Differential proteomic analysis of replanted Rehmannia glutinosa roots by iTRAQ reveals molecular mechanisms for formation of replant disease.

BACKGROUND: The normal growth of Rehmannia glutinosa, a widely used medicinal plant in China, is severely disturbed by replant disease. The formation of replant disease commonly involves interactions among plants, allelochemicals and microbes; however, these relationships remain largely unclear. As a result, no effective measures are currently available to treat replant disease. RESULTS: In this study, an integrated R. glutinosa transcriptome was constructed, from which an R. glutinosa protein library was obtained. iTRAQ technology was then used to investigate changes in the proteins in replanted R. glutinosa roots, and the proteins that were expressed in response to replant disease were identified. An integrated R. glutinosa transcriptome from different developmental stages of replanted and normal-growth R. glutinosa produced 65,659 transcripts, which were accurately translated into 47,818 proteins. Using this resource, a set of 189 proteins was found to be significantly differentially expressed between normal-growth and replanted R. glutinosa. Of the proteins that were significantly upregulated in replanted R. glutinosa, most were related to metabolism, immune responses, ROS generation, programmed cell death, ER stress, and lignin synthesis. CONCLUSIONS: By integrating these key events and the results of previous studies on replant disease formation, a new picture of the damaging mechanisms that cause replant disease stress emerged. Replant disease altered the metabolic balance of R. glutinosa, activated immune defence systems, increased levels of ROS and antioxidant enzymes, and initiated the processes of cell death and senescence in replanted R. glutinosa. Additionally, lignin deposition in R. glutinosa roots that was caused by replanting significantly inhibited tuberous root formation. These key processes provide important insights into the underlying mechanisms leading to the formation of replant disease and also for the subsequent development of new control measures to improve production and quality of replanted plants.

Chloroplast DNA sequencing and detailed microsatellite genotyping of all remnant populations suggests that only a single genet survives of the critically endangered plant Rehmannia japonica.

Rehmannia japonica (Thunb.) Makino ex T. Yamaz. is an endangered perennial herb species in Japan. Although earlier the Japanese considered it a variety of R. glutinosa, recent Japanese taxonomists have consistently regarded it as an independent species. According to the historical literature, Rehmannia japonica seems to have been known in China and Japan in the past. However, Chinese taxonomists do not recognize R. japonica at present. In Japan, only two populations are known, and although these populations flower every year, seed reproduction has not been observed. In this study, we aimed to reveal the phylogenetic relationships and levels of genetic diversity of R. japonica. A haplotype network based on two chloroplast DNA regions (trnL-trnF and rps16) showed that the sequences of R. japonica were distinguishable by three or four sites of indels from the most closely related species, R. chingii, consistent with the separate species status of R. japonica. An analysis of genetic diversity using twelve microsatellite loci showed that all of the ramets of R. japonica collected from two geographically isolated populations had an identical multilocus genotype, including identical heterozygous genotypes at six loci. This result indicated asexual origin of all sampled ramets. This study also suggests that the absence of sexual reproduction of R. japonica is explained by self-incompatibility combined with only a single genet remaining in the R. japonica populations.

[Advances on molecular mechanisms of Rehmannia glutinosa consecutive monoculture problem formation in multi-omics era].

Although consecutive monoculture problems have been studied for many years, no effective treatments are currently available. The complexity of systems triggered the formation of consecutive monoculture problems was one major cause. This paper elaborated the physiological and ecological mechanisms of consecutive monoculture problem formation based on the interaction relationship among multiple factors presented in the rhizosphere soil of consecutive monoculture plants. At same time, in this paper the multiple interactions among cultivated medicinal plants, autotoxic allelochemicals and rhizosphere microbial were proposed to be most important causes that derived the formation of consecutive monoculture problem. The paper also highlighted the advantage of 'omics' technologies integrating plant functional genomics and metabolomics as well as microbial macro-omics in understanding the multiple factor interaction under a particular ecological environment. Additionally, taking R. glutinosa as an example, the paper reviewed the molecular mechanism for the formation of R. glutinosa consecutive monoculture problem from the perspective of the accumulation of allelopathic autotoxins, the rhizosphere microecology catastrophe and theresponding of consecutive monoculture plants. Simultaneously, the roles of mutilple 'omics' technologies in comprehending these formation mechanism were described in detail. This paper provides finally a new insight to solve systematically the mechanism of consecutive monoculture problem formation on molecular level.

[Research progress of relationship between continuous cropping obstacles and microRNAs in Rehmannia glutinosa].

The efficacy of Rehmannia glutinosa which as a large quantity of traditional Chinese medicine is significant. However, the land must be given up after one season of R. glutinosa cultivation or replanted after a period of 8-10 years because of the severe continuous cropping obstacles. MicroRNAs is a class of endogenous non-coding small RNAs, which participate in regulation of physiological activities by target mRNA cleavage or translational repression in plants. In recent years,studies on the role of miRNAs in plants have made significant progresses,especially in medicinal plants．MiRNAs from some different medicinal plant species have been identified with regulatory effects．When plants are exposed to environmental stress, miRNAs act on stress-related genes and initiate stress-resistance mechanisms in the body against adverse factors. R. glutinosa is also a kind of environmental stress. It is conducive to deciphering the molecular mechanism of continuous cropping obstacles for us by researching miRNAs. This article reviews the production of miRNAs, mechanism, research approaches and characteristics of resisting the environmental stresses in plants, the development trends and future prospect of R. glutinosa miRNAs research.

Analysis of integrated multiple 'omics' datasets reveals the mechanisms of initiation and determination in the formation of tuberous roots in Rehmannia glutinosa.

All tuberous roots in Rehmannia glutinosa originate from the expansion of fibrous roots (FRs), but not all FRs can successfully transform into tuberous roots. This study identified differentially expressed genes and proteins associated with the expansion of FRs, by comparing the tuberous root at expansion stages (initiated tuberous root, ITRs) and FRs at the seedling stage (initiated FRs, IFRs). The role of miRNAs in the expansion of FRs was also explored using the sRNA transcriptome and degradome to identify miRNAs and their target genes that were differentially expressed between ITRs and FRs at the mature stage (unexpanded FRs, UFRs, which are unable to expand into ITRs). A total of 6032 genes and 450 proteins were differentially expressed between ITRs and IFRs. Integrated analyses of these data revealed several genes and proteins involved in light signalling, hormone response, and signal transduction that might participate in the induction of tuberous root formation. Several genes related to cell division and cell wall metabolism were involved in initiating the expansion of IFRs. Of 135 miRNAs differentially expressed between ITRs and UFRs, there were 27 miRNAs whose targets were specifically identified in the degradome. Analysis of target genes showed that several miRNAs specifically expressed in UFRs were involved in the degradation of key genes required for the formation of tuberous roots. As far as could be ascertained, this is the first time that the miRNAs that control the transition of FRs to tuberous roots in R. glutinosa have been identified. This comprehensive analysis of 'omics' data sheds new light on the mechanisms involved in the regulation of tuberous roots formation.

[Study on distribution and dynamic accumulation of catalpol and total iridoid in fresh Rehmannia glutinosa].

Iridoid glycosides were the main active ingredient of Rehmannia glutinosa, of which catalpol has the highest content. This work will provide theoretical basis for metabolic study and cultivation of iridoids on the basis of the dynamic accumulation of catalpol and total iridoids in the growth of R. glutinosa. The samples of rehmannia 85-5 were gathered in the same filed from July to October. The contents of catalpol and total iridoid glycosides were measured by HPLC and specteophotometric, respectively. The results showed that youngest leaves had the higher content of catalpol and total iridoid glyosides than that of the other two leaf ages in the same growth stage from July to September, while their content of catalpol and total iridoid glycosides were all decreased as the growth of leaves of R. glutinosa. The content of catalpol didn't differ significantly from July to September, whereas it has significantly increased in October in the three leaf stage. In the same stage, the wider the root diameter is, the higher content of the effective components are. In August and September, the total iridoid glycosides have the fastest accumulation. The content of catalpol was increased as the accumulation of total iridoid glycosides.

[Effect of substrate of edible mushroom on continuously cropping obstacle of Rehmannia glutinosa].

The continuous cultivation of Rehmannia glutinosa causes the accumulation of phenolic acids in soil. It is supposed to be the reason of the so called "continuously cropping obstacle". In this study, phenolic acids (hydroxybenzoic acid, vanillic acid, eugenol, vanillin and ferulic acid) were degraded by the extracta of all the tested spent mushroom substrate (SMS) and the maximal degradation rate was 75.3%, contributed by extraction of SMS of Pleurotus eryngii. Pot experiment indicated that hydroxybenzoic acid and vanillin in soil were also degraded effectively by SMS of P. eryngii. The employment of SMS enhanced ecophysiology index to near the normal levels, such as crown width, leaves number, leaf length, leaf width and height. At the same time, the fresh and dry weight and total catalpol concentration of tuberous root weight of R. glutinosa was increased to 2.70, 3.66, 2.25 times by employment of SMS, respectively. The increase of bacteria, fungi and actinomycetes numbers in rhizosphere soil were observed after the employment of SMS by microbial counts. The employment of SMS also enhanced the enzyme activity in soils, such as sucrase, cellulase, phosphalase, urease and catelase. These results indicated that the employment of SMS alleviated the continuously cropping obstacle of R. glutinosa in some extent.

[Observation of prime position and driving zones in process of tuberous root expanding and expression analysis of phytohormone relative genes in Rehmannia glutinosa].

In order to study the development characteristics of Rehmannia glutinosa tuberous root expansion and reveal the regulation mechanism of the genes related to hormones in this process, R. glutinosa "wen-85" was used as the experimental material in this study. R. glutinosa tuberous roots of different developmental stages were collected to observe phenotype and tissue morphology using resin semi-thin sections method. The genes related to hormone biosynthesis and response were chosen from the transcriptome of R. glutinosa, which was previously constructed by our laboratory, their expression levels at different development stages were measured by real-time quantitative PCR. The results showed that the root development could be divided into six stages: seeding, elongation, pre-expanding, mid-expanding, late-expanding and maturity stage. The anatomic characteristics indicated that the fission of secondary cambium initiated the tuberous root expansion, and the continuous and rapid division of secondary cambium and accessory cambium kept the sustained and rapid expansion of tuberous root. In addition, a large number oleoplasts were observed in root on the semi-thin and ultra-thin section. The quantitative analysis suggested that the genes related to biosynthesis and response of the IAA, CK, ABA,ethylene, JA and EB were up-regulated expressed, meanwhile, GA synthesis and response genes were down-regulated expressed and the genes of GA negative regulation factors were up-regulated expressed. The maximum levels of most genes expression occurred in the elongation and pre-expansion stage, indicating these two stages were the key periods to the formation and development of tuberous roots. Oleoplasts might be the essential cytological basis for the formation and storage of the unique medicinal components in R. glutinosa. The results of the study are helpful for explanation of development and the molecular regulation mechanism of the tuberous root in R. glutinosa.

[Abnormal change of calcium signal system on consecutive monoculture problem of Rehmannia glutinosa].

Based on the early transcriptome and digital differentially expressed profiling library construction in consecutive monoculture (two-year culturing) Rehmannia glutinosa, we screened and chose the twelve differentially expressed protein genes which might be related with calcium signal system. The spatiotemporal expression of these genes was measured by the real-time quantitative PCR, and the relative expression values of the genes related with calcium signal system in different development stages and tissues of normal growth (one-year culturing) and succession cropping of R. glutinosa (two-year culturing) was elaborated in detail. In addition, disposed succession cropping of R. glutinosa was treated with different levels of calcium signal blocking agents in order to verify the mode of action of calcium signal system on consecutive monoculture problem in R. glutinosa. Among the twelve genes, two calcium channels away from the cytoplasm were down-regulated expressed, while the ten calcium channels toward the cytoplasm were up-regulated expressed. The results implied that succession cropping caused calcium ions flowing from endoplasmic reticulum to cytoplasm. While the key genes in calcium signal respond components such as CBL, CBP, CIBP, PLC, etc. were down-regulated expressed significantly in succession cropping of R. glutinosa which were disposed with calcium signal blocking agents, the extent of the damage was relieved, and approached the normal growth (one-year culturing) level. This result strongly showed that calcium signal system participated in the perceiving, conducting and magnifying processes of succession cropping obstacles of R. glutinosa.

[Effect of continuous cropping of Rehmannia on its morphological and physiological characteristics].

OBJECTIVE: In contrast to the newly-planted plants, through measuring and analyzing the chlorophyll content, photosynthetic characteristics, root activity and enzyme activity of Rehmannia glutinosa in growth stages, the differentiation manifestation of R. glutinosa physiological activity mediated by continuous cropping was studied. METHODS: SPAD-502 chlorophyll meter was used to measure chlorophyll content and LI-6400 portable photosynthetic apparatus to determine plant photosynthetic characteristics. Plant root vigor and enzyme system were measured following reference literature. RESULTS: The problems of Rehmannia caused by continuous cropping had happened since the early stage of its growth period, and lasted throughout the whole growth period. Under the condition of continuous cropping, the chlorophyll content, photosynthetic characteristics and root activity remained at a lower level compared with the newly-planted plants, among which, the chlorophyll content and the root activity (100 days after planting) had significant differences. CONCLUSION: The insufficient photosynthesis source and the reducing of the storage capacity (root tuber) under the condition of continuous cropping might be the main reasons for these problems of R. glutinosa.

[Effects of seedling quality on growth of Rehmannia glutinosa and oligosaccharide content].

OBJECTIVE: To study the effect of seedling quality on growth, yield and quality of Rehmannia glutinosa at harvest and build a basis for its GAP. METHOD: The seedling quality of R. glutinosa in main producing regions was surveyed to understand the current status of seedling quality. Field experiments with different varieties and seedling quality were conducted to measure dry matter accumulation with different growth of R. glutinosa and oligosaccharide content, and economic yield at harvest. RESULT: The seedling was randomly selected by farmers in R. glutinosa producing regions. Seedling quality could significantly improve on seedling emergence rate, and promote seedling growth, especially with early stage R. glutinosa, finally increase yield at harvest. At harvest, 63% and 50% of yield with A and B seedling could be improved for variety of 85-5, and 50% and 47% of yield could be increased for variety of Beijing No. 1, compared to the C seeding. CONCLUSION: In cultivation, the seedlings with the diameter > 1.5 cm should be transplanted firstly.

[Spatiotemporal expression and analysis of responding consecutive monoculture genes in Rehmannia glutinosa].

OBJECTIVE: Based on previous study, authors used the suppression subtractive hybridization (SSH) technique to construct the forward and reverse subtractive cDNA libraries of consecutive monoulture Rehmannia glutinosa. Five genes related with consecutive monoculture problem of R. glutinosa were chosen from the each of two subtractive libraries. And their spatiotemporal expression was measured in order to explore the functions in consecutive monoculture problem of R. glutinosa. METHOD: Using the real-time quantitative PCR, we tested the relative expression values of the genes in different development stages and tissues of normal growth (one-year culturing) and consecutive monoculture (two-year culturing) R. glutinosa. RESULT: The five genes (calcium-dependent protein kinase, s-adenosyl-methionine synthetase, Aminocyclopropane-1-carboxylate oxidase, methyltransferase, calpain), which were chosen from the forward library had high expression in consecutive monoculture R. glutinosa, especially in root, and were hardly expression in normal growth R. glutinosa. On the contrary, the other five genes (RNA-dependent RNA polymerase, RNA replicase, DNA-directed RNA polymerase IIa, cyclin D, RNA binding protein) chosen from the reverse library had high expression in one-year R. glutinosa, but were down regulated or shut down in consecutive monoculture R. glutinosa. CONCLUSION: The key genes, which regulate inessential metabolism parthway (such as cyclin D, DNA-directed RNA polymerase IIa), were restrained or shut down in consecutive monoculture R. glutinosa. Calcium and ethylene signaling might played key roles in the formation of consecutive monoculture problem, resulting in disturbing normal metabolic process and syndrome of disease in R. glutinosa appeared in turn.

[Study on the HPCE fingerprint of Rehmannia glutinosa].

OBJECTIVE: To establish the analytical method for the fingerprint of Rehmannia glutinosa by HPCE and compare the fingerprints of Rehmannia glutinosa and its processed products. METHODS: Based on the mode of high performance capillary electrophoresis, 60 mmol/L sodium borate was used as buffer solution (5% MeOH, pH 9.5). The separation voltage was 20 kV and the detection wavelength was set at 210 nm. Catalpol was used as a reference standard, the chromatographic fingerprint were determined. The data were analyzed by fuzzy cluster and fingerprint similarity evaluation software was used to compare the similarity of samples. RESULTS: HPCE fingerprints with 7 common peaks of Rehmannia glutinosa were established preliminarily. It was discovered that a small number of samples differed from others. Regarding to the fingerprints of Rehmannia glutinosa and its processed products, there were obvious differences in the relative areas of common peaks. CONCLUSION: The method is reliable, accurate and can be used for quality control of Rehmannia glutinosa.

[Study on optimization of induction system of test-tube tuberous roots from leaves of Rehmannia glutinosa].

OBJECTIVE: To study the effect of sucrose and plant growth substances of different concentrations on the induction of test-tube tuberous roots of Rehmannia glutinosa, in order to establish an efficient system for the induction of test-tube tuberous roots from leaves of R. glutinosa. METHOD: Leaves from test-tube seedlings of 85-5 R. glutinosa were used as explants. After rooting induction, they were transferred to medium with orthogonal design for inducing test-tube tuberous roots of R. glutinosa. RESULT AND CONCLUSION: NAA played a significant role in induction of test-tube tuberous roots of R. glutinosa, followed by sucrose and 6-BA. With leaves from test-tube seedlings as the explants, the optimal medium for inducing test-tube tuberous roots of R. glutinosa was MS + BA 3.0 mg x L(-1) + NAA 0.1 mg x L(-1) + sucrose 7%. The study provides an efficient induction system for studies on artificial seeds and secondary metabolism with test-tube tuberous roots of R. glutinosa.

Differential miRNA expression in Rehmannia glutinosa plants subjected to continuous cropping.

BACKGROUND: The productivity of the medicinally significant perennial herb Rehmannia glutinosa is severely affected after the first year of cropping. While there is some information available describing the physiological and environmental causes of this yield decline, there is as yet no data regarding the changes in gene expression which occur when the species is continuously cropped. RESULTS: Using a massively parallel (Solexa) DNA sequencing platform, it was possible to identify and quantify the abundance of a large number of R. glutinosa miRNAs. We contrasted the miRNA content of first year crop plants with that of second year crop ones, and were able to show that of 89 conserved (belonging to 25 families) and six novel miRNAs (six families), 29 of the former and three of the latter were differentially expressed. The three novel miRNAs were predicted to target seven genes, and the 29 conserved ones 308 genes. The potential targets of 32 of these differentially expressed miRNAs involved in the main transcription regulation, plant development and signal transduction. A functional analysis of the differentially expressed miRNAs suggested that several of the proposed targets could be directly or indirectly responsible for the development of the tuberous root. CONCLUSION: We have compared differential miRNAs expression in the first year crop (FP) R. glutinosa plants and second year crop (SP) ones. The outcome identifies some potential leads for understanding the molecular basis of the processes underlying the difficulty of maintaining the productivity of continuously cropped R. glutinosa.

[Research on abatement measures of allelopathic autotoxicity of Rehmannia glutinosa].

OBJECTIVE: To explore effects on allelopathic autotoxicity of Rehmannia glutinosa of different abatement measures. METHOD: The experiments for abating allelopathic effects of R. glutinosa were designed with the reducing rate as a indication, three measures of the treating soil with lime nitrogen, and water washing were employed, R. glutinosa- Achyranthes bidentata rotation system and using Achyranthes bidentata as green manure, and seedling transplant were also studied for the abatement effect. RESULT: Effect of seedling transplant was the best, reducing rate of transplant and bare root transplant on the 20th day after emergence was 76.80%, 71.70%, respectively. The reducing rate of the treating soil with microorganism reached 54.25%. The effects of water washing and R. glutinosa-A. bidentata rotation system and using A. bidentata as green manure were not satisfied. Especially only using A. bidentata as green manure without rotation system worsened the allelopathic effects of R. glutinosa. CONCLUSION: All measures can abate allelopathic effects of R. glutinosa to some extent except only using A. bidentata as green manure.

[Responses of physiological ecology and quality evaluation of Rehmannia gltinosa in continuous cropping].

OBJECTIVE: To study responses of physiological ecology and quality evaluation of Rehmannia glutinosa in continuous cropping. METHOD: The potted plant R. glutinosa which consists of first cropping, 1 year continuous cropping and 2 year continuous cropping were used as experimental materials. The photosynthetic activity, descending axis vitality, the protective enzymes system and MDA content were measured, the quality was evaluated by FTIR and HPLC. RESULT: Continuous cropping reduced the content of chlorophyll in the non-first cropping R. glutinos, the photosynthetic activity and descending axis vitality were weakened. Because of the increase of the free radical in the R. glutinos due to the continuous cropping, the activity of protective enzymes including POD, SOD and CAT were enhanced and MDA content were increased, more importantly the medical potency declined . And along with the increasing years of the continuous cropping, this effect becomes even stronger. CONCLUSION: Continuous cropping affects the descending axis ability of absorbing water and nutrition and photosynthesis are inhibited R. glutinosa, at the same time, it also causes the disorders of antioxidation systems in R. glutinos, resulting in continuous cropping obstacle and decline of the medicinal materials quality.

[Preliminary study on promoting effects of endophytic fungi to growth of Rehmannia glutinosa].

In previous studies, four endophytic fungi were isolated from different swollen roots of Rehmannia glutinosa. It's thought that Ceratobasidium sp. , one of the discovered endophytic fingi, was a major promoter for the growth of the roots. In this study, symbiotic experiments were performed to measure the effects of different endophytic fingi cultivated with R. glutinosa. The results showed that the R. glutinosa had significant increases in the size of roots and amount of chlorophyll cultivated with Ceratobasidium sp. And it was tested that indoleacetic acid secreted by Ceratobasidium sp. maybe the effective factor for the promotion of the growth.

[Effects of leaf removal on growth and physiological characteristics of Rehmannia glutinosa].

Effects of the leaf-clipped treatment on growth and physiological properties of Rehmannia glutinosa were studied. Result showed that with the increase of the cutting leaves degree, growth rates of shoots and roots were decreased, sugar contents declined, chlorophyll contents decreased and root activities also inhibited. Compared with the normal plant (CK), the root inhibit rates in T1, T2, T3 were 17.53%, 33.41%, 59.47%, respectively. Physiological indexes including chlorophyll contents, root activities and sugar contents also were impacted by the leaf-clipped treatment. The results indicate that to balance source-sink relationship is a very essential method for improving production of R. glutinosa.

Comparative analysis of tuberous root metabolites between cultivated and wild varieties of Rehmannia glutinosa by widely targeted metabolomics.

Differential metabolites between tuberous roots from cultivated variety (ZP) and wild variety (YS) of Rehmannia glutinosa were analyzed by widely targeted metabolomics, and annotated to KEGG pathways. 228 secondary metabolites (SM) in ZP and YS were detected, of which 58 were differential metabolites (DM), including 41 flavonoids, 10 phenolic acids, 3 terpenoids, 2 alkaloids and 2 others, and 170 were unchanged; Among 58 DMs, 44 (75.9%) were up-regulated in YS, of which 30 were unique to YS, while 14 (24.1%) were down-regulated in YS, of which 10 were unique to ZP; Among flavonoids, 33 (80.5%) were more highly expressed in YS than in ZP; Among phenolic acids, 7 (70%) were more highly expressed in YS than in ZP; 12 of 58 DMs were annotated into 17 types of KEGG pathways. Among them, benzoic acid and p-Coumaryl alcohol were up-regulated in YS, and annotated into 10 pathways (58.8%) and 4 pathways (23.5%), respectively. In addition, much of DMs possess various pharmacological effects. These results indicated better quality of YS than ZP and the necessity of YS domestication. Taken together, this study will provide a reference for the scientific introduction, comprehensive development and utilization of wild Rehmannia glutinosa.