Overexpression of a Ramie (Boehmaeria nivea L. Gaud) Group I WRKY Gene, BnWRKY49, Increases Drought Resistance in Arabidopsis thaliana.

Plants face multiple stresses in their natural habitats. WRKY transcription factors (TFs) play an important regulatory role in plant stress signaling, regulating the expression of multiple stress-related genes to improve plant stress resistance. In this study, we analyzed the expression profiles of 25 BnWRKY genes in three stages of ramie growth (the seedling stage, the rapid-growth stage, and the fiber maturity stage) and response to abiotic stress through qRT-PCR. The results indicated that 25 BnWRKY genes play a role in different growth stages of ramie and were induced by salt and drought stress in the root and leaf. We selected BnWRKY49 as a candidate gene for overexpression in Arabidopsis. BnWRKY49 was localized in the nucleus. Overexpression of BnWRKY49 affected root elongation under drought and salt stress at the Arabidopsis seedling stage and exhibited increased tolerance to drought stress. Further research found that BnWRKY49-overexpressing lines showed decreased stomatal size and increased cuticular wax deposition under drought compared with wild type (WT). Antioxidant enzyme activities of SOD, POD, and CAT were higher in the BnWRKY49-overexpressing lines than the WT. These findings suggested that the BnWRKY49 gene played an important role in drought stress tolerance in Arabidopsis and laid the foundation for further research on the functional analysis of the BnWRKYs in ramie.

Comparative biochemical and transcriptomic analysis reveals the phosphate-starving tolerance of two ramie varieties.

Ramie (Boehmeria nivea L.) is a highly valued fiber crop. Its yield is often limited by lack of available phosphate (Pi) in the soil, but the underlying molecular mechanisms of ramie's response to Pi deficiency remain largely unknown. To investigate how ramie adapts to low Pi stress, we selected a low Pi-tolerant variety (H-5) and a low Pi-sensitive variety (XYL), and conducted a biochemical and transcriptomic analysis on roots and leaves of both varieties. After subjecting the plants to Pi-deficient and Pi-sufficient conditions for 15 days, we found that H-5 exhibited higher dry weight, longer root systems, and higher levels of Pi, galactolipids, and organic acids when subjected to Pi deprivation, compared to XYL. Transcriptomic analysis further revealed that Pi-responsive genes involved in lipid metabolism, Pi transport, organic acid synthesis, and acid phosphatase activities were more induced in the tolerant variety H-5. Furthermore, weighted gene co-expression network analysis (WGCNA) identified five hub genes, including phosphate transporter, SPX domain-containing protein and sulfoquinovosyl transferase, which played key roles in low Pi tolerance in ramie. The present study will broaden our comprehension of the differences and molecular mechanisms of different ramie cultivars in response to Pi starvation, and lay a foundation for future agronomic improvements in ramie and other fiber crops.

Medium nitrogen optimized Boehmeria nivea L. growth in copper contaminated soil.

Copper (Cu) pollution in agricultural soils is considered as a serious health risk due to its accumulation in plants. Thus, there is an urgent need to optimize nutrient application for higher yield with lower Cu uptake to ensure food security. A pot experiment was conducted to investigate the effectiveness of nitrogen fertilizer (N) on Boehmeria nivea growth, gas exchange characteristics, antioxidant capacity and uptake of Cu in contaminated soil. Therefore, combinations of Cu levels (0, 100, 300 mg kg-1) and N levels (0, 140, 280, 420 kg ha-1) were applied. The results showed that N at 280 kg ha-1 significantly (≤0.05) increased plant growth in terms of fresh biomass, plant height, stem diameter and number of leaves per plant up to100 mg kg-1 Cu in soil for all harvests (H1, H2, H3 and H4). However, the interactive effect of Cu and N on Cu uptake by plant varied among N levels. Furthermore, N at 280 kg ha-1 also improved the gas exchange characteristics viz., net photosynthesis (Pn), transpiration rate (Tr) and stomatal conductance (gs), while decreased oxidative stress in B. nivea up to 100 mg kg-1 Cu in soil, relative to control. Thus N at 280 kg ha-1 can be considered as an effective dose for high fresh biomass with lower Cu uptake by B. nivea grown as fodder in Cu contaminated soils (≤100 mg kg-1). Overall, present research highlighted the necessity of balanced or optimum N application for sustainable B. nivea forage production in Cu contaminated agricultural lands.

Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers.

Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Genetic diversity and population structure were estimated using the 59 (72 loci) validated polymorphic SSRs and three phenotypic markers. Three hundred ten alleles were identified, and the major allele frequency ranged from 0.26 to 0.85 (average: 0.56), Nei's genetic diversity ranged from 0.28 to 0.82 (average: 0.56), and the expected heterozygosity ranged from 0.28 to 0.81 (average: 0.56). The polymorphism information content ranged from 0.25 to 0.79 (average: 0.50), the observed number of alleles ranged from 2 to 8 (average: 4.13), and the effective number of alleles ranged from 0.28 to 0.81 (average: 0.5). The Cannabis population did not show mutation-drift equilibrium following analysis via the infinite allele model. A cluster analysis was performed using the unweighted pair group method using arithmetic means based on genetic distances. Population structure analysis was used to divide the germplasms into two subgroups. These results provide guidance for the molecular breeding and further investigation of Cannabis.

Promoter P PSP1-5-BnPSP-1 From Ramie (Boehmeria nivea L. Gaud.) Can Drive Phloem-Specific GUS Expression in Arabidopsis thaliana.

Isolation of phloem-specific promoters is one of the basic conditions for improving the fiber development and resistance of ramie phloem using genetic engineering. In this study, we isolated a ramie endogenous promoter (named P PSP1 -BnPSP-1) and analyzed the function of its truncated fragments in Arabidopsis. The results show that P PSP1 -BnPSP-1 can drive the GUS reporter gene to be specifically expressed in the veins of Arabidopsis. After hormone and simulated drought treatment of the independent Arabidopsis lines carrying P PSP1 -BnPSP-1 and its truncated fragments, only P PSP1-5-BnPSP-1 (-600 to -1 bp region of P PSP1 -BnPSP-1) is stably expressed and exhibits phloem specificity. Our findings suggest that P PSP1-5-BnPSP-1 can be used as a phloem specific promoter for further research.

Copper environmental toxicology, recent advances, and future outlook: a review.

Copper (Cu) is one of the micronutrients needed by living organisms. In plants, Cu plays key roles in chlorophyll formation, photosynthesis, respiratory electron transport chains, oxidative stress protection as well as protein, carbohydrate, and cell wall metabolism. Therefore, deficiency of Cu can alter various functions of plant metabolism. However, Cu-based agrochemicals have traditionally been used in agriculture and being excessively released into the environment by anthropogenic activities. Continuous and extensive release of Cu is an imperative issue with various documented cases of phytotoxicity by the overproduction of reactive oxygen species (ROS) and damage to carbohydrates, lipids, proteins, and DNA. The mobility of Cu from soil to plant tissues has several concerns including its adverse effects on humans. In this review, we have described about importance and occurrence of Cu in environment, Cu homeostasis and toxicity in plants as well as remediation and progress in research so far done worldwide in the light of previous findings. Furthermore, present review provides a comprehensive ecological risk assessment on Cu in soils and thus provides insights for agricultural soil management and protection.

Influence of rice straw biochar on growth, antioxidant capacity and copper uptake in ramie (Boehmeria nivea L.) grown as forage in aged copper-contaminated soil.

Copper (Cu) contamination in agricultural soil poses severe threats to living organisms, and possible ecofriendly solutions need to be considered for Cu immobilization, such as using biochar. A pot study was conducted to examine the effectiveness of biochar derived from rice straw (RSB) at various application rates (0, 2.5, 5 and 10% w/w) to mitigate possible risks of Cu solubility and its uptake by ramie (Boehmeria nivea L.) as forage. The plant growth parameters as well as soil chemical properties (pH, electrical conductivity and cation exchange capacity) notably improved with the increasing RSB application. Moreover, prominent reduction was observed in soil bioavailable Cu concentration by 96% with RSB application of 10% relative to control. In addition, Cu content in B. nivea roots, leaves and stems decreased by 60, 28 and 22%, respectively, for 10% RSB application. It was noted that chlorophyll content and gas exchange parameters in leaves were significantly higher at 10% RSB application than in control. Furthermore, 10% RSB resulted in a greater reduction in oxidative stress from the Cu in soil. Thus, soil amendment with RSB demonstrated positive results for Cu stabilization in aged Cu-contaminated soil, thereby reducing its accumulation and translocation in B. nivea and mitigating livestock feed security risks.

Morpho-physiological traits, antioxidant capacity and phytoextraction of copper by ramie (Boehmeria nivea L.) grown as fodder in copper-contaminated soil.

Ramie (Boehmeria nivea L.), the oldest fiber crop in China, can also be grown as fodder crop because of its huge biomass production. Moreover, it has the potential to colonize heavy metal-contaminated soils which showed the possibilities of phytoremediation using B. nivea. Therefore, the present study was conducted to investigate the potential of B. nivea for phytoextraction of copper (Cu)-contaminated soil. Moreover, the impact of different concentrations of Cu on growth and antioxidant enzymatic activity by B. nivea were also studied. For this purpose, a pot experiment was conducted to examine the growth, antioxidative response, and localization (distribution) of Cu in B. nivea plant under different Cu concentrations (0, 50, 100, 200, 300, and 400 mg kg-1 soil). Results revealed that B. nivea tolerated up to 100 mg kg-1 Cu concentration without a significant decrease in biomass, but further increase in Cu concentration from 200 to 400 mg kg-1 exhibited a significant reduction in chlorophyll content, fresh and dry biomass, plant height, and number of leaves. It was further observed that B. nivea accumulated more Cu in roots (26 to 53 mg kg-1), followed by the leaves (23 to 28 mg kg-1) and stems (14 to 21 mg kg-1), while the values for both bioaccumulation factor (BAF) and translocation factor (TF) at all treatments were less than 1. Moreover, activities of antioxidative enzymes (superoxide dismutase and peroxidase) were initially increased with the exposure of 50, 100, and 200 mg kg-1 Cu, but decreased by further increasing the Cu concentration to 300 and 400 mg kg-1 indicating the oxidative stress which is manifested by high malondialdehyde (MDA) and proline contents also. Thus, based on results, it can be concluded that B. nivea accumulated relatively low Cu contents in aboveground parts and could be grown as fodder crop for phytoremediation of Cu-contaminated sites.

Isolation and functional characterization of SUCROSE SYNTHASE 1 and SUCROSE TRANSPORTER 2 promoters from ramie (Boehmeria nivea L. Gaudich).

Sucrose synthase and sucrose transporter are involved in sucrose metabolism and partitioning of photosynthetic products, respectively. In this study, we cloned SUCROSE SYNTHASE 1 and SUCROSE TRANSPORTER 2 genes from ramie. Real-time quantitative PCR revealed that BnSUS1 and BnSUT2 were widely expressed in the analyzed tissues. Subsequently, the two promoters of BnSUS1 and BnSUT2 were isolated and truncated. The two promoters and their truncated fragments were fused GUS to transform into Arabidopsis. GUS staining showed that BnSUS1pro-1690 and BnSUS1pro-1420 had vascular specificity in cotyledons and mature leaves while BnSUT2pro-2239, BnSUT2pro-1681, BnSUT2pro-1199 and BnSUT2pro-618 had a constitutive function in seedlings and mature organs. Notably, the activity of BnSUT2pro-2239 and its fragments (except that of BnSUT2pro-231) are strongly induced by mechanical wounding. Moreover, BnSUS1pro-1051 and BnSUS1pro-485 are sensitive to CuSO4 treatment while BnSUT2pro-2239 and BnSUT2pro-1681 are sensitive to PEG and ABA treatments, respectively. Our findings will provide the foundation for deciphering the functions of BnSUS1 and BnSUT2, and also expand the promoter library to provide more options for plant genetic engineering.

Identification and expression characterization of the Phloem Protein 2 (PP2) genes in ramie (Boehmeria nivea L. Gaudich).

Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in sieve elements and companion cells, which play important roles in the maintenance of morphology, photoassimilate transportation and wound protection in higher plants, but to date, no PP2 (BnPP2) genes had been identified in ramie. Here, a total of 15 full-length BnPP2 genes were identified. These BnPP2 genes exhibited different responses to abiotic stresses. Interestingly, the BnPP2 genes are more sensitive to insect pests than to other stresses. A study of the BnPP2-15 promoter revealed that pBnPP2-15 could drive specific GUS expression in the petiole, root and stamen and could also be induced by mechanical wounding and aphid infection in transgenic Arabidopsis lines. The subcellular localization of six BnPP2 proteins showed that GFP-BnPP2-1, GFP-BnPP2-6, GFP-BnPP2-7, GFP-BnPP2-9, GFP-BnPP2-11 and GFP-BnPP2-12 were predominantly located in the cytoplasm. These results provide useful information elucidating the functions of BnPP2 genes in ramie.

Light-emitting diodes: whether an efficient source of light for indoor plants?

Availability of sufficient light for growth optimization of plants in greenhouse environment during winter is a major challenge, as light during winter is significantly lower than that in the summer. The most commonly used artificial light sources (e.g., metal halide lamps, high pressure sodium lamps, and high fluorescent lamps) are of low quality and inefficient. Therefore, better options should be developed for sustaining agricultural food production during low levels of solar radiation. In recent advances, light-emitting diodes (LEDs) have remarkable potential as supplemental source of light for promoting plant growth. LEDs are novel and versatile source of light with cool emitting surface, wavelength specificity, and low electric power requirement. In the present study, we provided a contemporary synthesis of existing evidence along with our hypothetical concepts to clarify how LED approach could be an efficient and cost-effective source of light for plant growth and development especially in closed production system. In comparative analysis of common artificial vs. LED lighting, we revealed that spectral quality of LEDs can have vivid effects on plant morphogenesis and anatomy. We also discussed the influence of different colors of LEDs on growth performance of plants and provided the cost benefit analysis of using LEDs compared with other traditional sources. Overall, we hope that this article will be of great worth in future due to its practical implications as well as research directions.

Interactive effect of gibberellic acid and NPK fertilizer combinations on ramie yield and bast fibre quality.

Understanding the effects of different combinations of nitrogen (N), phosphorus (P) and potassium (K) fertilizers and the effects of GA3 (gibberellic acid) foliar spray on the fiber quality and yield of ramie are important for maximizing the economic value of these plants. Three pot experiments were conducted using low NPK (140:70:140 kg/ha), normal NPK (280:140:280 kg/ha), and low NPK + GA3 (10 mg/L) treatments. In each experiment, following fertilizers were applied: no fertilizer (control), N, P, K, NP, NK, PK, and NPK. Ramie was harvested three times from each plant; ramie grown without fertilizers had significantly lower biomass and yield than plants grown with fertilizers. At both normal and low fertilization rates, application of NPK resulted in greater growth and yield than application of N, P, K, NP, NK, or PK. Unfertilized plants produced the thinnest fibres (22-24 µm), with lowest elongation rate (3.0-3.1%) and breaking strength (22.7-23.3 cN). Fibre yield and fibre quality were improved by application of GA3 + fertilizers. Maximum fibre yield was obtained at low NPK + GA3 treatment, resulting in 65-81% more yield than low NPK alone. GA3 with low NPK treatment significantly improved fibre diameter, fibre elongation, and breaking strength compared to both NPK alone and control treatment.

Senescence is delayed when ramie (Boehmeria nivea L.) is transformed with the isopentyl transferase (ipt) gene under control of the SAG12 promoter.

Ramie is an economically important industrial fiber crop widely planted in China, India, and other Southeast Asian and Pacific Rim countries. It plays an important role in China's economy, where ramie farming, industry, and trade provide livelihood support to about five million people. However, poor fiber production resulting from leaf senescence and leaf abscission is a significant problem. In this study, we report the successful production of transgenic ramie plants which delayed leaf senescence and enhanced biomass. Transgenic ramie plants were obtained via transformation with the Agrobacterium tumefaciens strain harboring the binary vector pSG529 containing the isopentyl transferase (ipt) gene under control of the SAG12 promoter (PSAG12-ipt construct). Agrobacterium tumefaciens strain EHA105 was used for the midrib explant transformation. The transformation frequency was 28.29%. Southern blot confirmed the integration of 1-4 copies of the NPTII gene into the ramie genome in the tested lines. At the fiber maturation stage, the transgenic plants had higher photosynthesis rates, chlorophyll content (SPAD values), and stronger resistance to exogenous ethylene compared with wild-type plants.

Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-Based Comparative Proteome Analysis of the Response of Ramie under Drought Stress.

In this study, we conducted the first isobaric tags for relative and absolute quantitation (isobaric tags for relative and absolute quantitation (iTRAQ))-based comparative proteomic analysis of ramie plantlets after 0 (minor drought stress), 24 (moderate drought stress), and 72 h (severe drought stress) of treatment with 15% (w/v) poly (ethylene glycol)6000 (PEG6000) to simulate drought stress. In our study, the association analysis of proteins and transcript expression revealed 1244 and 968 associated proteins identified in leaves and roots, respectively. L1, L2, and L3 are leaf samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups, a total of 118, 216, and 433 unique proteins were identified as differentially expressed during L1 vs. L2, L2 vs. L3, and L1 vs. L3, respectively. R1, R2, and R3 are root samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups，a total of 124, 27, and 240 unique proteins were identified as differentially expressed during R1 vs. R2, R2 vs. R3, and R1 vs. R3, respectively. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was significantly upregulated in roots in response to drought stress. This enhancement may result in more glycolytically generated adenosine triphosphate (ATP) in roots to adapt to adverse environmental conditions. To obtain complementary information related to iTRAQ data, the mRNA levels of 12 proteins related to glycolysis/gluconeogenesis in leaves and 7 in roots were further analyzed by qPCR. Most of their expression levels were higher in R3 than R1 and R2, suggesting that these compounds may promote drought tolerance by modulating the production of available energy.

Identification of small auxin-up RNA (SAUR) genes in Urticales plants: mulberry (Morus notabilis), hemp (Cannabis sativa) and ramie (Boehmeria nivea).

Small auxin-up RNA (SAUR) genes are important gene families in auxin signalling transduction and are commonly used as early auxin responsive markers. Till date, no SAUR gene is identified in Urticales plants despite of the published bioinformation of mulberry, hemp and ramie. In this study, we used Arabidopsis sequences as query to search against mulberry, hemp genomes and ramie transcriptome database. In total, we obtained 62, 56 and 71 SAUR genes in mulberry, hemp and ramie, respectively. Phylogenetic analysis revealed the Urticales specific expansion of SAUR genes. Expression analysis showed 15 randomly selected ramie SAUR genes that were diversely functioned in ramie tissues and revealed a series of IAA-responsive, drought-responsive and high temperature-responsive genes. Moreover, comparison of qRT-PCR data and previous RNA-Seq data suggested the reliability of our work. In this study, we first report the identification of SAUR genes in Urticales plants. These results will provide a foundation for their function validation in Urticales plant growth and development.

Large-scale developing of simple sequence repeat markers and probing its correlation with ramie (Boehmeria nivea L.) fiber quality.

Marker-assisted selection is an important component of the discipline of molecular breeding. Using DNA markers to assist in plant breeding, the efficiency and precision could be greatly increased. However, the scarcity number of identified DNA markers has hindered the research and the breeding process of ramie (Boehmeria nivea L.) in many aspects, especially fiber quality, one of the top-priority breeding objectives of ramie. In this study, 4230 SSR loci were identified in 3969 unigenes (6.80 % of 58,369), which were de novo assembled from the transcriptome involving different ramie fiber developmental stages. Among these SSRs, the dinucleotides (1599, 37.80 %) and trinucleotides (772, 18.25 %) were most abundant; the motifs AG/CT (1140, 26.94 %), AT/AT (407, 9.62 %) and AGA/TCT (246, 8.31 %) comprised the three most abundant repeats. A total of 2431 primer pairs were designed flanking the SSRs and 1050 of them were employed in PCR amplification for their usefulness using three ramie cultivars. The results showed that 88.10 % of these primers could generate positive PCR bands in any of the three cultivars. Further phylogenetic analysis that conducted from the PCR amplification of 52 specifically sifted SSR primers within 17 cultivars approved that the possible correlation may exist between the primers and ramie fiber quality. These developed SSR markers could be applied in downstream studies, like genetic and physical maps, quantitative trait loci mapping, genetic diversity studies and cultivar fingerprinting, and breeding processes of ramie with better fiber quality under further confirmation of the correlation with ramie fiber quality.

Transcriptome profiling and identification of transcription factors in ramie (Boehmeria nivea L. Gaud) in response to PEG treatment, using illumina paired-end sequencing technology.

Ramie (Boehmeria nivea L. Gaud), commonly known as China grass, is a perennial bast fiber plant of the Urticaceae. In China, ramie farming, industry, and trade provide income for about five million people. Drought stress severely affects ramie stem growth and causes a dramatic decrease in ramie fiber production. There is a need to enhance ramie's tolerance to drought stress. However, the drought stress regulatory mechanism in ramie remains unknown. Water stress imposed by polyethylene glycol (PEG) is a common and convenient method to evaluate plant drought tolerance. In this study, transcriptome analysis of cDNA collections from ramie subjected to PEG treatment was conducted using Illumina paired-end sequencing, which generated 170 million raw sequence reads. Between leaves and roots subjected to 24 (L2 and R2) and 72 (L3 and R3) h of PEG treatment, 16,798 genes were differentially expressed (9281 in leaves and 8627 in roots). Among these, 25 transcription factors (TFs) from the AP2 (3), MYB (6), NAC (9), zinc finger (5), and bZIP (2) families were considered to be associated with drought stress. The identified TFs could be used to further investigate drought adaptation in ramie.

Cloning of expansin genes in ramie (Boehmeria nivea L.) based on universal fast walking.

Gene cloning is the first step to study the expression profiles and functions of a particular gene; considerable cloning methods have been developed. Expansin, thought to involve in the cell-wall modification events, was not cloned in ramie (Boehmeria nivea L.), which is one of the most important bast fiber crops with little conducted molecular research, especially on its fiber development. Studying the expansin gene family will uncover its possible relationship with ramie fiber development and other growth events. As a result, five expansin genes were cloned with full-length and their sequence information was investigated. Additionally, the phylogenetic analysis was conducted, which suggested that the cloned genes belong to the α-subfamily, and these genes expressed differently during ramie fiber developmental process. In this study, we aimed to apply a strategy for cloning novel full-length genes from genomic DNA of ramie, based on using degenerate primers, touchdown polymerase chain reaction and universal fast walking protocols. By cloning five full-length expansin genes, we believe the polymerase chain reaction-based gene cloning strategy could be applied to general gene studies in ramie and other crops.

Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud).

In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.

Transcriptome profiling using pyrosequencing shows genes associated with bast fiber development in ramie (Boehmeria nivea L.).

BACKGROUND: Ramie (Boehmeria nivea L.), popularly known as "China grass", is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is important in the textile industry. However, the molecular mechanism of ramie fiber development remains unknown. RESULTS: A whole sequencing run was performed on the 454 GS FLX + platform using four separately pooled parts of ramie bast. This generated 1,030,057 reads with an average length of 457 bp. Among the 58,369 unigenes (13,386 contigs and 44,983 isotigs) that were generated through de novo assembly, 780 were differentially expressed. As a result, 13 genes that belong to the cellulose synthase gene family (four), the expansin gene family (three) and the xyloglucan endotransglucosylase/hydrolase (XTH) gene family (six) were up-regulated in the top part of the bast, which was in contrast to the other three parts. The identification of these 13 concurrently up-regulated unigenes indicated that the early stage (represented by the top part of the bast) might be important for the molecular regulation of ramie fiber development. Further analysis indicated that four of the 13 unigenes from the expansin (two) and XTH (two) families shared a coincident expression pattern during the whole growth season, which implied they were more relevant to ramie fiber development (fiber quality, etc.) during the different seasons than the other genes. CONCLUSIONS: To the best of our knowledge, this study is the first to characterize ramie fiber development at different developmental stages. The identified transcripts will improve our understanding of the molecular mechanisms involved in ramie fiber development. Moreover, the identified differentially expressed genes will accelerate molecular research on ramie fiber growth and the breeding of ramie with better fiber yields and quality.