Transcriptomic and metabolomic analyses reveal that ABA increases the salt tolerance of rice significantly correlated with jasmonic acid biosynthesis and flavonoid biosynthesis

Abstract Abscisic acid (ABA) has been shown to mitigate the deleterious effects of abiotic stresses and to regulate plant growth and development. Salinity is one of the important abiotic stresses affecting plant cell metabolism and physiology, which causes serious damages to crops. In this study, we investigated the protective role of exogenous ABA on leaves in response to salinity stress using rice seedlings (two leaf-one heart) subjected to three treatments: ZCK (control), ZS (50 mM NaCl), and ZSA (5 mg L–1 ABA + 50 mM NaCl). We carried out transcriptomic and metabolomic analyses to identify the molecular mechanisms by which ABA protects plants against salt stress. Results showed that 1159 differentially expressed genes (DEGs) (916 up-regulated, 243 down-regulated) and 63 differentially accumulated metabolites (DAMs) (42 up-regulated, 21 down-regulated) were identified between the ZS and ZSA treatments, respectively. In addition, ABA pretreatment regulated the expression pattern of genes responsible for oxidation redox, starch and sucrose metabolism, and phenylpropanoid biosynthesis. The combined transcriptomic and metabolomic analysis revealed that 16 DEGs and 2 DAMs were involved in Flavonoid biosynthesis and 8 DEGs and 2 DAMs were involved alpha-Linolenic acid metabolism which are responsible for salinity stress tolerance through induced by exogenous ABA. Overall, ABA could enhance rice leaves growth and development mainly by regulating flavonoid biosynthesis and linoleic acid metabolism pathway

Prohexadione-calcium alleviates saline-alkali stress in soybean seedlings by improving the photosynthesis and up-regulating antioxidant defense

Soil salinization seriously restricts the growth and yield of soybeans. However, little information is available on the early growth stages of soybeans which are subjected to the gibberellin biosynthesis inhibitor, prohexadione-calcium (Pro-Ca). This study aimed to investigate the effects of exogenous Pro-Ca on saline-alkali stress-induced damages to photosynthesis and antioxidant defenses in soybean (Glycine max L.) seedlings. At the V3 growth stage, salt-tolerant genotype Hefeng 50 (HF50) and salt-sensitive genotype Kenfeng 16 (KF16) were subjected to 110 mmol L−1 mixed saline-alkali stress respectively, and then 100 mg L−1 Pro-Ca was sprayed on the leaves. Our results showed that saline-alkali stress accelerated the degradation of thylakoids, inhibited chlorophyll synthesis, reduced shoot dry weight, electron transfer rate (ETR), and peroxidase (POD) activity, the concentration of ascorbic acid (AsA) and soluble sugar, but enhanced the concentration of proline, hydrogen peroxide (H2O2) and the rate of superoxide radical (O2∙−) generation. Additionally, saline-alkali stress induced a lower decrease of the net photosynthetic rate (Pn), potential activity of PSII (Fv/F0), and maximum quantum yield of PSII (Fv/Fm) in salt-tolerant HF50 than in salt-sensitive KF16. Nevertheless, foliar spraying of exogenous Pro-Ca increased the chlorophyll content, Pn, Fv/F0, and Fv/Fm. These results were more prominent when Pro-Ca was applied to KF16 under saline-alkali conditions. Furthermore, exogenous application of Pro-Ca retarded the degradation of thylakoids, increased the ETR and the accumulation of AsA, soluble sugar, and proline, activated the activities of superoxide dismutase (SOD), catalase (CAT), and POD, and decreased the concentration of malondialdehyde (MDA), electrolyte leakage (EL), O2∙−, and H2O2. These results indicated that Pro-Ca could effectively protect soybean seedlings against damage from saline-alkali stress by regulating seedling phenotype, photosynthetic apparatus, antioxidant defense, and osmoregulation

Joint analysis of transcriptome and metabolome revealed the difference in carbohydrate metabolism between super hybrid rice and conventional rice under salt stress

With the increasingly severe problem of soil salinization worldwide, exploring the molecular mechanism of salt tolerance of super hybrid rice has become an important scientific issue. In this study, the super hybrid rice Chaoyou1000 was used as the focus of attention, and the conventional rice Huanghuazhan was used as the control to explore the molecular mechanism of salt tolerance in super hybrid rice. The joint analysis of transcriptome and metabolome found 4661 DEGs, of which 2130 were up-regulated and 2531 were down-regulated; 70 named differential metabolites were found in the positive ion mode, and 32 were found in the negative ion mode. KEGG enrichment analysis showed that the carbohydrate metabolism-related pathways enriched by DEGs and differential metabolites were “starch and sucrose metabolism”, “galactose metabolism”, “glyoxylate and dicarboxylate metabolism”, and “citrate cycle (TCA cycle)”. Specifically, we found that some critical genes involved in carbohydrate metabolism, such as LOC4330753, LOC4325448, and LOC4341069, were up-regulated; some key metabolites, such as cis-aconitate, sucrose, and raffinose, were up-regulated. The difference in the expressions of these critical genes and metabolites between the two varieties is one of the most important reasons for the high resistance of Chaoyou1000. In addition, this study found that a large number of DEGs had a strong correlation with D-pipecolic acid, niveusin C, Gly-Val Ala-Ile, 2-(3-hydroxyphenyl)ethanol 1′-glucoside, 2,6-dimethyl-7-octene-1,6-diol 8-O-glucoside, (+)-syringaresinol, 2-indanone, 2-keto-6-acetamidocaproate, 3-dehydroquinate, IRETOL, and estrone glucuronide, suggesting that these genes and corresponding metabolites may exist with functional associations and regulatory relationships. The results of this study will provide a reference for the breeding of salt-tolerant rice

Fresh perspectives on an established technique: Pulsed amplitude modulation chlorophyll <i>a</i> fluorescence.

Pulsed amplitude modulation (PAM) chlorophyll a fluorescence provides information about photosynthetic energy transduction. When reliably measured, chlorophyll a fluorescence provides detailed information about critical in vivo photosynthetic processes. Such information has recently provided novel and critical insights into how the yield potential of crops can be improved and it is being used to understand remotely sensed fluorescence, which is termed solar-induced fluorescence and will be solely measured by a satellite scheduled to be launched this year. While PAM chlorophyll a fluorometers measure fluorescence intensity per se, herein we articulate the axiomatic criteria by which instrumentally detected intensities can be assumed to assess fluorescence yield, a phenomenon quite different than fluorescence intensity and one that provides critical insight about how solar energy is variably partitioned into the biosphere. An integrated mathematical, phenomenological, and practical discussion of many useful chlorophyll a fluorescence parameters is presented. We draw attention to, and provide examples of, potential uncertainties that can result from incorrect methodological practices and potentially problematic instrumental design features. Fundamentals of fluorescence measurements are discussed, including the major assumptions underlying the signals and the methodological caveats about taking measurements during both dark- and light-adapted conditions. Key fluorescence parameters are discussed in the context of recent applications under environmental stress. Nuanced information that can be gleaned from intra-comparisons of fluorescence-derived parameters and intercomparisons of fluorescence-derived parameters with those based on other techniques is elucidated

Fresh perspectives on an established technique: Pulsed amplitude modulation chlorophyll a fluorescence.

Funder: University of Cambridge; Id: http://dx.doi.org/10.13039/501100000735Funder: Kansas State University; Id: http://dx.doi.org/10.13039/100007765Funder: Texas A&M University; Id: http://dx.doi.org/10.13039/100007904Pulsed amplitude modulation (PAM) chlorophyll a fluorescence provides information about photosynthetic energy transduction. When reliably measured, chlorophyll a fluorescence provides detailed information about critical in vivo photosynthetic processes. Such information has recently provided novel and critical insights into how the yield potential of crops can be improved and it is being used to understand remotely sensed fluorescence, which is termed solar-induced fluorescence and will be solely measured by a satellite scheduled to be launched this year. While PAM chlorophyll a fluorometers measure fluorescence intensity per se, herein we articulate the axiomatic criteria by which instrumentally detected intensities can be assumed to assess fluorescence yield, a phenomenon quite different than fluorescence intensity and one that provides critical insight about how solar energy is variably partitioned into the biosphere. An integrated mathematical, phenomenological, and practical discussion of many useful chlorophyll a fluorescence parameters is presented. We draw attention to, and provide examples of, potential uncertainties that can result from incorrect methodological practices and potentially problematic instrumental design features. Fundamentals of fluorescence measurements are discussed, including the major assumptions underlying the signals and the methodological caveats about taking measurements during both dark- and light-adapted conditions. Key fluorescence parameters are discussed in the context of recent applications under environmental stress. Nuanced information that can be gleaned from intra-comparisons of fluorescence-derived parameters and intercomparisons of fluorescence-derived parameters with those based on other techniques is elucidated

Integrated Analysis of Transcriptome and Metabolome Reveals the Regulation of Chitooligosaccharide on Drought Tolerance in Sugarcane (<i>Saccharum</i> spp. Hybrid) under Drought Stress

Sugarcane (Saccharum spp. hybrid) is an important crop for sugar and biofuels, and often suffers from water shortages during growth. Currently, there is limited knowledge concerning the molecular mechanism involved in sugarcane response to drought stress (DS) and whether chitooligosaccharide could alleviate DS. Here, we carried out a combined transcriptome and metabolome of sugarcane in three different treatment groups: control group (CG), DS group, and DS + chitooligosaccharide group (COS). A total of 12,275 (6404 up-regulated and 5871 down-regulated) differentially expressed genes (DEGs) were identified when comparing the CG and DS transcriptomes (T_CG/DS), and 2525 (1261 up-regulated and 1264 down-regulated) DEGs were identified in comparing the DS and COS transcriptomes (T_DS/COS). GO and KEGG analysis showed that DEGs associated with photosynthesis were significantly enriched and had down-regulated expression. For T_DS/COS, photosynthesis DEGs were also significantly enriched but had up-regulated expression. Together, these results indicate that DS of sugarcane has a significantly negative influence on photosynthesis, and that COS can alleviate these negative effects. In metabolome analysis, lipids, others, amino acids and derivatives and alkaloids were the main significantly different metabolites (SDMs) observed in sugarcane response to DS, and COS treatment reduced the content of these metabolites. KEGG analysis of the metabolome showed that 2-oxocarboxylic acid metabolism, ABC transporters, biosynthesis of amino acids, glucosinolate biosynthesis and valine, leucine and isoleucine biosynthesis were the top-5 KEGG enriched pathways when comparing the CG and DS metabolome (M_CG/DS). Comparing DS with COS (M_DS/COS) showed that purine metabolism and phenylalanine metabolism were enriched. Combined transcriptome and metabolome analysis revealed that pyruvate and phenylalanine metabolism were KEGG-enriched pathways for CG/DS and DS/COS, respectively. For pyruvate metabolism, 87 DEGs (47 up-regulated and 40 down-regulated) and five SDMs (1 up-regulated and 4 down-regulated) were enriched. Pyruvate was closely related with 14 DEGs (|r| > 0.99) after Pearson’s correlation analysis, and only 1 DEG (Sspon.02G0043670-1B) was positively correlated. For phenylalanine metabolism, 13 DEGs (7 up-regulated and 6 down-regulated) and 6 SDMs (1 up-regulated and 5 down-regulated) were identified. Five PAL genes were closely related with 6 SDMs through Pearson’s correlation analysis, and the novel.31257 gene had significantly up-regulated expression. Collectively, our results showed that DS has significant adverse effects on the physiology, transcriptome, and metabolome of sugarcane, particularly genes involved in photosynthesis. We further show that COS treatment can alleviate these negative effects

Prohexadione-calcium alleviates the leaf and root damage caused by salt stress in rice (Oryza sativa L.) at the tillering stage.

Salt stress, as a principal abiotic stress, harms the growth and metabolism of rice, thus affecting its yield and quality. The tillering stage is the key growth period that controls rice yield. Prohexadione-calcium (Pro-Ca) can increase the lodging resistance of plants by reducing plant height, but its effects on rice leaves and roots at the tillering stage under salt stress are still unclear. This study aimed to evaluate the ability of foliar spraying of Pro-Ca to regulate growth quality at the rice tillering stage under salt stress. The results showed that salt stress reduced the tillering ability of the rice and the antioxidant enzyme activity in the roots. Salt stress also reduced the net photosynthetic rate (Pn), stomatal conductance (Gs) and intercellular CO2 concentration (Ci) of the rice leaves and increased the contents of osmotic regulatory substances in the leaves and roots. The application of exogenous Pro-Ca onto the leaves increased the tiller number of the rice under salt stress and significantly increased the photosynthetic capacity of the leaves. Additionally, it increased the activities of antioxidant enzymes and the AsA content. The contents of an osmotic regulation substance, malondialdehyde (MDA), and H2O2 in the leaves and roots also decreased. These results suggested that Pro-Ca can increase the tillering ability, photosynthetic capacity, osmotic adjustment substance content levels and antioxidant enzyme activity levels in rice and reduce membrane lipid peroxidation, thus improving the salt tolerance of rice at the tillering stage

High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean

Abstract Background Continuous cropping stress involves such factors as biological barriers, allelopathic autotoxicity, deterioration of soil physicochemical properties, and soil fertility imbalance and is regarded as a kind of comprehensive stress limiting soybean yield and quality. Genomic DNA methylation is an important regulatory mechanism for plants to resist various environmental stresses. Therefore, it is especially worthwhile to reveal genomic methylation characteristics under stress and clarify the relationship between DNA methylation status and continuous cropping stress adaptability in soybean. Results We generated a genome-wide map of cytosine methylation induced by this kind of comprehensive stress in a tolerant soybean variety (Kang Xian 2, KX2) and a sensitive variety (He Feng, HF55) using whole-genome bisulfite sequencing (WGBS) technology. The expression of DNA demethylase genes was detected using real-time quantitative PCR (qRT-PCR). The functions of differentially methylated genes (DMGs) involved in stress response in biochemical metabolism and genetic information transmission were further assessed based on Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results showed that genomic DNA demethylation was closely related to continuous cropping comprehensive stress adaptability in soybean, which was further verified by the increasing expression of DNA demethylases ROS1 and DML. The demethylation of mCpG and mCpHpG (mCpApG preferred) contexts was more critical, which mainly occurred in gene-regulatory regions at the whole-chromosome scale. Moreover, this kind of stress adaptability may be related to various stress responders generated through strengthened glucose catabolism and amino acid and fatty acid anabolism, as well as fidelity transmission of genetic information. Conclusions Genomic DNA demethylation was closely associated with continuous cropping comprehensive stress adaptability, highlighting the promising potential of screening continuous cropping-tolerant cultivars by DNA methylation index and further exploring the application of DNA demethylases in soybean breeding