts

BACKGROUND

Rheum nobile is an alpine plant with translucent bracts concealing the inflorescence which produce a "glasshouse" effect promoting the development of fertile pollen grains in such conditions. The current understanding of the adaptation of such bracts to alpine environments mainly focuses on the phenotypic and physiological changes while the genetic basis is very limited. By sequencing the upper bract and the lower rosulate leaf from the same R. nobile stem, we identified candidate genes that may be involved in alpine adaption of the translucent bract in "glasshouse" plants and illustrated the changes in gene expression underlying the adaptive and complex evolution of the bracts phenotype.

RESULTS

A total of 174.2 million paired-end reads from each transcriptome were assembled into 25,249 unigenes. By comparing the gene expression profiles, we identified 1,063 and 786 genes up-regulated respectively in the upper bract and the lower leaf. Functional enrichment analyses of these genes recovered a number of differential important pathways, including flavonoid biosynthesis, mismatch repair and photosynthesis related pathways. These pathways are mainly involved in three types of functions: 9 genes in the UV protective process, 9 mismatch repair related genes and 88 genes associated with photosynthesis.

CONCLUSIONS

This study provides the first comprehensive dataset characterizing Rheum nobile gene expression at the transcriptomic scale, and provides novel insights into the gene expression profiles associated with the adaptation of the "glasshouse" plant bracts. The dataset will be served as a public genetic resources for further functional and evolutionary studies of "glasshouse" plants.

Evaluation of drought tolerance of the Vietnamese soybean cultivars provides potential resources for soybean production and genetic engineering

Drought is one of the greatest constraints to soybean production in many countries, including Vietnam. Although a wide variety of the newly produced cultivars have been produced recently in Vietnam through classical breeding to cope with water shortage, little knowledge of their molecular and physiological responses to drought has been discovered. This study was conducted to quickly evaluate drought tolerance of thirteen local soybean cultivars for selection of the best drought-tolerant cultivars for further field test. Differences in drought tolerance of cultivars were assessed by root and shoot lengths, relative water content, and drought-tolerant index under both normal and drought conditions. Our data demonstrated that DT51 is the strongest drought-tolerant genotype among all the tested cultivars, while the highest drought-sensitive phenotype was observed with MTD720. Thus, DT51 could be subjected to further yield tests in the field prior to suggesting it for use in production. Due to their contrasting drought-tolerant phenotypes, DT51 and MTD720 provide excellent genetic resources for further studies underlying mechanisms regulating drought responses and gene discovery. Our results provide vital information to support the effort of molecular breeding and genetic engineering to improve drought tolerance of soybean.

Rice and cold stress: methods for its evaluation and summary of cold tolerance-related quantitative trait loci

Cold stress adversely affects rice (Oryza sativa L.) growth and productivity, and has so far determined its geographical distribution. Dissecting cold stress-mediated physiological changes and understanding their genetic causes will facilitate the breeding of rice for cold tolerance. Here, we review recent progress in research on cold stress-mediated physiological traits and metabolites, and indicate their roles in the cold-response network and cold-tolerance evaluation. We also discuss criteria for evaluating cold tolerance and evaluate the scope and shortcomings of each application. Moreover, we summarize research on quantitative trait loci (QTL) related to cold stress at the germination, seedling, and reproductive stages that should provide useful information to accelerate progress in breeding cold-tolerant rice.

Molecular characterization of ferulate 5-hydroxylase gene from kenaf (Hibiscus cannabinus L.)

The purpose of this study is to clone and characterize the expression pattern of a F5H gene encoding ferulate 5-hydroxylase in the phenylpropanoid pathway from kenaf (Hibiscus cannabinus L.). Kenaf is a fast-growing dicotyledonous plant valued for its biomass. F5H, a cytochrome P450-dependent monooxygenase (CYP84), is a key enzyme for syringyl lignin biosynthesis. The full length of the F5H ortholog was cloned and characterized. The full-length F5H ortholog consists of a 1,557-bp open reading frame (ORF) encoding 518 amino acids (GenBank Accession number JX524278). The deduced amino acid sequence showed that kenaf F5H had the highest similarity (78%) with that of Populus trichocarpa. Transcriptional analysis of F5H ortholog was conducted using quantitative real-time PCR during the developmental stages of various tissues and in response to various abiotic stresses. The highest transcript level of the F5H ortholog was observed in immature flower tissues and in early stage (6 week-old) of stem tissues, with a certain level of expression in all tissues tested. The highest transcript level of F5H ortholog was observed at the late time points after treatments with NaCl (48 h), wounding (24 h), cold (24 h), abscisic acid (24 h), and methyl jasmonate (24 h).

OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors

High salinity causes remarkable losses in rice productivity worldwide mainly because it inhibits growth and reduces grain yield. To cope with environmental changes, plants evolved several adaptive mechanisms, which involve the regulation of many stress-responsive genes. Among these, we have chosen OsRMC to study its transcriptional regulation in rice seedlings subjected to high salinity. Its transcription was highly induced by salt treatment and showed a stress-dose-dependent pattern. OsRMC encodes a receptor-like kinase described as a negative regulator of salt stress responses in rice. To investigate how OsRMC is regulated in response to high salinity, a salt-induced rice cDNA expression library was constructed and subsequently screened using the yeast one-hybrid system and the OsRMC promoter as bait. Thereby, two transcription factors (TFs), OsEREBP1 and OsEREBP2, belonging to the AP2/ERF family were identified. Both TFs were shown to bind to the same GCC-like DNA motif in OsRMC promoter and to negatively regulate its gene expression. The identified TFs were characterized regarding their gene expression under different abiotic stress conditions. This study revealed that OsEREBP1 transcript level is not significantly affected by salt, ABA or severe cold (5 °C) and is only slightly regulated by drought and moderate cold. On the other hand, the OsEREBP2 transcript level increased after cold, ABA, drought and high salinity treatments, indicating that OsEREBP2 may play a central role mediating the response to different abiotic stresses. Gene expression analysis in rice varieties with contrasting salt tolerance further suggests that OsEREBP2 is involved in salt stress response in rice.

Ionomic profiling of Nicotiana langsdorffii wild-type and mutant genotypes exposed to abiotic stresses

To provide a new insight into the response of plants to abiotic stresses, the ionomic profiles of Nicotiana langsdorffii specimens have been determined before and after exposure to toxic metals (chromium) or drought conditions. The plants were genetically transformed with the rat glucocorticoid receptor (GR) or the gene for Agrobacterium rhizogenes rolC, because these modifications are known to produce an imbalance in phytohormone equilibria and a significant change in the defence response of the plant. Elemental profiles were obtained by developing and applying analytical procedures based on inductively coupled plasma atomic emission and mass spectrometry (ICP-AES/MS). In particular, the removal of isobaric interferences affecting the determination of Cr and V by ICP-MS was accomplished by use of a dynamic reaction cell, after optimization of the relevant conditions. The combined use of ICP atomic emission and mass spectrometry enabled the determination of 29 major and trace elements (Ba, Bi, Ca, Cd, Co, Cr, Cu, Eu, Fe, Ga, K, Li, Mg, Mn, Mo, Na, P, Pb, Pt, Rb, S, Sb, Sn, Sr, Te, V, W, Y, and Zn) in different parts of the plants (roots, stems, and leaves), with high accuracy and precision. Multivariate data processing and study of element distribution patterns provided new information about the ionomic response of the target organism to chemical treatment or water stress. Genetic modification mainly affected the distribution of Bi, Cr, Mo, Na, and S, indicating that these elements were involved in biochemical processes controlled by the GR or rolC genes. Chemical stress strongly affected accumulation of several elements (Ba, Ca, Fe, Ga, K, Li, Mn, Mo, Na, P, Pb, Rb, S, Sn, Te, V, and Zn) in different ways; for Ca, Fe, K, Mn, Na, and P the effect was quite similar to that observed in other studies after treatment with other transition elements, for example Cu and Cd. The effect of water deficit was less evident, mainly consisting in a decrease of Ba, Cr, Na, and Sr in roots.

The homologous homeodomain-leucine zipper transcription factors HaHB1 and AtHB13 confer tolerance to drought and salinity stresses via the induction of proteins that stabilize membranes

Transgenic approaches to conferring tolerance to abiotic stresses have mostly resulted in some degree of plant yield penalty under normal or mild stress conditions. Recently, we have reported that the homeodomain-leucine zipper transcription factors (TFs) HaHB1 and AtHB13 were able to confer tolerance to freezing temperatures via the induction of glucanase (GLU and PR2) and chitinase (PR4) proteins. In the present study, we show that the expression of these TFs, as well as that of their putative targets AtPR2, AtPR4 and AtGLU, is up-regulated by drought and salinity stresses. Transgenic plants overexpressing separately these five genes exhibited tolerance to severe drought and salinity stresses, displaying a cell membrane stabilization mechanism. Under normal or mild stress conditions, these plants achieved an improved yield associated with higher chlorophyll content. Moreover, overexpression of the sunflower HaHB1 gene from its own, inducible, promoter conferred a high drought-stress tolerance without yield penalty under normal or mild stress conditions. We propose these TFs as potential biotechnological tools to breed crops for tolerance to multiple stresses and for increased yield.

Identification of sense and antisense transcripts regulated by drought in sugarcane

Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90%. From the probes presented on the array, 75% of the sense probes and 11.9% of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

Signal transduction during cold, salt, and drought stresses in plants

Abiotic stresses, especially cold, salinity and drought, are the primary causes of crop loss worldwide. Plant adaptation to environmental stresses is dependent upon the activation of cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Plants have stress-specific adaptive responses as well as responses which protect the plants from more than one environmental stress. There are multiple stress perception and signaling pathways, some of which are specific, but others may cross-talk at various steps. In this review article, we first expound the general stress signal transduction pathways, and then highlight various aspects of biotic stresses signal transduction networks. On the genetic analysis, many cold induced pathways are activated to protect plants from deleterious effects of cold stress, but till date, most studied pathway is ICE-CBF-COR signaling pathway. The Salt-Overly-Sensitive (SOS) pathway, identified through isolation and study of the sos1, sos2, and sos3 mutants, is essential for maintaining favorable ion ratios in the cytoplasm and for tolerance of salt stress. Both ABA-dependent and -independent signaling pathways appear to be involved in osmotic stress tolerance. ROS play a dual role in the response of plants to abiotic stresses functioning as toxic by-products of stress metabolism, as well as important signal transduction molecules and the ROS signaling networks can control growth, development, and stress response. Finally, we talk about the common regulatory system and cross-talk among biotic stresses, with particular emphasis on the MAPK cascades and the cross-talk between ABA signaling and biotic signaling.

Advances and prospects: biotechnologically improving crop water use efficiency

Bio-water saving can be defined as the reduction of crop water consumption employing biological measures. This is the focus of efforts to save water in agriculture. Different levels of water-use efficiency (WUE) have been developed. The genetic diversity of WUE has been confirmed in several crops. WUE is the basis of bio-watering and physiological WUE is the key. The degree to develop physiological WUE potential decides the performance of bio-watering in the field. During this process, fine management is important. Thus bio-watering is closely related to WUE. Crop WUE has improved and evolved as a result of breeding programs. Many WUE genes have been located in different genomic and aneuploid materials and have been mapped by various molecular markers in a number of crops. Two genes, (Erecta and alx8), which control water use efficiency; have been cloned in Arabidopsis thaliana. Eleven WUE genes have been identified by microarray analysis. Six genes associated with drought resistance and photosynthesis have been transfered into crops which have resulted in improving WUE and drought resistance. WUE is important on the basis of functional identification of more drought resistant gene resources. The popularity on the industrial-scale of transgenic plants is still in its infancy and one of the reasons for this is the lack of knowledge regarding molecular mechanisms and it is a very immature technology. Enhanced agricultural practices and the theoretical aspects of improving crop WUE have been developed and are discussed in this review paper. Rapid progress will be made in bio-water savings and that crop WUE can be substantially improved under both favorable and unfavorable water-limited environments. This will be achieved by a combination of traditional breeding techniques and the introduction of modern biotechnology.

Ecological functions and differentially expressed transcripts of translucent bracts in an alpine 'glasshouse' plant Rheum nobile (Polygonaceae)

The molecular basis of many physiological and/or phenotypic adaptations of alpine plants remains largely unknown. The upper leaves of what are termed "glasshouse plants" have been transformed into translucent bracts that cover their inflorescences. This change in appearance is believed to allow such plants to maintain normal sexual reproduction under very cold conditions. Thus, it is hypothesized that the foliar roles of these bracts have been altered as an adaptation to alpine environments. In the present study, a test of this hypothesis revealed distinct physiological and anatomical differences (especially related to photosynthesis) between the bracts and normal leaves in one 'glasshouse' species, Rheum nobile Hook. f. and Thomson. A cDNA-AFLP analysis, was conducted to identify candidate genes involving differential expression in bracts and normal leaves, detected 323 (5.4%) transcript-derived fragments (TDFs) that were differentially expressed (up- or down-regulated) among 6,000 TDFs recovered. In total, 110 differentially expressed TDFs were sequenced, of which 52 were homologous to genes reported from other plants. More than half of the candidate genes represented by the unidentified TDFs may be specific to the Rheum lineage or have arisen through adaptive processes in alpine plants. All putative genes involved in photosynthesis had been down-regulated, while those related to stress and defense response were up-regulated in the bracts. These differentially expressed genes are highly congruent with physiological and anatomical differences between the bracts and normal leaves, indicating that they are associated with functions that confer a physiological advantage in alpine conditions.

The arsenic hyperaccumulator fern Pteris vittata L

Arsenic (As) contaminated soils and waters are becoming major global environmental and human health risks. The identification of natural hyperaccumulators of As opens the door for phytoremediation of the arsenic contaminant. Pteris vittata is the first identified naturally evolving As hyperaccumulator. More than a decade after its discovery, we have made great progress in understanding the uptake, transport, and detoxification of As in the fern. The molecular mechanisms controlling As accumulation in P. vittata are now beginning to be recognized. In this review, we will try to summarize what we have learned about this As accumulator, with particular emphasis on the current knowledge of the physiological and molecular mechanisms of arsenic phytoremediation. We also discuss the potential strategies to further enhance phytoextraction abilities of P. vittata.

Understanding water deficit stress-induced changes in the basic metabolism of higher plants - biotechnologically and sustainably improving agriculture and the ecoenvironment in arid regions of the globe

Water is vital for plant growth, development and productivity. Permanent or temporary water deficit stress limits the growth and distribution of natural and artificial vegetation and the performance of cultivated plants (crops) more than any other environmental factor. Productive and sustainable agriculture necessitates growing plants (crops) in arid and semiarid regions with less input of precious resources such as fresh water. For a better understanding and rapid improvement of soil-water stress tolerance in these regions, especially in the water-wind eroded crossing region, it is very important to link physiological and biochemical studies to molecular work in genetically tractable model plants and important native plants, and further extending them to practical ecological restoration and efficient crop production. Although basic studies and practices aimed at improving soil water stress resistance and plant water use efficiency have been carried out for many years, the mechanisms involved at different scales are still not clear. Further understanding and manipulating soil-plant water relationships and soil-water stress tolerance at the scales of ecology, physiology and molecular biology can significantly improve plant productivity and environmental quality. Currently, post-genomics and metabolomics are very important in exploring anti-drought gene resources in various life forms, but modern agriculturally sustainable development must be combined with plant physiological measures in the field, on the basis of which post-genomics and metabolomics have further practical prospects. In this review, we discuss physiological and molecular insights and effects in basic plant metabolism, drought tolerance strategies under drought conditions in higher plants for sustainable agriculture and ecoenvironments in arid and semiarid areas of the world. We conclude that biological measures are the bases for the solutions to the issues relating to the different types of sustainable development.

Higher plant antioxidants and redox signaling under environmental stresses

Main antioxidants in higher plants include glutathione, ascorbate, tocopherol, proline, betaine, and others, which are also information-rich redox buffers and important redox signaling components that interact with biomembrane-related compartments. As an evolutionary consequence of aerobic life for higher plants, reactive oxygen species (ROS) are formed by partial reduction of molecular oxygen. The above enzymatic and non-enzymatic antioxidants in higher plants can protect their cells from oxidative damage by scavenging ROS. In addition to crucial roles in defense system and as enzyme cofactors, antioxidants influence higher plant growth and development by modifying processes from mitosis and cell elongation to senescence and death. Most importantly, they provide essential information on cellular redox state, and regulate gene expression associated with biotic and abiotic stress responses to optimize defense and survival. An overview of the literature is presented in terms of main antioxidants and redox signaling in plant cells. Special attention is given to ROS and ROS-antioxidant interaction as a metabolic interface for different types of signals derived from metabolism and from the changing environment, which regulates the appropriate induction of acclimation processes or, execution of cell death programs, which are the two essential directions for higher plants.

Water-deficit stress-induced anatomical changes in higher plants

Water is vital for plant growth and development. Water-deficit stress, permanent or temporary, limits the growth and the distribution of natural vegetation and the performance of cultivated plants more than any other environmental factors do. Although research and practices aimed at improving water-stress resistance and water-use efficiency have been carried out for many years, the mechanism involved is still not clear. Further understanding and manipulating plant-water relations and water-stress tolerance at the scale of physiology and molecular biology can significantly improve plant productivity and environmental quality. Currently, post-genomics and metabolomics are very important to explore anti-drought gene resource in different life forms, but modern agricultural sustainable development must be combined with plant physiological measures in the field, on the basis of which post-genomics and metabolomics will have further a practical prospect. In this review, we discussed the anatomical changes and drought-tolerance strategies under drought condition in higher plants.

Primary antioxidant free radical scavenging and redox signaling pathways in higher plant cells

Antioxidants in plant cells mainly include glutathione, ascorbate, tocopherol, proline, betaine and others, which are also information-rich redox buffers and important redox signaling components that interact with cellular compartments. As an unfortunate consequence of aerobic life for higher plants, reactive oxygen species (ROS) are formed by partial reduction of molecular oxygen. The above enzymatic and non-enzymatic antioxidants in higher plant cells can protect their cells from oxidative damage by scavenging ROS. In addition to crucial roles in defense system and as enzyme cofactors, antioxidants influence higher plant growth and development by modifying processes from miotosis and cell elongation to senescence and death. Most importantly, they provide essential information on cellular redox state, and regulate gene expression associated with biotic and abiotic stress responses to optimize defense and survival. An overview of the literature is presented in terms of primary antioxidant free radical scavenging and redox signaling in plant cells. Special attention is given to ROS and ROS-anioxidant interaction as a metabolic interface for different types of signals derived from metabolisms and from the changing environment. This interaction regulates the appropriate induction of acclimation processes or execution of cell death programs, which are the two essential directions for higher plant cells.

The mutual responses of higher plants to environment: physiological and microbiological aspects

Higher plants are different from animals in many aspects, but the important difference may be that plants are more easily influenced by environment. Plants have a series of fine mechanisms for responding to environmental changes, which has been established during their long-period evolution and artificial domestication. The relationship between higher plants and environment is influenced mutually. The component in environment provides higher plants with nutrients for shaping themselves and higher plants simultaneously bring photosynthetic products and metabolites to surroundings, which is the most important part of natural circle. Photosynthetic products are realized mainly by physiological mechanisms, and microbiological aspects in environment (for instance, soil environment) impact the above processes greatly. The complete understanding of the relationship will extremely promote the sustainable utilization of plant resources and make the best use of its current potential under different scales.

Secondary succession and its effects on soil moisture and nutrition in abandoned old-fields of hilly region of Loess Plateau, China

Floristic composition, community structure and soil moisture and nutrient contents in abandoned fields of different ages were analyzed to clarify the regenerative aspects of succession as a tool for vegetation restoration. The results indicated that secondary succession in this region can be interpreted as an auto-succession: there are main changes in species-relative abundance and species turnover. Annual or biennial species (e.g. Artemisia scoparia), acted as pioneers and strongly dominated the early stages. Then, they underwent a progressive decline, while forbs (e.g. Artemisia sacrorum) and grasses (e.g. Xanthium sibiricum) had their peak abundance at intermediate stages. Dwarf shrubs (e.g. Lespedeza dahurica) and short rhizome grass (e.g. Bothriochloa ischaemum) appeared at mid-succession stage and gradually increased in abundance during succession, becoming dominant at late stages. The first axis of detrended correspondence canonical analysis arranged the sites according to their fallow time, indicating a successional sere. The second axis, associated with diverging pathways of regeneration, correlated with topographic factors and soil moisture and nutrition. Structural divergence between plots increased as succession went on, attained the highest at the mid-succession stage, decreased at the late stage. Soil moisture and available phosphorus content decreased steadily with field age after their abandonment, whereas pools of organic matter, total and available nitrogen, potassium and total phosphorus increased with field age. The pace and direction of recovery of native vegetation and natural soil properties in these abandoned fields resembled classic old-field succession, which is a form of secondary succession that often serves as a template for guiding restoration efforts. Interface between the abandoned field soil and plant system was crucial to the above process. Our current study supported the generally accepted hypothesis in the succession literature.