The miRNAome of ramie (Boehmeria nivea L.): identification, expression, and potential roles of novel microRNAs in regulation of cadmium stress response.

BACKGROUND: MicroRNAs (miRNAs) regulate numerous crucial abiotic stress processes in plants. However, information is limited on their involvement in cadmium (Cd) stress response and tolerance mechanisms in plants, including ramie (Boehmeria nivea L.) that produces a number of economic valuable as an important natural fibre crop and an ideal crop for Cd pollution remediation. RESULTS: Four small RNA libraries of Cd-stressed and non-stressed leaves and roots of ramie were constructed. Using small RNA-sequencing, 73 novel miRNAs were identified. Genome-wide expression analysis revealed that a set of miRNAs was differentially regulated in response to Cd stress. In silico target prediction identified 426 potential miRNA targets that include several uptake or transport factors for heavy metal ions. The reliability of small RNA sequencing and the relationship between the expression levels of miRNAs and their target genes were confirmed by quantitative PCR (q-PCR). We showed that the expression patterns of miRNAs obtained by q-PCR were consistent with those obtained from small RNA sequencing. Moreover, we demonstrated that the expression of six randomly selected target genes was inversely related to that of their corresponding miRNAs, indicating that the miRNAs regulate Cd stress response in ramie. CONCLUSIONS: This study enriches the number of Cd-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in ramie during Cd stress.

Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.).

BACKGROUND: Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known. RESULTS: A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170-64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170-64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie. CONCLUSIONS: The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.

Hydroponic method for ramie and removal of nitrogen and phosphorus from livestock wastewater.

By using a hydroponic culture system, the terrestrial fiber crop ramie can growth optimally in aquatic environment and enhance exponentially quantities of high quality seedlings for subsequent field cultivation. In this study, the survival rate of ramie seedling was more than 97% when cultured using the novel hydroponic method. Further physiological analysis of the hydroponic ramie to different concentration of livestock wastewater demonstrated that all of these ramies can survival in livestock wastewater, but the 4 times diluted livestock wastewater (total N: 100.9 mg L-1, total P: 2.69 mg L-1) was more appropriate for ramie growth. The nutrients N and P in livestock wastewater were significantly decreased by the growth of ramie, and the removal efficiency of total N and total P in the 4 times diluted livestock wastewater achieved 78.1% and 43.1% respectively within 5 weeks. In conclusion, our studies highlight that the combination of ramie and the hydroponic technology resulted to be effective in the phytoremediation of livestock wastewater.

Systematic evaluation of ramie (Boehmeria nivea L.) for phytoremediation of cadmium contaminated soil and the mechanism of microbial regulation.

Ramie is an ideal crop for remediation of cadmium (Cd) contaminated soil. However, there is a lack of rapid and effective evaluation system for Cd tolerance of ramie germplasms, and also a lack of systematic and in-depth research under Cd contaminated field conditions. This study innovatively developed a rapid screening system of "hydroponics-pot planting", and 196 core germplasms were used to quickly and effectively identify their Cd tolerance and Cd enrichment capacity. Then, two excellent varieties were selected to carry out a 4 years of field experiment under Cd contaminated field to study the remediation model, evaluation of reuse after repair and the mechanism of microbial regulation. The results showed that ramie adopted the cycle mode of "Absorption-activating soil Cd-Migration-Absorption" to remediate on Cd contaminated field, and the application of ramie for remediation had good ecological and economic benefits. Ten dominant genera such as Pseudonocardiales, as well as the key functional genes (mdtC, mdtB, mdtB/yegN, actR, rpoS, and ABA transporter gene) in rhizosphere soil, were identified to participate in activating Cd in rhizosphere soil and promoting ramie to enrich Cd. This study provides a technical route and practical production experience for the research field of phytoremediation of heavy metal pollution.

Transcriptome Analysis of High-NUE (T29) and Low-NUE (T13) Genotypes Identified Different Responsive Patterns Involved in Nitrogen Stress in Ramie (Boehmeria nivea (L.) Gaudich).

Nitrogen-use efficiency (NUE) has significant impacts on plant growth and development. NUE in plants differs substantially in physiological resilience to nitrogen stress; however, the molecular mechanisms underlying enhanced resilience of high-NUE plants to nitrogen deficiency remains unclear. We compared transcriptome-wide gene expression between high-NUE and low-NUE ramie (Boehmeria nivea (L.) Gaudich) genotypes under nitrogen (N)-deficient and normal conditions to identify the transcriptomic expression patterns that contribute to ramie resilience to nitrogen deficiency. Two ramie genotypes with contrasting NUE were used in the study, including T29 (NUE = 46.01%) and T13 (NUE = 15.81%). Our results showed that high-NUE genotypes had higher gene expression under the control condition across 94 genes, including frontloaded genes such as GDSL esterase and lipase, gibberellin, UDP-glycosyltransferase, and omega-6 fatty acid desaturase. Seventeen stress-tolerance genes showed lower expression levels and varied little in response to N-deficiency stress in high-NUE genotypes. In contrast, 170 genes were upregulated under N deficiency in high-NUE genotypes but downregulated in low-NUE genotypes compared with the controls. Furthermore, we identified the potential key genes that enable ramie to maintain physiological resilience under N-deficiency stress, and categorized these genes into three groups based on the transcriptome and their expression patterns. The transcriptomic and clustering analysis of these nitrogen-utilization-related genes could provide insight to better understand the mechanism of linking among the three gene classes that enhance resilience in high-NUE ramie genotypes.

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich.

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae.

Gene expression profiling of ramie roots during hydroponic induction and adaption to aquatic environment.

Ramie (Boehmeria nivea (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems was grown in the soil or in a hydroponic water solution, and cultured in the same environmental conditions. Root samples of terrestrial ramie, and different developmental stages of hydroponic ramie (5 days, 30 days), were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000. Gene expression levels of each samples were quantified using the BGISEQ500 platform to help understand the distribution of aquatic root development related genes at the macro level (GSE98903). Our data resources provided an opportunity to elucidate the adaptation mechanisms of ramie seedlings roots in aquatic environment.