Untargeted and targeted metabolomics analyses of blackberries – Understanding postharvest red drupelet disorder

Critical Review of Selected Analytical Platforms for GC-MS Metabolomics Profiling-Case Study: HS-SPME/GC-MS Analysis of Blackberry's Aroma

Data processing and data extraction are the first, and most often crucial, steps in metabolomics and multivariate data analysis in general. There are several software solutions for these purposes in GC-MS metabolomics. It becomes unclear which platform offers what kind of data and how that information influences the analysis's conclusions. In this study, selected analytical platforms for GC-MS metabolomics profiling, SpectConnect and XCMS as well as MestReNova software, were used to process the results of the HS-SPME/GC-MS aroma analyses of several blackberry varieties. In addition, a detailed analysis of the identification of the individual components of the blackberry aroma club varieties was performed. In total, 72 components were detected in the XCMS platform, 119 in SpectConnect, and 87 and 167 in MestReNova, with automatic integral and manual correction, respectively, as well as 219 aroma components after manual analysis of GC-MS chromatograms. The obtained datasets were fed, for multivariate data analysis, to SIMCA software, and underwent the creation of PCA, OPLS, and OPLS-DA models. The results of the validation tests and VIP-pred. scores were analyzed in detail.

ShinyFruit: interactive fruit phenotyping software and its application in blackberry

Introduction

Horticultural plant breeding programs often demand large volumes of phenotypic data to capture visual variation in quality of harvested products. Increasing the throughput potential of phenomic pipelines enables breeders to consider data-hungry molecular breeding strategies such as genome-wide association studies and genomic selection.

Methods

We present an R-based web application called ShinyFruit for image-based phenotyping of size, shape, and color-related qualities in fruits and vegetables. Here, we have demonstrated one potential application for ShinyFruit by comparing its estimates of fruit length, width, and red drupelet reversion (RDR) with ImageJ and analogous manual phenotyping techniques in a population of blackberry cultivars and breeding selections from the University of Arkansas System Division of Agriculture Fruit Breeding Program.

Results

ShinyFruit results shared a strong positive correlation with manual measurements for blackberry length (r = 0.96) and ImageJ estimates of RDR (r = 0.96) and significant, albeit weaker, correlations with manual RDR estimation methods (r = 0.62 - 0.70). Neither phenotyping method detected genotypic differences in blackberry fruit width, suggesting that this trait is unlikely to be heritable in the population observed.

Discussion

It is likely that implementing a treatment to promote RDR expression in future studies might strengthen the documented correlation between phenotyping methods by maximizing genotypic variance. Even so, our analysis has suggested that ShinyFruit provides a viable, open-source solution to efficient phenotyping of size and color in blackberry fruit. The ability for users to adjust analysis settings should also extend its utility to a wide range of fruits and vegetables.

Integrated Transcriptomic and Metabolomic Analyses Uncover the Differential Mechanism in Saline-Alkaline Tolerance between Indica and Japonica Rice at the Seedling Stage

Saline-alkaline stress is one of the major damages that severely affects rice (Oryza sativa L.) growth and grain yield; however, the mechanism of the tolerance remains largely unknown in rice. Herein, we comparatively investigated the transcriptome and metabolome of two contrasting rice subspecies genotypes, Luohui 9 (abbreviation for Chao2R under study, O. sativa ssp. indica, saline-alkaline-sensitive) and RPY geng (O. sativa ssp. japonica, saline-alkaline-tolerant), to identify the main pathways and important factors related to saline-alkaline tolerance. Transcriptome analysis showed that 68 genes involved in fatty acid, amino acid (such as phenylalanine and tryptophan), phenylpropanoid biosynthesis, energy metabolism (such as Glycolysis and TCA cycle), as well as signal transduction (such as hormone and MAPK signaling) were identified to be specifically upregulated in RPY geng under saline-alkaline conditions, implying that a series of cascade changes from these genes promotes saline-alkaline stress tolerance. The transcriptome changes observed in RPY geng were in high accordance with the specifically accumulation of metabolites, consisting mainly of 14 phenolic acids, 8 alkaloids, and 19 lipids based on the combination analysis of transcriptome and metabolome. Moreover, some genes involved in signal transduction as hub genes, such as PR5, FLS2, BRI1, and NAC, may participate in the saline-alkaline stress response of RPY geng by modulating key genes involved in fatty acid, phenylpropanoid biosynthesis, amino acid metabolism, and glycolysis metabolic pathways based on the gene co-expression network analysis. The present research results not only provide important insights for understanding the mechanism underlying of rice saline-alkaline tolerance at the transcriptome and metabolome levels but also provide key candidate target genes for further enhancing rice saline-alkaline stress tolerance.

Genome-wide association identifies key loci controlling blackberry postharvest quality

Introduction

Blackberry (Rubus subgenus Rubus) is a soft-fruited specialty crop that often suffers economic losses due to degradation in the shipping process. During transportation, fresh-market blackberries commonly leak, decay, deform, or become discolored through a disorder known as red drupelet reversion (RDR). Over the past 50 years, breeding programs have achieved better fruit firmness and postharvest quality through traditional selection methods, but the underlying genetic variation is poorly understood.

Methods

We conducted a genome-wide association of fruit firmness and RDR measured in 300 tetraploid fresh-market blackberry genotypes from 2019-2021 with 65,995 SNPs concentrated in genic regions of the R. argutus reference genome.

Results

Fruit firmness and RDR had entry-mean broad sense heritabilities of 68% and 34%, respectively. Three variants on homologs of polygalacturonase (PG), pectin methylesterase (PME), and glucan endo-1,3-β-glucosidase explained 27% of variance in fruit firmness and were located on chromosomes Ra06, Ra01, and Ra02, respectively. Another PG homolog variant on chromosome Ra02 explained 8% of variance in RDR, but it was in strong linkage disequilibrium with 212 other RDR-associated SNPs across a 23 Mb region. A large cluster of six PME and PME inhibitor homologs was located near the fruit firmness quantitative trait locus (QTL) identified on Ra01. RDR and fruit firmness shared a significant negative correlation (r = -0.28) and overlapping QTL regions on Ra02 in this study.

Discussion

Our work demonstrates the complex nature of postharvest quality traits in blackberry, which are likely controlled by many small-effect QTLs. This study is the first large-scale effort to map the genetic control of quantitative traits in blackberry and provides a strong framework for future GWAS. Phenotypic and genotypic datasets may be used to train genomic selection models that target the improvement of postharvest quality.

Study on the Effect of Molecular Weight on the Gut Microbiota Fermentation Properties of Blackberry Polysaccharides In Vitro

This study aimed to investigate the effect of different molecular weights on the metabolic characteristics of blackberry polysaccharides (BBP). After degradation, three fractions, namely, BBP-8, BBP-16, and BBP-24, were obtained. During fermentation, all polysaccharide fractions were significantly degraded and utilized by the intestinal microbiota, and the lower-molecular-weight polysaccharides were easier to be fermented with higher gas production and carbohydrate consumption rates. Furthermore, the monosaccharide utilization sequence of all polysaccharides was glucose > galactose > arabinose > galacturonic acid. In addition, the lower-molecular-weight polysaccharides had a faster short-chain fatty acid (SCFA) production rate but did not affect the final SCFA yields. The fermentation of BBP promoted the increase of Bacteroidetes and the decrease of Firmicutes. The proportions of Bacteroidetes in BBP, BBP-8, BBP-16, and BBP-24 were 45.41, 47.50, 48.08, and 50.09%, respectively.

Mass Spectrometry-Based Nontargeted and Targeted Analytical Approaches in Fingerprinting and Metabolomics of Food and Agricultural Research

Mass spectrometry (MS)-based techniques have been extensively applied in food and agricultural research. This review aims to address the advances and applications of MS-based analytical strategies in nontargeted and targeted analysis and summarizes the recent publications of MS-based techniques, including flow injection MS fingerprinting, chromatography-tandem MS metabolomics, direct analysis using ambient mass spectrometry, as well as development in MS data deconvolution software packages and databases for metabolomic studies. Various nontargeted and targeted approaches are employed in marker compounds identification, material adulteration detection, and the analysis of specific classes of secondary metabolites. In the newly emerged applications, the recent advances in computer tools for the fast deconvolution of MS data in targeted secondary metabolite analysis are highlighted.

Delayed Senescence and Marketability Index Preservation of Blackberry Fruit by Preharvest Application of Chitosan and Salicylic Acid

Blackberry fruits are appreciated as a source of nutrients and compounds related to benefit human health. However, they are highly perishable and very susceptible to decay factors. Current methods to improve and maintain blackberry quality are limited in use because of the fruit's fragile physical properties. Regarding these properties, it has been reported that the activities of certain enzymes are linked to senescence and fruit softening processes. This study was aimed to assess the effect of salicylic acid (SA) and chitosan (COS) as preharvest treatments on the physiology related to improving fruit conservation and preserving the marketability index of blackberry fruit. The preharvest treatments were foliar sprayed on blackberry plants at different concentrations. The activities of enzymes superoxide dismutase (SOD), catalase (CAT), phenylalanine ammonia-lyase (PAL), and polygalacturonase (PG) were measured. Total soluble solids (TSS), titratable acidity (TA), TSS/TA ratio, and marketability index (MI) were analyzed after 144 h of storage. The application of 3 mM of SA and 0.25% of COS treatments preserved the MI of blackberries by reducing leakage, red drupelet reversion (RDR), and mycelium presence in the fruit. SA application increased SOD, CAT, and PAL activities. Our results also showed that SA and COS preharvest treatments modified the activity of the cell wall degrading enzyme PG, which might play a role in improving the shelf life and resistance to decay factors of blackberry fruit without any significant effects on physicochemical properties like TSS, TA, and the TSS/TA ratio.

Seasonal Effects of Glucosinolate and Sugar Content Determine the Pungency of Small-Type (Altari) Radishes (Raphanus sativus L.)

Kimchi made from small-type (Altari) radishes grown in late spring is more pungent than that made from autumn-grown Altari radishes, which poses a major challenge in the kimchi industry. The mechanism through which the pungency of Altari radish changes seasonally has not been intensively investigated. In this study, three small-type radish cultivars with different pungency levels were cultivated in spring and autumn to identify the factors affecting the seasonal-dependent pungency of small-type radishes. The contents of pungency-related metabolite glucoraphasatin and other polar metabolites were analyzed. Although a previous study reported that the glucoraphasatin concentration affects the pungency of radish, in the current study, the concentration of neither glucoraphasatin nor its hydrolysis product (raphasatin) could fully explain the change in the pungency associated with radish cultivars grown in the two seasons. The change in the pungency of radish by season may be explained by the ratio of raphasatin content to total sweetness of sugars. In addition, the polar metabolites that differ with season were analyzed to identify seasonal biomarkers and understand the seasonal changed physio-biochemistry.

Phytonutrients and Metabolism Changes in Topped Radish Root and Its Detached Leaves during 1 °C Cold Postharvest Storage

Glucosinolates, lipid-soluble vitamins E and K contents, primary metabolites and plant hormones were analyzed from topped radish root and detached leaf during storage at 1 °C. The topped root was analyzed at 0, 5, 15, 30, and 90 days after storage while the detached leaf was analyzed at 0, 5, 15, 30, and 45 days in an airtight storage atmosphere environment. The results showed that aliphatic glucosinolates were gradually decreased in leaf but not in root. There was a highly significant correlation between tryptophan and 4-methoxyindoleglucobrassicin in both tissues (r = 0.922, n = 10). There was no significant difference in vitamins E and K in leaf and root during storage. Plant hormones partially explained the significantly changed metabolites by tissue and time, which were identified during cold storage. Phenylalanine, lysine, tryptophan, and myo-inositol were the most important biomarkers that explained the difference in leaf and root tissue during cold storage. The most different metabolism between leaf and root tissue was starch and sucrose metabolism. Therefore, different postharvest technology or regimes should be applied to these tissues.

Metabolite and Elastase Activity Changes in Beach Rose (Rosa rugosa) Fruit and Seeds at Various Stages of Ripeness

Rose hips are the fruits of the beach rose (Rosa rugosa). To determine the optimal harvest time and to obtain the maximum functional compounds, rose hips at various stages of ripeness (immature, early, mid, and late) were harvested, and the flesh tissue and seeds were separated. The rose hip flesh showed the highest total phenolic content at the mid-ripeness stage (8.45 ± 0.62 mg/g gallic acid equivalent concentration (dry weight)). The early-, mid-, and late-ripeness stages of rose hip flesh did not show significantly different 2,2-diphenyl-1-picrylhydrazyl antioxidant capacities. The elastase inhibitory activity of the 95% ethanol extract from the rose hip seeds was highest at the mid-ripeness stage; however, the elastase inhibitory activity of the rose hip tissue was not significantly different from that of the seeds. Pathway analysis using MetaboAnalyst showed that sucrose, fructose, and glucose gradually increased as the fruit ripened. Ursolic acid was detected in the seeds but not in the flesh. Of the fatty acids, linoleic acid concentrations were highest in rose hip seeds, followed by linolenic acid, oleic acid, and palmitic acid. Fatty acids and ursolic acid might be the active compounds responsible for elastase inhibitory activity and can be utilized as a functional cosmetic material.

Effects of the Addition of Herbs on the Properties of Doenjang

Three types of doenjang, a fermented soybean paste, were prepared by adding coriander (CR), Korean mint (KM), and peppermint (PM) and compared to the control group (CN) by studying their metabolite profiles and antioxidant activities followed by different fermentation periods (1, 30, and 150 days, respectively). The primary metabolome was analyzed by GC-TOF-MS, and 36 of metabolites were identified in four types of doenjang samples (CN, CR, KM, and PM). Samples were clustered based on the herb type and fermentation period in PCA and PLS-DA analysis. For the secondary metabolome analysis, UHPLC-Q-orbitrap-MS was used, and 26 metabolites were identified. The statistical analysis showed that the samples were clustered by herb type rather than fermentation period, and the samples containing KM and PM were located in the same group. The DPPH assay showed that PM-containing doenjang had the highest antioxidant activity. Correlation analysis indicated that organic acids such as lactic acid, malonic acid, succinic acid, uracil, vanillic acid, and quinic acid showed positive correlation with the DPPH activity. Overall, our results demonstrated that incorporating herbs in doenjang during fermentation caused significant shifts (p-value < 0.05) in the doenjang metabolites and antioxidant activity. Hence, herbs could be utilized for enhancing doenjang fermentation.

Comparative Metabolomic and Transcriptomic Studies Reveal Key Metabolism Pathways Contributing to Freezing Tolerance Under Cold Stress in Kiwifruit

Cold stress poses a serious treat to cultivated kiwifruit since this plant generally has a weak ability to tolerate freezing tolerance temperatures. Surprisingly, however, the underlying mechanism of kiwifruit's freezing tolerance remains largely unexplored and unknown, especially regarding the key pathways involved in conferring this key tolerance trait. Here, we studied the metabolome and transcriptome profiles of the freezing-tolerant genotype KL (Actinidia arguta) and freezing-sensitive genotype RB (A. arguta), to identify the main pathways and important metabolites related to their freezing tolerance. A total of 565 metabolites were detected by a wide-targeting metabolomics method. Under (-25°C) cold stress, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway annotations showed that the flavonoid metabolic pathways were specifically upregulated in KL, which increased its ability to scavenge for reactive oxygen species (ROS). The transcriptome changes identified in KL were accompanied by the specific upregulation of a codeinone reductase gene, a chalcone isomerase gene, and an anthocyanin 5-aromatic acyltransferase gene. Nucleotides metabolism and phenolic acids metabolism pathways were specifically upregulated in RB, which indicated that RB had a higher energy metabolism and weaker dormancy ability. Since the LPCs (LysoPC), LPEs (LysoPE) and free fatty acids were accumulated simultaneously in both genotypes, these could serve as biomarkers of cold-induced frost damages. These key metabolism components evidently participated in the regulation of freezing tolerance of both kiwifruit genotypes. In conclusion, the results of this study demonstrated the inherent differences in the composition and activity of metabolites between KL and RB under cold stress conditions.

Comparative study on the effect of extraction solvent on the physicochemical properties and bioactivity of blackberry fruit polysaccharides

In this study, hot water, 0.1 M HCl and 0.1 M NaOH and 0.1 M NaCl solution were separately used for extraction of blackberry polysaccharides (BPs: Hw, Ac, Al and Na). The physicochemical properties and biological activities were then investigated and compared. Results showed that the extraction yield, molecular weight, monosaccharide composition, particle size, triple-helical structure, surface morphology and rheological properties of BPs were greatly affected by extraction solvents. Bioactivity assays implied that the four BPs showed that the polysaccharides (Hw and Na) with higher molecular weight had stronger antioxidant and α-glucosidase inhibitory activity. Moreover, anti-glycated assay indicated that BPs with higher molecular weight and higher content of galacturonic acid possessed better inhibition of AGEs formation. These results suggested that the higher molecular weight of blackberry polysaccharide could be developed as a beneficial bioactive ingredient for diabetes mellitus and complications.

Effect of PLA Active Packaging Containing Monoterpene-Cyclodextrin Complexes on Berries Preservation

Blackberries and raspberries are highly perishable and fragile products, which limits their shelf life. The effect of biodegradable active packaging of blackberries and raspberries containing 2.5% and 5.0% weight (wt%) of thymol or carvacrol complexed in β-cyclodextrins (β-CDs), successively added to poly (lactic acid) (PLA), and melt-processed by injection molding was evaluated under stored conditions at 4 °C for 21 days, using as reference commercial clamshell and PLA package control samples. Thus, physicochemical, headspace, microbiological, and sensory quality studies were carried out in order to compare the efficacy of the different packages. Concerning weight loss, color, and total phenolic and soluble solids content, significant differences were detected when compared with commercial clamshell packaging. The results show that the PLA packages containing thymol and carvacrol complexes maintained the color, weight, and phenolic content of berries until day 21, with a score up to 45% better compared to commercial clamshell. The headspace analysis detected 101 mg L⁻¹ (ppm) of thymol and 35 ppm of carvacrol on the first day of refrigeration; these concentrations decreased with time. This release mechanism of carvacrol and thymol into the PLA package modified the initial atmosphere composition. After 21 days of storage, the berries had 4.25 degrees of acceptance, without adverse perception of aroma or flavor for both carvacrol and thymol compounds. A general microbial inhibition was observed for yeast and molds, which increased with the concentration of monoterpene in PLA packages, and showed an inhibition of 3.5 log units for PLA packages containing thymol, and of 3 log units for those containing carvacrol. Overall results show that PLA/β-CD-thymol 5.0% packages prolonged raspberries’ and blackberries’ shelf life by one more week at 4 °C, compared with commercial clamshell packaging.

The structure, conformation, and hypoglycemic activity of a novel heteropolysaccharide from the blackberry fruit

A novel heteropolysaccharide fraction (BBP-24-3) with a relative molecular weight of 145.1 kDa was isolated from blackberry fruits. The BBP-24-3 was mainly composed of arabinose, glucose, and galacturonic acid with a ratio of 5.30 : 3.60 : 91.10 mol%. Structural analysis showed that BBP-24-3 possessed a 1,6-linked β-d-Glcp, 1, 2, 3, 5 linked α-l-Araf, and 1, 4 linked α-d-GalpA backbone with branches substituted at the C-2 and C-5 positions of arabinose units, which included 1, 2, 3, 4 linked β-d-Glcp and T-linked β-d-GalpA. The conformation analysis indicated that BBP-24-3 exhibited a solid spherical structure with a uniform distribution in 0.1 M NaCl solution. The BBP-24-3 exhibited excellent α-glucosidase inhibitory activity with an IC50 value of 3.70 mg mL-1, which was due to the structural change, including α-helix and random coil of α-glucosidase caused by BBP-24-3. The current work suggests the potential utilization of BBP-24-3 as an α-glucosidase inhibitor in healthy food for reducing the postprandial blood glucose level.

Comprehensive investigation on volatile and non-volatile metabolites in broccoli juices fermented by animal- and plant-derived Pediococcus pentosaceus

A metabolomics approach was employed to investigate differences and correlations among key odorants and non-volatile metabolites in broccoli juices fermented by plant- and animal-derived Pediococcus pentosaceus. Forty volatile metabolites were identified by headspace solid-phase microextraction/gas chromatography-mass spectrometry. According to orthogonal projections to latent structures-differential analysis, 24 and 21 differential volatiles were detected after fermentation by plant- and animal-derived P. pentosaceus, respectively. The concentrations of 10 odorants (OAV ≥ 1) detected by gas chromatography-olfactometry changed significantly after fermentation by P. pentosaceus. Using ultrahigh-pressure liquid chromatography/quadrupole time-of-flight mass spectrometry, 49.47% of the non-volatile metabolites were classified as lipids and lipid-like molecules. The relative expressions of five non-volatile metabolites that exhibited significant correlations with odorants using Spearman correlation analysis changed significantly after fermentation. Fermentation with animal- and plant-derived P. pentosaceus can therefore change key odorants and non-volatile metabolites in broccoli juice that contribute to the characteristic organoleptic properties of products.

Metabolite Changes during Postharvest Storage: Effects on Fruit Quality Traits

Metabolic changes occurring in ripe or senescent fruits during postharvest storage lead to a general deterioration in quality attributes, including decreased flavor and ‘off-aroma’ compound generation. As a consequence, measures to reduce economic losses have to be taken by the fruit industry and have mostly consisted of storage at cold temperatures and the use of controlled atmospheres or ripening inhibitors. However, the biochemical pathways and molecular mechanisms underlying fruit senescence in commercial storage conditions are still poorly understood. In this sense, metabolomic platforms, enabling the profiling of key metabolites responsible for organoleptic and health-promoting traits, such as volatiles, sugars, acids, polyphenols and carotenoids, can be a powerful tool for further understanding the biochemical basis of postharvest physiology and have the potential to play a critical role in the identification of the pathways affected by fruit senescence. Here, we provide an overview of the metabolic changes during postharvest storage, with special attention to key metabolites related to fruit quality. The potential use of metabolomic approaches to yield metabolic markers useful for chemical phenotyping or even storage and marketing decisions is highlighted.

The impact of phenanthrene on membrane phospholipids and its biodegradation by Sphingopyxis soli

The direct interactions of bacterial membranes and polycyclic aromatic hydrocarbons (PAHs) strongly influence the biological processes, such as metabolic activity and uptake of substrates due to changes in membrane lipids. However, the elucidation of adaptation mechanisms as well as membrane phospholipid alterations in the presence of phenanthrene (PHE) from α-proteobacteria has not been fully explored. This study was conducted to define the degradation efficiency of PHE by Sphingopyxis soli strain KIT-001 in a newly isolated from Jeonju river sediments and to characterize lipid profiles in the presence of PHE in comparison to cells grown on glucose using quantitative lipidomic analysis. This strain was able to respectively utilize 1-hydroxy-2-naphthoic acid and salicylic acid as sole carbon source and approximately 90% of PHE (50 mg/L) was rapidly degraded via naphthalene route within 1 day incubation. In the cells grown on PHE, strain KIT-001 appeared to dynamically change profiles of metabolite and lipid in comparison to cells grown on glucose. The levels of primary metabolites, phosphatidylethanolamines (PE), and phosphatidic acids (PA) were significantly decreased, whereas the levels of phosphatidylcholines (PC) and phosphatidylglycerols (PG) were significantly increased. The adaptation mechanism of Sphingopyxis sp. regarded mainly the accumulation of bilayer forming lipids and anionic lipids to adapt more quickly under restricted nutrition and toxicity condition. Hence, these findings are conceivable that strain KIT-001 has a good adaptive ability and biodegradation for PHE through the alteration of phospholipids, and will be helpful for applications for effective bioremediation of PAHs-contaminated sites.

1H-NMR Metabolomics Analysis of the Effect of Rubusoside on Serum Metabolites of Golden Hamsters on a High-Fat Diet

Rubusoside is a natural sweetener and the active component of Rubus suavissimus. The preventive and therapeutic effect of rubusoside on high-fat diet-induced (HFD) serum metabolite changes in golden hamsters was analyzed by ¹H-NMR metabolomics to explore the underlying mechanism of lipid metabolism regulation. ¹H-NMR serum metabolomics analyses revealed a disturbed amino acid-, sugar-, fat-, and energy metabolism in HFD animals. Animals supplemented with rubusoside can partly reverse the metabolism disorders induced by high-fat diet and exerted good anti-hypertriglyceridemia effect by intervening in some major metabolic pathways, involving amino acid metabolism, synthesis of ketone bodies, as well as choline and 4-hydroxyphenylacetate metabolism. This study indicates that rubusoside can interfere with and normalize high-fat diet-induced metabolic changes in serum and could provide a theoretical basis to establish rubusoside as a potentially therapeutic tool able to revert or prevent lipid metabolism disorders.