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The distribution of secondary metabolites in plant tissues plays a crucial role in determining their pharmacological properties. In this study, we investigated the dynamics of the bioactive compounds in Adenophora triphylla, a medicinal herb with diverse therapeutic applications.The anti-inflammatory properties of the EtOAc fraction from the aerial part extract (A_ EtF) exhibited an IC50 value of 27.2 ± 2.3 μg/mL, significantly surpassing that of the EtOAc fraction from the root extract (R_EtF) with an IC50 of 38.9 ± 2.9 μg/mL. Similarly, the anti-melanogenic activity of A_EtF (IC50 = 68.9 ± 2.3 μg/mL) outperformed that of R_EtF (IC50 = 90.0 ± 5.5 μg/mL). Analysis of the distinct chemical profiles of these tissues using UPLC-ESI-Q-TOF-MS revealed that the distribution of secondary metabolites contributes to the observed variations in pharmacological properties between the aerial parts and roots. Transcriptome analysis further elucidated spatially regulated genes associated with secondary metabolism, highlighting the role of AbtYABBYs as potential regulators of phenylpropanoid biosynthesis. To validate their function, these genes were transiently expressed in tobacco leaves via agro-infiltration, confirming their role in modulating polyphenolic compound biosynthesis. Our findings underscore the importance of understanding spatial gene expression patterns for harnessing the complete pharmacological potential of medicinal plants. This study provides valuable insights into the spatial regulation of secondary metabolism and lays the groundwork for targeted manipulation of plant bioactivity for therapeutic and industrial applications.

Waterlogging caused by climate change has threatened the growth and production yield of crops. Although morphological and physiological changes in major crops under waterlogging have been well-defined, the effect of waterlogging on the quality of medicinal plants remains largely unknown. In this study, we analysed waterlogging-induced variations in the anti-melanogenic properties of Platycodon grandiflorus roots. Based on the analysis of melanin production and the expression levels of melanogenic enzymes, we found that waterlogging negatively impacted the anti-melanogenic properties of P. grandiflorus roots. Using UPLC-ESI-Q-TOFMS, we identified 12 compounds including platycodin D3 and platycodin A, which showed differences between untreated and waterlogging-treated roots. In addition, waterlogging led to the suppression of the triterpenoid saponin biosynthetic pathway. Taken together, our results will form an important basis for understanding the impact of climate change on the quality of medicinal plants.

This study investigated the utilization of by-products from Platycodon grandiflorus and the role of genetic diversity in their anti-melanogenic properties, focusing on the purple-flower (PF) and white-flower (WF) varieties. Our results show that the WF variety exhibited significantly higher anti-melanogenic activity, attributed to higher concentrations of key saponins such as platycodin D3 and platycodin D. These saponins demonstrated strong tyrosinase inhibitory effects as confirmed by molecular docking analysis. Further, the WF variety showed increased expression of genes involved in saponin biosynthesis, highlighting the role of genetic diversity in determining phytochemical composition and pharmacological efficacy. The superior anti-melanogenic activity of WF suggests its potential as a valuable ingredient in the cosmetic industry for skin-whitening products. Our findings emphasize the importance of utilizing by-products and selecting specific genotypes to enhance the quality and efficacy of plant-derived products. Future research should explore the full spectrum of bioactive compounds in P. grandiflorus, investigate sustainable extraction methods, and conduct clinical trials to validate the safety and effectiveness of these compounds in cosmetic and therapeutic applications.

Amaranth is a nutritionally valuable crop, as it contains phenolic acids and flavonoids, yielding diverse plant secondary metabolites (PSMs) like phytosterol, tocopherols, and carotenoids. This study explored the variations in the contents of seventeen polyphenolic compounds within the leaves of one hundred twenty Amaranthus accessions representing nine Amaranthus species. The investigation entailed the analysis of phenolic content across nine Amaranthus species, specifically A. hypochondriacus, A. cruentus, A. caudatus, A. tricolor, A. dubius, A. blitum, A. crispus, A. hybridus, and A. viridis, utilizing ultra performance liquid chromatography with photodiode array detection (UPLC-PDA). The results revealed significant differences in polyphenolic compounds among accessions in which rutin content was predominant in all Amaranthus species in both 2018 and 2019. Among the nine Amaranthus species, the rutin content ranged from 95.72 ± 199.17 μg g−1 (A. dubius) to 1485.09 ± 679.51 μg g−1 (A. viridis) in 2018 and from 821.59 ± 709.95 μg g−1 (A. tricolor) to 3166.52 ± 1317.38 μg g−1 (A. hypochondriacus) in 2019. Correlation analysis revealed, significant positive correlations between rutin and kaempferol-3-O-β-rutinoside (r = 0.93), benzoic acid and ferulic acid (r = 0.76), and benzoic acid and kaempferol-3-O-β-rutinoside (r = 0.76), whereas gallic acid showed consistently negative correlations with each of the 16 phenolic compounds. Wide variations were identified among accessions and between plants grown in the two years. The nine species and one hundred twenty Amaranthus accessions were clustered into six groups based on their seventeen phenolic compounds in each year. These findings contribute to expanding our understanding of the phytochemical traits of accessions within nine Amaranthus species, which serve as valuable resources for Amaranthus component breeding and functional material development.

Cold stress is a major environmental factor limiting agricultural expansion and crop yields, and plants have developed diverse molecular mechanisms to cope with a lifetime of exposure to cold stress. Histone modifications play a fundamental role in regulating chromatin dynamics and transcriptional activation, either directly or through protein adaptors termed effectors. Growing evidence indicates that the chromatin remodeling caused by histone modifications, including acetylation, methylation, phosphorylation, and ubiquitination, is required for stress-responsive transcription, stress adaptation, and stress memory in plants. In this mini-review, I have summarized the current knowledge regarding the histone modifications associated with plant responses to cold stress, and discussed the roles of these modifications in improving plant cold tolerance.

Genetic diversity can remarkably impact the quality of derived products. This study focused on Adenophora triphylla, an herbaceous perennial used in East Asian traditional medicine. It is known for its diverse therapeutic effects that are attributed to phytochemicals. However, despite its therapeutic potential, a comprehensive exploration of the influence of genetic diversity on the pharmaceutical properties of various A. triphylla genotypes remains unknown. To address this knowledge gap, we employed DNA barcoding regions (ITS2, matK, and psbA-trnH) to elucidate the genetic diversity among the collected genotypes. The combined application of these barcoding regions is a robust method to identify A. triphylla genotypes. In addition, leaf extracts consistently exhibited higher antioxidant potential than root extracts. Nitric oxide production was strongly inhibited by the leaf extracts of the BG genotype (IC50 = 124.52 ± 12.97 µg/mL), and the leaf extracts (200 µg/mL) of the BT genotype contained significant antimelanogenic properties (IC50 = 181.56 ± 16.17 µg/mL). Various genotypes displayed diverse levels of phytochemical content, and the total saponin content exhibited a strong correlation with various biological activities of A. triphylla, suggesting a genetic influence on their pharmaceutical attributes. These findings highlight the significance of genotype selection for optimizing health benefits and promoting the potential utilization of specific genotypes in various industries, such as cosmetics and pharmaceuticals.

Plasmodesmata (PD) play a critical role in symplasmic communication, coordinating plant activities related to growth & development, and environmental stress responses. Most developmental and environmental stress signals induce reactive oxygen species (ROS)-mediated signaling in the apoplast that causes PD closure by callose deposition. Although the apoplastic ROS signals are primarily perceived at the plasma membrane (PM) by receptor-like kinases (RLKs), such components involved in PD regulation are not yet known. Here, we show that an Arabidopsis NOVEL CYS-RICH RECEPTOR KINASE (NCRK), a PD-localized protein, is required for plasmodesmal callose deposition in response to ROS stress. We identified the involvement of NCRK in callose accumulation at PD channels in either basal level or ROS-dependent manner. Loss-of-function mutant (ncrk) of NCRK induces impaired callose accumulation at the PD under the ROS stress resembling a phenotype of the PD-regulating GLUCAN SYNTHASE-LIKE 4 (gsl4) knock-out plant. The overexpression of transgenic NCRK can complement the callose and the PD permeability phenotypes of ncrk mutants but not kinase-inactive NCRK variants or Cys-mutant NCRK, in which Cys residues were mutated in Cys-rich repeat ectodomain. Interestingly, NCRK mediates plasmodesmal permeability in mechanical injury-mediated signaling pathways regulated by GSL4. Furthermore, we show that NCRK interacts with calmodulin-like protein 41 (CML41) and GSL4 in response to ROS stress. Altogether, our data indicate that NCRK functions as an upstream regulator of PD callose accumulation in response to ROS-mediated stress signaling pathways.

Melanin is a brown or black pigment that protects skin from ultraviolet radiation and reactive oxygen species (ROS). However, overproduction of melanin is associated with lentigines, melasma, freckles and skin cancer. Licorice has shown antioxidant, anti-tumor, anti-platelet, anti-inflammatory and immunomodulatory activities and is used as a natural treatment for skin whitening. We aimed to confirm the potential of Wongam, a new cultivar of licorice developed by the Rural Development Administration (RDA), as a whitening agent in cosmetics. In addition, we verified the effect of heat treatment on the bioactivity of licorice by comparing antioxidant and anti-melanogenic activities of licorice extract before and after heating (130 °C). The heat-treated licorice extract (WH-130) showed higher radical-scavenging activities in the ABTS+ (2,2′-azino-bis-(3-ethylbenzothiazolin-6-sulfonic acid) diammonium salt) and DPPH (2,2-diphenyl-1-picrylhydrazyl) assays. In addition, WH-130 inhibited melanogenesis more effectively due to downregulation of tyrosinase in B16F10 melanoma cells than non-heated licorice extract. Moreover, heat treatment increased total phenolic content. In particular, isoliquiritigenin, an antioxidant and anti-melanogenic compound of licorice, was produced by heat treatment. In conclusion, WH-130, with increased levels of bioactive phenolics such as isoliquiritigenin, has potential for development into a novel skin whitening material with applications in cosmetics.

While the status of histone acetylation is a critical regulator of chromatin’s structure with a significant impact on plant physiology, our understanding of epigenetic regulation in the biosynthesis of active compounds in plants is limited. In this study, Platycodon grandiflorus was treated with sodium butyrate (NaB), a histone deacetylase inhibitor, to investigate the influence of histone acetylation on secondary metabolism. Its treatment with NaB increased the acetylation of histone H3 at lysine 9, 14, and 27 and enhanced the anti-melanogenic properties of P. grandiflorus roots. Through transcriptome and differentially expressed gene analyses, we found that NaB influenced the expression of genes that were involved in both primary and secondary metabolic pathways. In addition, NaB treatment caused the accumulation of polyphenolic compounds, including dihydroquercetin, gallic acid, and 2,4-dihydroxybenzoic acid. The NaB-induced transcriptional activation of genes in the phenylpropanoid biosynthetic pathway influenced the anti-melanogenic properties of P. grandiflorus roots. Overall, these findings suggest the potential of an epigenomic approach to enhance the medicinal qualities of medicinal plants.

Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy–Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.

Epigenetics is the study of hereditary changes in gene expression under the premise that the nucleotide sequence is not changed. Such hereditary changes mainly involve DNA methylation, histone modification, and chromatin remodeling. These covalent modifications play indispensable roles in regulating gene expression; DNA replication, recombination, and repair; and cell differentiation. Epigenetic modifications can be partially inherited by daughter cells during mitosis and meiosis and influenced by external factors, such as environmental stresses and supply deficits. In this review, we summarize the current knowledge regarding epigenetic factors, such as DNA methylation, histone acetylation, and regulation by non-coding RNAs, in the development and stress response of plants.

In the present study, the chemical composition of the essential oil (EO) obtained from the flowers of Abeliophyllum distichum, commonly known as white forsythia, was examined by gas chromatography–mass spectrometry (GC/MS). Thirty-five components including epoxy linalool, methyl salicylate, linalool oxide (pyranoid), and L-linalool were identified in the EO of A. distichum flowers (AfEO). In addition, the AfEO exhibited a remarkable anti-inflammatory effect in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells. We found that this anti-inflammatory effect was mediated by inhibiting the expression of proinflammatory mediators, including IL-1β, IL-6, and IL-18. Taken together, these results confirm the potential use of the AfEO as an anti-inflammatory agent for topical application.

In higher plants, S1-basic region-leucine zipper (S1-bZIP) transcription factors fulfill crucial roles in the physiological homeostasis of carbon and amino acid metabolisms and stress responses. However, very little is known about the physiological role of S1-bZIP in cruciferous vegetables. Here, we analyzed the physiological function of S1-bZIP from Brassica rapa (BrbZIP-S) in modulating proline and sugar metabolism. Overexpression of BrbZIP-S in Nicotiana benthamiana resulted in delayed chlorophyll degradation during the response to dark conditions. Under heat stress or recovery conditions, the transgenic lines exhibited a lower accumulation of H2O2, malondialdehyde, and protein carbonyls compared to the levels in transgenic control plants. These results strongly indicate that BrbZIP-S regulates plant tolerance against dark and heat stress. We propose that BrbZIP-S is a modulator of proline and sugar metabolism, which are required for energy homeostasis in response to environmental stress conditions.

BackgroundVicia bungei is an economically important forage crop in South Korea and China. Although detailed genetic and genomic data can improve population genetic studies, conservation efforts, and improved breeding of crops, few such data are available for Vicia species in general and none at all for V. bungei. Therefore, the main objectives of this study were to sequence, assemble, and annotate V. bungei chloroplast genome and to identify simple sequence repeats (SSRs) as polymorphic genetic markers.ResultsThe whole-genome sequence of V. bungei was generated using an Illumina MiSeq platform. De novo assembly of complete chloroplast genome sequences was performed for the low-coverage sequence using CLC Genome Assembler with a 200–600-bp overlap size. Vicia bungei chloroplast genome was 130,796-bp long. The genome lacked an inverted repeat unit and thus resembled those of species in the inverted repeat-lacking clade within Fabaceae. Genome annotation using Dual OrganellarGenoMe Annotator (DOGMA) identified 107 genes, comprising 75 protein-coding, 28 transfer RNA, and 4 ribosomal RNA genes. In total, 432 SSRs were detected in V. bungei chloroplast genome, including 64 mononucleotides, 14 dinucleotides, 5 trinucleotides, 4 tetranucleotides, 233 pentanucleotides, 90 hexanucleotides, and 14 complex repeated motifs. These were used to develop 232 novel chloroplast SSR markers, 39 of which were chosen at random to test amplification and genetic diversity in Vicia species (20 accessions from seven species). The unweighted pair group method with arithmetic mean cluster analysis identified seven clusters at the interspecies level and intraspecific differences within clusters.ConclusionThe complete chloroplast genome sequence of V. bungei was determined. This reference genome should facilitate chloroplast resequencing and future searches for additional genetic markers using population samples. The novel chloroplast genome resources and SSR markers will greatly contribute to the conservation of the genus Vicia and facilitate genetic and evolutionary studies of this genus and of other higher plants.

Climate change is affecting agriculture in a number of ways, such as changing water distribution, daily temperatures and salinity patterns. In this regard, plant breeding innovations and genetic engineering approaches to improve abiotic stress tolerance are necessary to avoid a decline in crop yields caused by climate change during the 21st century. In the last few years, genome editing using the CRISPR/Cas system has attracted attention as a powerful tool that can generate hereditary mutations. So far, only a few studies using the CRISPR/Cas system have been reported to improve abiotic stress tolerance, but they have clearly suggested its effective role for future applications in molecular breeding to improve abiotic stress tolerance. Accordingly, the CRISPR/Cas system application is introduced in this mini-review as a way to improve abiotic stress tolerance. Although editing efficiency and target discovery for plant CRISPR/Cas systems require further improvement, CRISPR/Cas systems will be the key approach to maintaining global food security during climate change.

Among the several sucrose-catabolizing enzymes, neutral/alkaline invertases (NINs) play crucial roles in developmental processes as well as environmental stress responses in higher plants. Despite the fact that NINs are essential enzymes for plant life, the NIN family and their evolutionary relationships are poorly understood. Therefore, in this study, we identified 11 NINs in the Brassica rapa (Chinese cabbage; BraNINs) genome, and analyzed the evolutionary mechanisms of BraNIN genes. Evolution analysis suggested that the BraNIN genes were duplicated via a segmental duplication event originating 15.81–45.25 million years ago. Furthermore, two segmental duplicated pairs (BraNIN5/6 and BraNIN7/8) were subject to negative selection. Furthermore, expression analysis of BraNINs using RNA-sequencing data suggested various functions of BraNINs during responses to drought stress. Taken together, our comparative genomic analysis of NIN genes in B. rapa provides information that will assist future studies on sucrose metabolism in sinks and sources of higher plants.

Cold stress is known as the important yield-limiting factor of heading type Kimchi cabbage (HtKc, Brassica rapa L. ssp. pekinensis), which is an economically important crop worldwide. However, the biochemical and molecular responses to cold stress in HtKc are largely unknown. In this study, we conducted transcriptome analyses on HtKc grown under normal versus cold conditions to investigate the molecular mechanism underlying HtKc responses to cold stress. A total of 2131 genes (936 up-regulated and 1195 down-regulated) were identified as differentially expressed genes and were significantly annotated in the category of “response to stimulus”. In addition, cold stress caused the accumulation of polyphenolic compounds, including p-coumaric, ferulic, and sinapic acids, in HtKc by inducing the phenylpropanoid pathway. The results of the chemical-based antioxidant assay indicated that the cold-induced polyphenolic compounds improved the free-radical scavenging activity and antioxidant capacity, suggesting that the phenylpropanoid pathway induced by cold stress contributes to resistance to cold-induced reactive oxygen species in HtKc. Taken together, our results will serve as an important base to improve the cold tolerance in plants via enhancing the antioxidant machinery.

Platycodon grandiflorus roots have been used as a foodstuff and traditional medicine for thousands of years in East Asia. In order to increase the root development of P. grandiflorus, cultivators removed the inflorescences, suggesting the possible negative effect of flowering on root development. This indicates that the genetic improvement of P. grandiflorus by late flowering is a potential approach to increase productivity. However, nothing is known about key genes integrating multiple flowering pathways in P. grandiflorus. In order to fill this gap, we identified potential homologs of the FLOWERING LOCUS T (FT) gene in P. grandiflorus. The alignment with other FT members and phylogenetic analysis revealed that the P. grandiflorus FT (PlgFT) protein contains highly conserved functional domains and belongs to the FT-like clade. The expression analysis revealed spatial variations in the transcription of PlgFT in different organs. In addition, the expression level of PlgFT was increased by high temperature but not by photoperiodic light input signals, presumably due to lacking the CONSTANS binding motif in its promoter region. Furthermore, PlgFT induced early flowering upon its overexpression in P. grandiflorus, suggesting the functional role of PlgFT in flowering. Taken together, we functionally characterized PlgFT as a master regulator of P. grandiflorus flowering under inductive high temperature, which will serve as an important target gene for improving the root productivity.

Rosa rugosa is widely used as a health food and medicine due to its broad pharmacological properties. Although the bioactivities obtained from plant materials is related to the type and amount of phytochemicals in each extract, no systematic information is available on the organ-dependent bioactivities of R. rugosa. Here, the antioxidant, anticancer, and anti-inflammatory activities of R. rugosa stem, leaf, flower, and fruit ethanol extracts were evaluated. Overall, the stem extract exhibited the highest levels of DPPH radical scavenging activity, ferric reducing power, and oxygen radical antioxidant capacity compared with other organ extracts, whereas leaves contained potent anticancer compounds that were particularly effective against A549 cells. Additionally, the leaf extract inhibited the MEK/ERK signaling pathway, resulting in the transcriptional repression of pro-inflammatory mediators in LPS-stimulated RAW 264.7 cells. Furthermore, significant correlation between phytochemical content and bioactivities indicated that phenolic compounds play as a major antioxidant compound of R. rugosa. Taken together, these findings suggested that the spatial distribution of the phytochemicals contributed to the biological activities of R. rugosa. Given that R. rugosa fruits and flowers are already being used in health foods and medicine, these results indicate that the leaves and stems of R. rugosa should also be included and used as natural sources of antioxidant, anticancer, and anti-inflammatory agents.

Perilla frutescens var. crispa (Pfc) of the family Lamiaceae is used as a medicinal plant due to its pharmacological properties. Although Pfc is an important resource for the medical nutrition industry, the variability in phytonutrients and biological activities among genotypes of Pfc is not well understood. The effects of genotype on the phytochemical composition, antioxidant activities, antimelanogenic principles, and anti-inflammatory effects of Pfc were determined using eight Pfc genotypes. Using HPLC analysis, we identified 30 polyphenolic compounds from Pfc, although variation was observed in the polyphenolic composition of Pfc genotypes. Pfc 5 exhibited antimelanogenic activity in B16F10 melanoma cells via inhibition of tyrosinase activity. In addition, Pfc 2 strongly inhibited lipopolysaccharide-induced nitric oxide production through translational downregulation of inducible NOS in RAW264 murine macrophages. Taken together, the results of our study reveal the significant impacts of genotype on phytonutrients and biological activities. This finding will assist in the breeding and genetic engineering of Pfc in order to meet future phytonutrition and health challenges.

The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.

The presence of large amounts of bioactive compounds such as saponins and flavonoids in ginseng (Panax ginseng) berry suggests its potential as a functional resource for the food and medical industries, despite the fact that been considered a useless by-products of P. ginseng. In this study, we examined the variations in the antioxidant and anti-melanogenic potential of ginseng berry during the ripening process. We found that fully ripe berry extracts (Go-S3) contained the highest level of antioxidant and anti-melanogenic activities. Phytochemical screening suggested that alterations in polyphenol contents correlated with the variation in bioactive principles of ginseng berry during the ripening process. Furthermore, results obtained by quantitative real-time PCR, western blot, tyrosinase inhibition assay and molecular docking analysis suggested that Go-S3 probably inhibits tyrosinase activity by interacting with copper-coordinating histidines and second shell residues of tyrosinase, resulting in the reduction of melanin production in α-MSH-stimulated B16F10 cells. Taken together, these finding suggest the potential of ginseng berry as a resource for functional applications in the cosmetic industries and demonstrate that fruit ripening stages have profound effects on the pharmaceutical value of ginseng berry.

Agaricus bisporus is a globally cultivated mushroom with high economic value. Despite its widespread cultivation, commercial button mushroom strains have little genetic diversity and discrimination of strains for identification and breeding purposes is challenging. Molecular markers suitable for diversity analyses of germplasms with similar genotypes and discrimination between accessions are needed to support the development of new varieties. To develop cleaved amplified polymorphic sequences (CAPs) markers, single nucleotide polymorphism (SNP) mining was performed based on the A. bisporus genome and resequencing data. A total of 70 sets of CAPs markers were developed and applied to 41 A. bisporus accessions for diversity, multivariate, and population structure analyses. Of the 70 SNPs, 62.85% (44/70) were transitions (G/A or C/T) and 37.15% (26/70) were transversions (A/C, A/T, C/G, or G/T). The number of alleles per locus was 1 or 2 (average = 1.9), and expected heterozygosity and gene diversity were 0.0–0.499 (mean = 0.265) and 0.0–0.9367 (mean = 0.3599), respectively. Multivariate and cluster analyses of accessions produced similar groups, with F-statistic values of 0.134 and 0.153 for distance-based and model-based groups, respectively. A minimum set of 10 markers optimized for accession identification were selected based on high index of genetic diversity (GD, range 0.299–0.499) and major allele frequency (MAF, range 0.524–0.817). The CAPS markers can be used to evaluate genetic diversity and population structure and will facilitate the management of emerging genetic resources.

Superoxide dismutases (SODs) are key antioxidant enzymes that can detoxify the superoxide radicals generated by various stresses. Although various plant SODs have been suggested to improve stress tolerance, SODs in garlic, an economically important vegetable grown worldwide, remain relatively unknown. In this study, we found that heat stress strongly induced the activities of Cu/ZnSODs, FeSODs, and MnSODs in garlic leaves. In addition, we cloned four garlic SODs (AsSODs) and suggest that heat stress-increased SOD activity was reflected at least by the induction of these AsSODs. The results of the agro-infiltration assay suggested that the cloned AsSODs encoded functional SOD enzymes belonging to the Cu/ZnSOD and MnSOD families. As a first step toward understanding the enzymatic antioxidant system in garlic plants, our results provide a solid foundation for an in-depth analysis of the physiological functions of the AsSOD family.

Amaranthus species are widely used as grain and leaf vegetables around the world and are potential dietary sources of antioxidants and phenolic compounds. In this study, we examined the variation in total flavonoid contents, total polyphenol contents, and antioxidant activities among 120 accessions of nine Amaranthus species. The antioxidant activity of DPPH (2,2-diphenyl-1-picrylhydrazyl) of the 120 amaranth accessions ranged from 1.1 (A. tricolor) to 75.2 (A. tricolor mg ascorbic acid equivalents (AAE)/g in 2018, and 8.5 (A. tricolor) to 68.8 (A. dubius) mg AAE/g in 2019. ABTS (2,2′-azinobis (3-ethylbenzothiazoline 6-sulfonate)) antioxidant activity ranged from 16.7 (A. tricolor) to 78.3 (A. hypochondriacus) mg AAE/g in 2018, and 36.6 (A. tricolor) to 79.2 (A. dubius) mg AAE/g in 2019. Total flavonoid content (TFC) of 2018 and 2019 ranged from 21.7 (A. caudatus) to 52.7 (A. hybridus) and from 22.3 (A. viridis) to 54.7 (A. tricolor), respectively Antioxidant activities were compared using two methods and all components were measured in plants grown both in 2018 and 2019. We identified wide variation among the accessions and between plants grown in the two years. Antioxidant activities and phytochemical contents were consistently negatively correlated. The nine species and 120 accessions clustered into three groups according to their antioxidant activities, total flavonoid contents, and total polyphenol contents in each year. These results provide information about the nutritional profiles of different Amaranthus species.

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

Plant extracts have gained more attention as natural therapeutic agents against inflammation characterized by an overproduction of several inflammatory mediators such as reactive oxygen species and pro-inflammatory cytokines. Although Abeliophyllum distichum Nakai is generally known for its ornamental value, recent pharmacological research has demonstrated its potential therapeutic properties. Thus, to further evaluate the applicability of A. distichum in the food, cosmetic, and medical industries, we identified the phytochemicals in three organ extracts (fruits: AF, branches: AB, leaves: AL) of A. distichum and determined their antioxidant and anti-inflammatory activities. Using UPLC-ESI-Q-TOF-MS, a total of 19 compounds, including dendromoniliside D, forsythoside B, isoacteoside, isomucronulatol 7-O-Glucoside, plantamajoside, and wighteone were identified in the A. distichum organ extracts. AB exhibited a strong reducing power, an oxygen radical antioxidant capacity, and radical scavenging values compared with other samples, whereas AL exhibited the best anti-inflammatory properties. Gene expression, western blot, and molecular docking analyses suggested that the anti-inflammatory effect of AL was mediated by its ability to suppress lipopolysaccharide (LPS)-induced production of reactive oxygen species and/or inhibit LPS-stimulated activation of extracellular signal-regulated protein kinases (ERK1/2) in RAW264.7 cells. Collectively, these results indicate that AL is a potential source of phytochemicals that could be used to treat inflammation-associated diseases.

We used ultraperformance liquid chromatography coupled with a photodiode-array detector and electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-PDA/ESI-Q-TOF/MS) to rapidly and accurately quantify 17 phenolic compounds. Then, we applied this method to the seed and leaf extracts of two Amaranthus species to identify and quantify phenolic compounds other than the 17 compounds mentioned above. Compounds were eluted within 30 min on a C18 column using a mobile phase (water and acetonitrile) containing 0.1% formic acid, and the specific wavelength and ion information of the compounds obtained by PDA and ESI-Q-TOF/MS were confirmed. The proposed method showed good linearity (r2 > 0.990). Limits of detection and quantification were less than 0.1 and 0.1 μg/mL, respectively. Intra- and interday precision were less than 2.4% and 1.8%, respectively. Analysis of amaranth seed and leaf extracts using the established method showed that the seeds contained high amounts of 2,4-dihydroxybenzoic acid and kaempferol, and leaves contained diverse phenolic compounds. In addition, six tentatively new phenolic compounds were identified. Moreover, seeds potentially contained 2,3-dihydroxybenzaldehyde, a beneficial bioactive compound. Thus, our method was an efficient approach for the qualitative and quantitative analysis of phenolic compounds, and could be used to investigate phenolic compounds in plants.

The development of genetically engineered cell cultures has been suggested as a potential approach for the production of target compounds from medicinal plants. In this study, we generated PAP1 (production of anthocyanin pigment 1)-overexpressing ginseng (Panax ginseng C.A. Meyer) hairy roots to improve the production of anthocyanins, as well as the bioactivity (e.g., antioxidant and whitening activities) of ginseng. Based on differentially expressed gene analysis, we found that ectopic expression of PAP1 induced the expression of genes involved in the ‘phenylpropanoid biosynthesis’ (24 genes), and ‘flavonoid biosynthesis’ (17 genes) pathways, resulting in 191- to 341-fold increases in anthocyanin production compared to transgenic control (TC) hairy roots. Additionally, PAP1-overexpressing ginseng hairy roots exhibited an approximately seven-fold higher DPPH-free radical scavenging activity and 10-fold higher ORAC value compared to the TC. In α-melanocyte-stimulating hormone-stimulated B16F10 cells, PAP1-overexpressing ginseng hairy roots strongly inhibited the accumulation of melanin by 50 to 59% compared to mock-control. Furthermore, results obtained by quantitative real-time PCR, western blot, and tyrosinase inhibition assay suggested that the anti-melanogenic activity of PAP1-overexpressing ginseng hairy roots is mediated by tyrosinase activity inhibition. Taken together, our results suggested that the ectopic expression of PAP1 is an effective strategy for the enhancement of anthocyanin production, which improves the biological activities of ginseng root cultures.

Sorbus commixta Hedl. (Rosaceae family) has a long history as a medicinal plant in East Asian countries. In this study, we evaluated the effect of S. commixta fruit extracts prepared with different ethanol concentrations on anti-melanoma activity, and the extraction yield of phenolic compounds and flavonoids. Using the partitioned fractions from the EtOH extract, we found that the butanol fraction (BF) possessed strong cytotoxic activity against SK-MEL-2 cells (human melanoma cells) but not against HDFa cells (human dermal fibroblast adult cells). Additionally, BF-induced cell death was mediated by the inhibition of the mitogen-activated protein kinase/extracellular regulated kinase (MEK/ERK) signaling pathway, coupled with the upregulation of caspase-3 activity in SK-MEL-2 cells. Furthermore, HPLC analysis of polyphenolic compounds suggested that S. commixta fruits contained several active compounds including chlorogenic acid, rutin, protocatechuic acid, and hydroxybenzoic acid, all of which are known to possess anti-cancer activities. Although this study has been carried out by cell-based approach, these results suggest that S. commixta fruits contain promising anti-melanoma compounds.

Abeliophyllum distichum Nakai is known as a monotypic genus endemic to South Korea. Currently, several pharmacological studies have revealed that A. distichum extract exhibits diverse biological functions, including anti-cancer, anti-diabetic, anti-hypertensive, and anti-inflammatory activities. In this study, we present the anti-osteoporotic activity of A. distichum extract by inhibiting osteoclast formation. First, we show that the methanolic extract of the leaves of A. distichum, but not extracts of the branches or fruits, significantly inhibits receptor activator of the NF-κB ligand (RANKL)-induced osteoclast differentiation. Second, our transcriptome analysis revealed that the leaf extract (LE) blocks sets of RANKL-mediated osteoclast-related genes. Third, the LE attenuates the phosphorylation of extracellular signal-related kinase. Finally, treatment with the LE effectively prevents postmenopausal bone loss in ovariectomized mice and glucocorticoid-induced osteoporosis in zebrafish. Our findings show that the extract of A. distichum efficiently suppressed osteoclastogenesis by regulating osteoclast-related genes, thus offering a novel therapeutic strategy for osteoporosis.

Abeliophyllum distichum Nakai, commonly called white forsythia, is a monotypic genus endemic to Korea. Although A. distichum is mainly used as an ornamental plant because of its horticultural value, recent studies have demonstrated its bioactivities, including antioxidant and anti-inflammatory activities, prompting us to investigate the potential anticancer effect of A. distichum organ extracts (leaves, fruit, and branches) against human melanoma SK-MEL-2 cells. The methanol extract of A. distichum leaves (AL) exhibited dose- and time-dependent cytotoxicities against SK-MEL-2 cells but not against HDFa human dermal fibroblasts. Based on high-performance liquid chromatography analysis, we identified 18 polyphenolic compounds from A. distichum organ extracts and suggest that differences in anticancer activity between organ extracts should be caused by different compositions of polyphenolic compounds. Additionally, the Annexin V/propidium iodide staining assay and analysis of caspase activity and expression indicated that AL induced cell death, including early and late apoptosis, as well as necrosis, by inducing the extrinsic pathway. Furthermore, we analyzed the differentially expressed genes between mock- and AL-treated cells using RNA-seq technology, suggesting that the anti-melanoma action of AL is mediated by down-regulation of the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. Taken together, these results shed light on the potential use of A. distichum as a green resource with potent anti-melanoma activity.

Bone tissue is continuously remodeled by the coordinated action of osteoclasts and osteoblasts. Nuclear factor-activated T cells c1 (NFATc1) is a well-known transcription factor for osteoclastogenesis and transcriptionally activated by the c-Fos and nuclear factor-kappa B (NF-κB) signaling pathways in response to receptor activation of NF-κB ligand (RANKL). Since excessive RANKL signaling causes an increase of osteoclast formation and bone resorption, inhibition of RANKL or its signaling pathway is an attractive therapeutic approach to the treatment of pathologic bone loss. In this study, we show that an ethyl acetate fraction (LEA) from the shiitake mushroom, Lentinula edodes, inhibited RANKL-induced osteoclast differentiation by blocking the NFATc1 signaling pathway. We found that the water extract and its subsequent ethyl acetate fraction of L. edodes significantly suppressed osteoclast formation. Comparative transcriptome analysis revealed that LEA specifically downregulated a set of RANKL target genes, including Nfatc1. Next, we found that LEA suppresses Nfatc1 expression mainly through the inhibition of the transactivity of p65 and NFATc1. Moreover, treatment of LEA rescued an osteoporotic phenotype in a zebrafish model of glucocorticoid-induced osteoporosis. Collectively, our findings define an undocumented role of the shiitake mushroom extract in regulating bone development.

Rubus coreanus Miquel is a Korean black raspberry used in folk medicine and functional foods. To investigate the biosynthesis pathway of anthocyanin in R. coreanus Miquel, the complete coding sequence of flavonoid 3′-hydroxylase (F3′H), designated as RcMF3′H1, was cloned for the first time using the Korean black raspberry transcriptome library. The deduced amino acid sequence of RcMF3′H1 contained the proline-rich “hinge” region, P450 consensus heme-binding domain, and F3′H-specific motifs. Phylogenetic analysis revealed that RcMF3′H1 was clustered into the same subgroup as other plant F3′Hs. In addition, expression analysis by quantitative real-time PCR revealed the involvement of RcMF3′H1 in methyl jasmonate-mediated anthocyanin biosynthesis. Furthermore, the ability of the RcMF3′H1 gene to complement the Arabidopsis transparent testa 7-1 mutant suggested that RcMF3′H1 encodes the functional F3′H enzyme involved in anthocyanin biosynthesis. Taken together, the cloning and molecular characterization of RcMF3′H1 will facilitate a better insight into the anthocyanin biosynthesis pathway in R. coreanus Miquel.

The present study was conducted to evaluate the antioxidant and anti-inflammatory activities of crude methanolic extract of Abeliophyllum distichum Nakai, and those of its partitioned fractions, including hexane, ethyl acetate, n-butanol, and aqueous. The antioxidant activities were analyzed by DPPH free radical scavenging and oxygen radical antioxidant capacity assay. Results showed that the BuOH fraction possessed a strong antioxidant activity through a hydrogen atom transfer reaction-based mechanism and a single electron transfer reaction-based mechanism. In lipopolysaccharide (LPS)-stimulated RAW 264.7 cells, the BuOH fraction of A. distichum methanol extract exhibited a strong inhibitory effect on the nitric oxide production and inhibited the expression of pro-inflammatory mediators, including COX-2, TNF-α, and IL-6, through the inhibition of the MEK/ERK signaling pathway. In addition, the BuOH fraction inhibited the LPS-induced ROS level through the NADPH oxidase-independent mechanism. Furthermore, HPLC analysis identified chlorogenic acid, caffeic acid, gentisic acid, rutin, ferulic acid, and quercetin, and suggested that the antioxidant and anti-inflammatory activities of the BuOH fraction should be mediated by the presence of higher amounts of caffeic acid, rutin, and ferulic acid than other fractions. Taken together, these results suggest that A. distichum extract is a source of antioxidant and anti-inflammatory compounds, and could be developed as a potential source for functional food and dietary health supplement.

Oplopanax elatus is a valuable medicinal plant in the family Araliaceae that recommends itself as source of herbal preparations. Although, as in ginseng, triterpenoid saponins make up the major bioactive component of O. elatus, nothing is known about the genes that are involved in the biosynthesis of these complex compounds, as reflected also by a lack of genomic information in public databases. Using Illumina paired-end sequencing technology, we have therefore generated a transcriptome library of O. elatus from a pooled RNA sample from different organs. 208,959 unigenes were assembled from approximately 77 million high-quality reads, and 110,202 unigenes (52.7% of the unigenes) were annotated. In addition, 47,273 cDNA-derived SSRs in 38,446 unigenes were identified as potential molecular markers. Furthermore, 122 unigenes encoding 47 putative enzymes related to the biosynthesis of the backbone of triterpenoid saponins were identified by analyzing our library. The organ-specific expression of selected genes suggests that the leaves of O. elatus are the main site of triterpenoid saponin biosynthesis. The transcriptome data reported here provides valuable and comprehensive information for further research into the metabolic pathways of O. elatus as well as into genetic variation in the Oplopanax genus. The online version of this article (doi: 10.5073/JABFQ.2017.090.004) contains supplementary files.

In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potential mRNA targets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA−mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.

Despite the completion of the Arabidopsis genome sequence, for only a relatively low percentage of the encoded proteins experimental evidence concerning their function is available. Plant proteins that harbour a single PLAT (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase) domain and belong to the PLAT-plant-stress protein family are ubiquitously present in monocot and dicots. However, the function of PLAT-plant-stress proteins is still poorly understood. Therefore, we have assessed the function of the uncharacterised Arabidopsis PLAT-plant-stress family members through a combination of functional genetic and physiological approaches. PLAT1 overexpression conferred increased abiotic stress tolerance, including cold, drought and salt stress, while loss-of-function resulted in opposite effects on abiotic stress tolerance. Strikingly, PLAT1 promoted growth under non-stressed conditions. Abiotic stress treatments induced PLAT1 expression and caused expansion of its expression domain. The ABF/ABRE transcription factors, which are positive mediators of abscisic acid signalling, activate PLAT1 promoter activity in transactivation assays and directly bind to the ABRE elements located in this promoter in electrophoretic mobility shift assays. This suggests that PLAT1 represents a novel downstream target of the abscisic acid signalling pathway. Thus, we showed that PLAT1 critically functions as positive regulator of abiotic stress tolerance, but also is involved in regulating plant growth, and thereby assigned a function to this previously uncharacterised PLAT domain protein. The functional data obtained for PLAT1 support that PLAT-plant-stress proteins in general could be promising targets for improving abiotic stress tolerance without yield penalty.

The Korean black raspberry (Rubus coreanus Miquel, KB) on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits. Over 4.86 Gb of normalized cDNA prepared from fruits was sequenced using Illumina HiSeq™ 2000, and assembled into 43,723 unigenes. Secondly, we have reported that alterations in anthocyanins and proanthocyanidins are the major factors facilitating variations in these stages of fruits. In addition, up-regulation of F3'H1, DFR4 and LDOX1 resulted in the accumulation of cyanidin derivatives during the ripening process of KB, indicating the positive relationship between the expression of anthocyanin biosynthetic genes and the anthocyanin accumulation. Furthermore, the ability of RcMCHI2 (R. coreanus Miquel chalcone flavanone isomerase 2) gene to complement Arabidopsis transparent testa 5 mutant supported the feasibility of our transcriptome library to provide the gene resources for improving plant nutrition and pigmentation. Taken together, these datasets obtained from transcriptome library and metabolic profiling would be helpful to define the gene-metabolite relationships in this non-model plant.

As energy producers, mitochondria play a pivotal role in multiple cellular processes. Although several lines of evidence suggest that differential expression of mitochondrial respiratory complexes (MRCs) has a significant impact on mitochondrial function, the role of integrated MRCs in the whole coexpression network has yet to be revealed. In this study, we construct coexpression networks based on microarray datasets from different tissues and chemical treatments to explore the role of integrated MRCs in the coexpression network and the effects of different chemicals on the mitochondrial network. By grouping MRCs as one seed target, the hypergeometric distribution allowed us to identify genes that are significantly coexpress with whole MRCs. Coexpression among 46 MRC genes (approximately 78% of MRC genes tested) was significant in the normal tissue transcriptome dataset. These MRC genes are coexpressed with genes involved in the categories “muscle system process,” “metabolic process,” and “neurodegenerative disease pathways,” whereas, in the chemically treated tissues, coexpression of these genes mostly disappeared. These results indicate that chemical stimuli alter the normal coexpression network of MRC genes. Taken together, the datasets obtained from the different coexpression networks are informative about mitochondrial biogenesis and should contribute to understanding the side effects of drugs on mitochondrial function.

Heat and drought are prominent abiotic stressors that limit crop productivity and yield, particularly concerning climate change; therefore, understanding the molecular mechanisms underlying plant stress responses is crucial for stress-tolerant crop production. This study conducted a transcriptomic analysis to elucidate how garlic (Allium sativum L.) responds to drought and heat stress conditions. Transcriptome libraries were generated to identify differentially expressed genes (DEGs) induced by drought and heat stresses. Functional classification and clustering analysis of DEGs revealed stress-specific gene expression patterns. Notably, cell wall-related genes were implicated in the drought response, whereas heat stress was associated with heat stress transcription factors and heat shock proteins. Our results provide essential information for future studies on stress tolerances in garlic. [ABSTRACT FROM AUTHOR]