Genetic, epigenetic, and HPLC fingerprint differentiation between natural and ex situ populations of Rhodiola sachalinensis from Changbai Mountain, China

Comparative plastomes of eight subgenus Chamaesyce plants and system authentication of Euphorbiae Humifusae Herba

Euphorbiae Humifusae Herba (EHH) was provided with medicinal and edible uses, but frequently was adulterated with its closely related species. Hence, this study sought to identify EHH via an integrated approach comprising data from its morphological evaluation, HPLC analysis, comparative plastomes analysis and allele-specific PCR identification. First, the morphological characteristics of 8 subgenus Chamaesyce plants were summarized. Then, HPLC analysis showed that 18 batches of EHH were adulterated or unqualified. Furthermore, the plastomes of the 8 subg. Chamaesyce species were analyzed. Phylogenetic analysis revealed a sister relationship among the 8 subg. Chamaesyce species. The allele-specific PCR authentication was developed by the nucleotide polymorphisms (SNPs) and insertions or deletions (InDels) analysis. The results of allele-specific PCR showed that 27 batches of EHH were adulterated, indicating that the superior sensitivity of molecular authentication over the other methods used. This study provided a reference for rational use and phylogenetic research of EHH.

Overexpression of Rhodiola crenulata glutathione peroxidase 5 increases cold tolerance and enhances the pharmaceutical value of the hairy roots

Rhodiola crenulata, a plant of great medicinal value found in cold high-altitude regions, has been excessively exploited due to the difficulty in cultivation. Understanding Rhodiola crenulata's adaptation mechanisms to cold environment can provide a theoretical basis for artificial breeding. Glutathione peroxidases (GPXs), critical enzymes found in plants, play essential roles in antioxidant defense through the ascorbate-glutathione cycle. However, it is unknown whether GPX5 contributes to Rhodiola crenulata's cold tolerance. In this study, we investigated the role of GPX5 in Rhodiola crenulata's cold tolerance mechanisms. By overexpressing Rhodiola crenulata GPX5 (RcGPX5) in yeast and Arabidopsis thaliana, we observed down-regulation of Arabidopsis thaliana GPX5 (AtGPX5) and increased cold tolerance in both organisms. Furthermore, the levels of antioxidants and enzyme activities in the ascorbate-glutathione cycle were elevated, and cold-responsive genes such as AtCBFs and AtCORs were induced. Additionally, RcGPX5 overexpressing lines showed insensitivity to exogenous abscisic acid (ABA), suggesting a negative regulation of the ABA pathway by RcGPX5. RcGPX5 also promoted the expression of several thioredoxin genes in Arabidopsis and interacted with two endogenous genes of Rhodiola crenulata, RcTrx2-3 and RcTrxo1, located in mitochondria and chloroplasts. These findings suggest a significantly different model in Rhodiola crenulata compared to Arabidopsis thaliana, highlighting a complex network involving the function of RcGPX5. Moreover, overexpressing RcGPX5 in Rhodiola crenulata hairy roots positively influenced the salidroside synthesis pathway, enhancing its pharmaceutical value for doxorubicin-induced cardiotoxicity. These results suggested that RcGPX5 might be a key component for Rhodiola crenulata to adapt to cold stress and overexpressing RcGPX5 could enhance the pharmaceutical value of the hairy roots.

Clustering Analysis of Natural D-borneol Resource Plants Based on Simple Sequence Repeat (SSR) Markers, Leaf Morphology, and Chemical Composition

D-borneol is a double-loop monoterpene with a wide use in the pharmaceutical, food, and cosmetics industries. Natural D-borneol can be extracted from branches and leaves of D-borneol resource plants. With the widespread use of natural D-borneol, the identification of D-borneol resource plants and the protection of germplasm resources have become the focus of research. In this study, plant leaf morphology, chemical composition, and simple sequence repeat (SSR) molecular marker analysis were used to analyze and cluster 5 species of D-borneol resource plants and their closely related species. It was found that all three analysis methods could distinguish and cluster these D-borneol resource plants to some degree. The result of SSR analysis using capillary electrophoresis was the best, and it could distinguish Mei Pian tree from Yin Xiang as well as Longnao Zhang from An Zhang. The correlation analysis between SSR similarity matrix and leaf morphology analysis and between SSR similarity matrix and chemical composition similarity matrix revealed that they both had significant correlations (P < 0.0001) and the correlation (r = 0.588) between SSR and leaf morphology was a little higher than that (r = 0.519) between SSR and chemical composition. This indicated that the environment had a greater impact on the chemical composition than on leaf morphology. The research findings will offer efficient techniques to cluster natural D-borneol resource plants and establish a theoretical basis for their future development and utilization.

Pseudotargeted metabolomics revealed the adaptive mechanism of Draba oreades Schrenk at high altitude

Strong ultraviolet radiation and low temperature environment on Gangshika Mountain, located in the eastern part of the Qilian Mountains in Qinghai Province, can force plants to produce some special secondary metabolites for resisting severe environmental stress. However, the adaptive mechanism of Draba oreades Schrenk at high altitude are still unclear. In the current study, Draba oreades Schrenk from the Gangshika Mountain at altitudes of 3800 m, 4000 m and 4200 m were collected for comprehensive metabolic evaluation using pseudotargeted metabolomics method. Through KEGG pathway enrichment analysis, we found that phenylpropanoid biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis and phenylalanine metabolism related to the biosynthesis of flavonoids were up-regulated in the high-altitude group, which may enhance the environmental adaptability to strong ultraviolet intensity and low temperature stress in high altitude areas. By TopFc20 distribution diagram, the content of flavonoids gradually increased with the elevation of altitude, mainly including apigenin, luteolin, quercetin, hesperidin, kaempferol and their derivatives. Based on the random forest model, 10 important metabolites were identified as potential biomarkers. L-phenylalanine, L-histidine, naringenin-7-O-Rutinoside-4'-O-glucoside and apigenin related to the flavonoids biosynthesis and plant disease resistance were increased with the elevation of altitude. This study provided important insights for the adaptive mechanism of Draba oreades Schrenk at high altitude by pseudotargeted metabolomics.

Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions

Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.

Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

Evaluation of Two Major Rhodiola Species and the Systemic Changing Characteristics of Metabolites of Rhodiola crenulata in Different Altitudes by Chemical Methods Combined with UPLC-QqQ-MS-Based Metabolomics

Rhodiola species have a long history of use in traditional medicine in Asian and European countries and have been considered to possess resistance to the challenges presented by extreme altitudes. However, the influence of different Rhodiola species on quality is unclear, as well as the influence of altitude on phytochemicals. In this study, the phenolic components and antioxidant abilities of two major Rhodiola species are compared, namely Rhodiolacrenulata and Rhodiola rosea, and the metabolomes of Rhodiolacrenulata from two representative elevations of 2907 and 5116 m are analyzed using a UPLC-QqQ-MS-based metabolomics approach. The results show that the phenolic components and antioxidant activities of Rhodiolacrenulata are higher than those of Rhodiola rosea, and that these effects in the two species are positively correlated with elevation. Here, 408 metabolites are identified, of which 178 differential metabolites (128 upregulated versus 50 downregulated) and 19 biomarkers are determined in Rhodiola crenulata. Further analysis of these differential metabolites showed a significant upregulation of flavonoids, featuring glucosides, the enhancement of the phenylpropanoid pathway, and the downregulation of hydrolyzed tannins in Rhodiola crenulata as elevation increased. Besides, the amino acids of differential metabolites were all upregulated as the altitude increased. Our results contribute to further exploring the Rhodiola species and providing new insights into the Rhodiola crenulata phytochemical response to elevation.

There "ain't no mountain high enough"?: The drivers, diversity and sustainability of China's Rhodiola trade

ETHNOPHARMACOLOGICAL RELEVANCE

Across Asia, Rhodiola species have been used in Bhutanese, Mongolian, Nepalese, Kazakh, Kyrgyz and Uzbek traditional medical systems. China is globally significant in terms of Rhodiola species diversity, with over 60% (55 species) of the world's 90 Rhodiola species, including 16 species found nowhere else in the world. Since the late 1980's there has been a shift from relatively low demand for infusions using chopped dried Rhodiola roots, to high 21st century demand for a wide variety of processed products. China's trade in Rhodiola products is now very diverse, with use in cosmetics and foods in addition to herbal products. Rhodiola crenulata (Hook.f. & Thomson) H.Ohba is the most widely traded species in China. In addition to R. crenulata and Rhodiola rosea L., 19 Rhodiola other species are used.

AIMS OF THE STUDY

These were to: (i) better understand why adulteration occurs in Rhodiola products; (ii) become more aware of what drives the growing market demand for Rhodiola products in China; (iii) find out whether increased demand is reflected in wholesale prices for Rhodiola raw materials traditional medicine markets; (iv) to examine Rhodiola supply chains and (v) given that wild populations are the primary supply source, to review the implications of growing demand for conservation and sustainable use.

MATERIALS AND METHODS

Firstly, we assessed growth in the diversity of Rhodiola products using three approaches: (i) by assessing patent applications for Rhodiola products in China (1990-2019); (ii) in 2018, through on-line searches of CFDA (China Food and Drug Administration) records for medicines and dietary supplements that had Rhodiola as an ingredient and (iii) by visiting retail stores in 2018 and 2019 to assess the diversity of commercial Rhodiola based products in trade. Secondly, we visited traditional medicine markets in Yunnan, Sichuan, and Qinghai provinces to investigate the trade in Rhodiola (folk taxonomy, trade names, prices, source areas, levels of processing and grading). Thirdly, we analysed the wholesale price data for Rhodiola raw materials in trade over a 16-year period (2002-2018). Fourthly, as most products come from wild collected Rhodiola species, we documented the extent of Rhodiola cultivation in China.

RESULTS

International exports of Rhodiola products from China, particularly extracts, is a major driver of commercial trade. One proxy indicator of Rhodiola product diversification in China has been the rapid rise in patent applications from single applications in 1990 and 1991, to a peak of 1017 patent applications in 2015. Wholesale price data from 2002 to 2018 shows a steady increase in wholesale prices. As the growing market for Rhodiola products in China is currently supplied entirely from wild collection, there are justifiable concerns about sustainability. Commercial cultivation needs to expand to meet future demand.

CONCLUSIONS

In contrast to Europe and North America, where R. rosea is the focal species in commerce, the trade in Rhodiola products in China is much more diverse. In the face of growing demand, both effective conservation of wild populations and cultivation are needed.

ISSR Characterization and Quantification of Purpurin and Alizarin in Rubia cordifolia L. Populations from India

Rubia cordifolia L., is an industrially viable medicinal crop and is widely exploited for the therapeutic potential of its bioactive metabolite, purpurin. The present investigation aimed to explore the chemotypic and molecular variability in seven wild populations of R. cordifolia from South Eastern Ghats region of India. Thirty-eight individuals were assessed for molecular fingerprinting (ISSR markers) and densitometric quantification of purpurin and alizarin. The populations of Yelagiri Hills and Shervaroy Hills contained the highest levels of alizarin (0.115 and 0.093%, respectively) while Pachamalai and Kolli Hills revealed the highest purpurin content (0.284 and 0.280%, respectively). Genetic diversity was generally higher in the same populations that produced higher metabolite content, with the exception of Pachamalai, suggesting a highly prioritized conservation concern. The study revealed a Nei's total gene diversity at species level of 0.266 and of 0.187 at population level, with an average population genetic differentiation of 0.28. No clear genetic or chemical structure was retrieved between the studied populations, with individuals from different locations clustering together, and no significant correlation was obtained between metabolites and genetic diversity or between these and the populations' geographic distances.

Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence

PREMISE OF THE STUDY

Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae).

METHODS

Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation.

KEY RESULTS

Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances.

CONCLUSIONS

Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations.

Molecular and chemotypic variability of forskolin in Coleus forskohlii Briq., a high value industrial crop collected from Western Himalayas (India)

Two elite germplasm(s) ofC. forskohlii viz.NBC-24 (0.728%) and NBC-16 (0.641%) were obtained as the highest accumulator of forskolin with high genetic variability (92%).

Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism

The stress-induced epimutations could be inherited over generations and play important roles in plant adaption to stressful environments. Upland rice has been domesticated in water-limited environments for thousands of years and accumulated drought-induced epimutations of DNA methylation, making it epigenetically differentiated from lowland rice. To study the epigenetic differentiation between upland and lowland rice ecotypes on their drought-resistances, the epigenetic variation was investigated in 180 rice landraces under both normal and osmotic conditions via methylation-sensitive amplified polymorphism (MSAP) technique. Great alterations (52.9~54.3% of total individual-locus combinations) of DNA methylation are recorded when rice encountering the osmotic stress. Although the general level of epigenetic differentiation was very low, considerable level of ΦST (0.134~0.187) was detected on the highly divergent epiloci (HDE). The HDE detected in normal condition tended to stay at low levels in upland rice, particularly the ones de-methylated in responses to osmotic stress. Three out of four selected HDE genes differentially expressed between upland and lowland rice under normal or stressed conditions. Moreover, once a gene at HDE was up-/down-regulated in responses to the osmotic stress, its expression under the normal condition was higher/lower in upland rice. This result suggested expressions of genes at the HDE in upland rice might be more adaptive to the osmotic stress. The epigenetic divergence and its influence on the gene expression should contribute to the higher drought-resistance in upland rice as it is domesticated in the water-limited environment.