Untargeted metabolomics of strawberry (Fragaria x ananassa 'Camarosa') fruit from plants grown under osmotic stress conditions

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

Multiplatform untargeted metabolomics

Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize a few hundred metabolites at best. The uncertainty in metabolite identification commonly encountered in untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple analytical techniques) approach can improve upon the number of metabolites reliably detected and correctly assigned. This can be further improved by applying synergistic sample preparation along with the use of combinatorial or sequential non-destructive and destructive techniques. Similarly, peak detection and metabolite identification strategies that employ multiple probabilistic approaches have led to better annotation decisions. Applying these techniques also addresses the issues of reproducibility found in single platform methods. Nevertheless, the analysis of large data sets from disparate analytical techniques presents unique challenges. While the general data processing workflow is similar across multiple platforms, many software packages are only fully capable of processing data types from a single analytical instrument. Traditional statistical methods such as principal component analysis were not designed to handle multiple, distinct data sets. Instead, multivariate analysis requires multiblock or other model types for understanding the contribution from multiple instruments. This review summarizes the advantages, limitations, and recent achievements of a multiplatform approach to untargeted metabolomics.

Magnesium Nutrient Application Induces Metabolomics and Physiological Responses in Mulberry (Morus alba) Plants

Mulberry (Morus alba) is a significant plant with numerous economic benefits; however, its growth and development are affected by nutrient levels. A high level of magnesium (Mg) or magnesium nutrient starvation are two of the significant Mg factors affecting plant growth and development. Nevertheless, M. alba's metabolic response to different Mg concentrations is unclear. In this study, different Mg concentrations, optimal (3 mmol/L), high (6 mmol/L and 9 mmol/L), or low (1 and 2 mmol/L) and deficient (0 mmol/L), were applied to M. alba for three weeks to evaluate their effects via physiological and metabolomics (untargeted; liquid chromatography-mass spectrometry (LC-MS)) studies. Several measured physiological traits revealed that Mg deficiency and excess Mg altered net photosynthesis, chlorophyll content, leaf Mg content and fresh weight, leading to remarkable reductions in the photosynthetic efficiency and biomass of mulberry plants. Our study reveals that an adequate supply of the nutrient Mg promoted the mulberry's physiological response parameters (net photosynthesis, chlorophyll content, leaf and root Mg content and biomass). The metabolomics data show that different Mg concentrations affect several differential metabolite expressions (DEMs), particularly fatty acyls, flavonoids, amino acids, organic acid, organooxygen compounds, prenol lipids, coumarins, steroids and steroid derivatives, cinnamic acids and derivatives. An excessive supply of Mg produced more DEMs, but negatively affected biomass production compared to low and optimum supplies of Mg. The significant DEMs correlated positively with mulberry's net photosynthesis, chlorophyll content, leaf Mg content and fresh weight. The mulberry plant's response to the application of Mg used metabolites, mainly amino acids, organic acids, fatty acyls, flavonoids and prenol lipids, in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. These classes of compounds were mainly involved in lipid metabolism, amino acid metabolism, energy metabolism, the biosynthesis of other secondary metabolites, the biosynthesis of other amino acids, the metabolism of cofactors and vitamin pathways, indicating that mulberry plants respond to Mg concentrations by producing a divergent metabolism. The supply of Mg nutrition was an important factor influencing the induction of DEMs, and these metabolites were critical in several metabolic pathways related to magnesium nutrition. This study provides a fundamental understanding of DEMs in M. alba's response to Mg nutrition and the metabolic mechanisms involved, which may be critical to the mulberry genetic breeding program.

Study on the Comprehensive Phytochemicals and the Anti-Ulcerative Colitis Effect of Saussurea pulchella

BACKGROUND

Saussurea pulchella (SP) is a traditional medicinal plant that is widely used in folk medicine because of its diverse biological activities, particularly its anti-inflammatory effects. However, the alleviation effect of SP on ulcerative colitis (UC) has not yet been realized.

PURPOSE

To investigate the chemical composition and therapeutic effect of SP extract against UC.

METHODS

First, qualitative and quantitative analysis of SP 75% ethanol extract was performed by UPLC-Q/TOF-MS. Second, a dextran sodium sulfate (DSS) model of UC mice was developed to study the effects of SP on the symptoms, inflammatory factors, oxidative stress indexes and colon histopathology. Third, an integration of network pharmacology with metabolomics was performed to investigate the key metabolites, biological targets and metabolisms closely related to the effect of SP.

RESULTS

From the SP ethanol extract, 149 compounds were identified qualitatively and 20 were determined quantitatively. The SP could dose-dependently decrease the DAI score, spleen coefficient and the levels of TNF-α, IL-6, iNOS, MPO and MDA; increase the colon length, GSH level and SOD activity; and protect the intestinal barrier in the UC mice. Moreover, 10 metabolite biomarkers,18 targets and 5 metabolisms were found to play crucial roles in the treatment of UC with SP.

CONCLUSIONS

SP 75% ethanol extract could effectively alleviate the progression of UC and, therefore, could be classified as a novel natural treatment for UC.

Total Syntheses and Anti-inflammatory Activities of Syringin and Its Natural Analogues

Syringin (1), a natural bioactive glucoside isolated from the root of Acanthopanax senticosus (Rupr. Maxim.) Harms, possesses significant anti-inflammatory activity. In this study, we have accomplished the total syntheses of syringin (1), along with its natural analogues 2-12, from a common starting material, syringaldehyde (13), in 4-8 steps with an overall yields of 11.8-61.3%. The anti-inflammatory activities of these compounds were determined against NO production in the LPS-stimulated RAW264.7 cells. Among them, compounds 1-5, 7, and 9 exhibited different levels of anti-inflammatory activity.

Metabolomics Response to Drought Stress in Morus alba L. Variety Yu-711

Mulberry is an economically significant crop for the sericulture industry worldwide. Stresses such as drought exposure have a significant influence on plant survival. Because metabolome directly reflects plant physiological condition, performing a global metabolomic analysis is one technique to examine this influence. Using a liquid chromatography-mass spectrometry (LC-MS) technique based on an untargeted metabolomic approach, the effect of drought stress on mulberry Yu-711 metabolic balance was examined. For this objective, Yu-711 leaves were subjected to two weeks of drought stress treatment and control without drought stress. Numerous differentially accumulated metabolic components in response to drought stress treatment were revealed by multivariate and univariate statistical analysis. Drought stress treatment (EG) revealed a more differentiated metabolite response than the control (CK). We found that the levels of total lipids, galactolipids, and phospholipids (PC, PA, PE) were significantly altered, producing 48% of the total differentially expressed metabolites. Fatty acyls components were the most abundant lipids expressed and decreased considerably by 73.6%. On the other hand, the prenol lipids class of lipids increased in drought leaves. Other classes of metabolites, including polyphenols (flavonoids and cinnamic acid), organic acid (amino acids), carbohydrates, benzenoids, and organoheterocyclic, had a dynamic trend in response to the drought stress. However, their levels under drought stress decreased significantly compared to the control. These findings give an overview for the understanding of global plant metabolic changes in defense mechanisms by revealing the mulberry plant metabolic profile through differentially accumulated compounds.

Metabolomics-Based Evaluation of Crop Quality Changes as a Consequence of Climate Change

Fruit composition determines the fruit quality and, consequently, consumer acceptance. As fruit quality can be modified by environmental conditions, it will be impacted by future alterations produced by global warming. Therefore, agricultural activities will be influenced by the changes in climatological conditions in cultivable areas, which could have a high socioeconomic impact if fruit production and quality decline. Currently, different stresses are being applied to several cultivated species to evaluate their impact on fruit metabolism and plant performance. With the use of metabolomic tools, these changes can be precisely measured, allowing us to determine changes in the patterns of individual compounds. As these changes depend on both the stress severity and the specific species involved and even on the specific cultivar, individual analysis must be conducted. To date, the most-studied crops have mainly been crops that are widely cultivated and have a high socioeconomic impact. In the near future, with the development of these metabolomic strategies, their implementation will be extended to other species, which will allow the adaptation of cultivation conditions and the development of varieties with high adaptability to climatological changes.

Comprehensive Lipidome and Metabolome Profiling Investigations of Panax quinquefolius and Application in Different Growing Regions Using Liquid Chromatography Coupled with Mass Spectrometry

Panax quinquefolius is one of the most recognized ginseng species. In this study, lipidome and metabolome extraction methods for P. quinquefolius were optimized with methanol/methyl-tert-butyl ether/water (0.3 mg/1 μL/6 μL/8 μL). A total of 497 metabolites were identified, including 365 lipids and 76 ginsenosides. Comprehensive lipidome profiling was first performed for P. quinquefolius, in which 32.6% glycerophospholipids, 39.5% glycerolipids, 9.3% sphingolipids, 3.3% sterol lipids, and 15.3% fatty acyls were identified. Orthogonal partial least squares discrimination analysis (OPLS-DA) showed obvious metabolomic differences in two growing regions of China. In the northern growing region, the ratio of bilayer- to nonbilayer-forming membrane lipids (PCs/PEs, DGDGs/MGDGs), the degree of unsaturation of acyl chains in galactolipids, and the content of membrane glycerophospholipids were increased. In the eastern growing region, the synthesis of storage lipids, ceramides, and fatty acyls was increased, and secondary metabolism was enhanced with 24 differential ginsenosides found. The investigation deepens the understanding of metabolic regulation mechanisms of P. quinquefolius.

Characteristics of Fragaria vesca Yield Parameters and Anthocyanin Accumulation under Water Deficit Stress

Plants exposed to drought stress conditions often increase the synthesis of anthocyanins—natural plant pigments and antioxidants. However, water deficit (WD) often causes significant yield loss. The aim of our study was to evaluate the productivity as well as the anthocyanin content and composition of berries from cultivated Fragaria vesca “Rojan” and hybrid No. 17 plants (seedlings) grown under WD. The plants were grown in an unheated greenhouse and fully irrigated (control) or irrigated at 50% and 25%. The number of berries per plant and the berry weight were evaluated every 4 days. The anthocyanin content and composition of berries were evaluated with the same periodicity using HPLC. The effect of WD on the yield parameters of two evaluated F. vesca genotypes differed depending on the harvest time. The cumulative yield of plants under WD was not less than that of the control plants for 20–24 days after the start of the experiment. Additionally, berries accumulated 36–56% (1.5–2.3 times, depending on the harvest time) more anthocyanins compared with fully irrigated plants. Our data show that slight or moderate WD at a stable air temperature of about 20 °C positively affected the biosynthesis of anthocyanins and the yield of F. vesca berries.

Atheroprotective Properties of Costus spicatus (Jacq.) Sw. in Female Rats

Background: Costus spicatus (Jacq.) Sw. is a medicinal species frequently prescribed for the treatment of cardiovascular diseases. This study aims to evaluate the effects of this species against the development of atherosclerosis. Methods: First, an anatomical study of the C. spicatus leaves was performed. Then, the extract (ESCS) was obtained and submitted to phytochemical analysis. Female rats were treated with a single dose of ESCS (2000 mg/kg) to assess acute toxicity. Other groups of female rats received an atherogenic diet for 60 days. After 30 days, the animals were treated orally with ESCS (30 and 300 mg/kg), rosuvastatin (5 mg/kg), or vehicle once daily for 30 days. Serum lipids oxidized low-density lipoprotein, soluble adhesion molecules, interleukins 1β and 6, and markers of renal and liver function were measured. Renal function, blood pressure, electrocardiography, and vascular reactivity were also evaluated. Arteries, heart, liver, and kidney were also collected to evaluate the tissue redox state and histopathological analysis. Results: Prolonged treatment with ESCS induces significant hypolipidemic and antioxidant effects, that prevent endothelial dysfunction and modulated the local inflammatory process, reducing the evolution of the atherosclerotic disease. Conclusions: This study provides a scientific basis for the popular use of C. spicatus for the treatment of atherosclerosis.

Genome-wide identification, and characterization of the CDPK gene family reveal their involvement in abiotic stress response in Fragaria x ananassa

Calcium-dependent protein kinases (CDPKs) are encoded by a large gene family and play important roles against biotic and abiotic stresses and in plant growth and development. To date, little is known about the CDPK genes in strawberry (Fragaria x ananassa). In this study, analysis of Fragaria x ananassa CDPK gene family was performed, including gene structures, phylogeny, interactome and expression profiles. Nine new CDPK genes in Fragaria x ananassa were identified based on RNA-seq data. These identified strawberry FaCDPK genes were classified into four main groups, based on the phylogenetic analysis and structural features. FaCDPK genes were differentially expressed during fruit development and ripening, as well as in response to abiotic stress (salt and drought), and hormone (abscisic acid) treatment. In addition, the interaction network analysis pointed out proteins involved in the ABA-dependent response to plant stress via Ca²⁺ signaling, especially RBOHs. To our knowledge, this is the first report on CDPK families in Fragaria x ananassa, and it will provide valuable information for development of biofortified fruits and stress tolerant plants.

The postharvest ripening of strawberry fruits induced by abscisic acid and sucrose differs from their in vivo ripening

In this study, we compared the chemical composition of strawberry (Fragaria × ananassa) fruits that were ripened in vivo (attached to plant) to those ripened during postharvest storage. The effects of the application of abscisic acid (ABA) and sucrose on the postharvest ripening were also evaluated. The results suggested that the postharvest ripening process was dependent on the signal triggered by ABA and differed from in vivo ripening, resulting in fruits with altered chemical composition and firmness. The application of sucrose in unripe strawberries resulted in the induction of ripening, which is dependent on ABA and its derivatives. This induction was more pronounced during the first days of storage and associated with the application of mannitol rather than water, suggesting that mannitol negatively regulated the postharvest strawberry ripening. These results provide further insights into the role of ABA and sucrose in the regulation of postharvest ripening of strawberry.