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Miscanthus spp. show excellent application prospects due to its bioenergy potential and multiple ecological services. Annual N export with biomass harvest from Miscanthus, even without fertilizer supplement, do not reduce soil N levels. The question arises regarding how Miscanthus can maintain stable soil N levels. Metagenomic strategies were used to reveal soil N‐cycling‐related microbiome and their functional contributions to processes of soil N‐cycling based on the comparison among the bare land, cropland, 10‐year Miscanthus × giganteus, and 15‐year Miscanthus sacchariflorus fields. The results showed that, after long‐term cropland‐to‐Miscanthus conversion (LCMC), 16 of 21 bacterial phyla and all the archaeal phyla exhibited significant changes. Soil microbial denitrification and nitrification functions were significantly weakened, and N fixation (NF) was significantly enhanced. The biosynthesis of amino acids, especially alanine, aspartate, and glutamate metabolism, in soil N‐cycling‐related microbiome was dramatically promoted. The genus Anaeromyxobacter contributed largely to the NF process after LCMC. Variations in the soil available potassium, available N, organic C, and total N contents drove a functional shift of soil microbiome from cropland to Miscanthus pattern. We conclude that Miscanthus can recruit Anaeromyxobacter communities to enhance NF benefiting its biomass sustainability and soil N balance. [ABSTRACT FROM AUTHOR]

Switchgrass (Panicum virgatum L.) shows great bioenergy potential and provides multiple ecological services. However, its severe seed shedding causes biomass waste and seed diffusion risk. Questions arise as to the production performance of switchgrass after panicle removal (PR), which remains unknown. We revealed switchgrass growth responses to PR and illustrated physiological reasons. Compared to the untreated switchgrass, PR significantly stimulated stem elongation (32.13%) and increased tiller number (39.70%), as well as aboveground biomass (24.69%). Importantly, PR significantly increased contents of nonstructural carbohydrates (NSCs) in the stem, which was directly beneficial to the ethanol conversion, and in the rhizome and root. The chlorophyll contents, net photosynthetic efficiency, and photochemical quantum efficiencies of flag leaf increased significantly. PR switchgrass allocated more assimilates into the stem, root, rhizome, and NSCs. Activities of phosphoenolpyruvate carboxylase, ribulose-1, 5-diphosphate carboxylase, sucrose phosphate synthase (SPS) in flag leaf and adenosine diphosphate glucose pyrophosphorylase (AGPase) and SPS in the stem and rhizome all increased significantly. In contrast, activities of the AGPase in flag leaf and sheath decreased significantly. Contents of zeatin nucleoside, gibberellins, and indoleacetic acid in flag leaf, stem, and rhizome all increased. Abscisic acid contents in flag leaf and stem decreased significantly while increased significantly in the rhizome. In conclusion, growth-promoting hormones delayed plant senescence, enhanced leaf photosynthesis, and enhanced vegetative growth through regulating assimilates-metabolism-related enzymes, which increased biomass accumulation in PR switchgrass. This work provided new insights for yield and digestibility improvement in switchgrass through field management practices, hormones regulation, or genetic modification strategies. [Display omitted] • Panicle removal (PR) retarded plant senescence in switchgrass. • PR increased biomass dry weights of switchgrass. • PR increased contents of nonstructural carbohydrates in stem, root and rhizome. • AGPase and SPS facilitated storage and transport of C assimilates in PR switchgrass. • Growth promoting hormones played critical roles in delaying plant senescence. [ABSTRACT FROM AUTHOR]

Switchgrass ( Panicum virgatum L.) has been developed into a major herbaceous bioenergy crop for the production of cellulosic biofuels in North America and many counties in European. As cultivar selection has a major impact on the ultimate biomass productivity, we evaluated the adaptability and yield potential of 12 switchgrass cultivars including both upland and lowland ecotypes from 2010 to 2013 in the Beijing region, Northern China. Plant height was measured after anthesis, but phytomer number and tiller density were investigated at harvest. One single autumn harvest was carried out each year and biomass yields were determined. It was found that the lowland cultivars ‘Alamo’, ‘Kanlow’ and ‘NewYork’ produced the most biomass for their better performances in number of phytomers per tiller and mass per phytomer, though upland cultivars had higher tiller density. ‘Cave-in-rock’ and ‘Trailblazer’ had better biomass production among the upland cultivars and they were also recommended for planting together with lowland ones for their excellent cold tolerance in this region. [ABSTRACT FROM AUTHOR]

As an important bioenergy crop, switchgrass (Panicum virgatum L.) can produce high biomass yield. However, its biomass yield could be further increased by using beneficial microbe inoculation methods. In this study, a plant beneficial symbiotic microbe strain 11F was isolated and identified as Streptomyces alfalfae , which can produce IAA and siderophore. It is also known to have phosphate-solubilizing and N 2 fixing abilities. In addition, the promoting effects of strain 11F on seed germination and plant growth were evaluated. The results indicated that seeds treated with 11F showed higher germination rates, which observed an increase of 21.9%. Compared with the control, the switchgrass plants treated with strain 11F were found to have longer leaf lengths; greater plant heights, shoot fresh weights and root fresh weights; longer overall total lengths; and larger total plant root surface areas, which were significantly increased, by 30.7%, 25.8%, 49.5%, 42.9%, 39.3%, and 44.8%, respectively. Moreover, an egfp -tagged 11F strain was constructed and the mycelium of the 11F strain was observed on the surfaces of the switchgrass root hairs. The colonization dynamics of the egfp -tagged 11F strain to the rhizosphere soil of the switchgrass showed that it remained stable up to 30 days at 2.65 × 105 CFU g−1 dry weight from the initial inoculums. All of the aforementioned observational results suggest the potential of the S. alfalfae 11F strain in improving establishment and biomass yield of switchgrass. • The strain 11F was isolated and identified as Streptomyces alfalfa based on 16S rRNA and the genomic collinearity. • The S. alfalfa 11F strain can produce IAA and siderophore and have phosphate-solubilizing and N 2 fixing abilities. • The S. alfalfa 11F strain inoculations can effectively promote the seed germination and growth of switchgrass. • The colonization of S. alfalfa 11F strain in the switchgrass rhizosphere was investigated using an egfp -tagged one. [ABSTRACT FROM AUTHOR]

Zoysia japonica is an important warm-season turfgrass used worldwide. The decreased aesthetic quality and functionality during leaf senescence hamper its further utilization. However, information about the transcriptional mechanism and genes involved in leaf senescence in Z. japonica needs to be more extensive. Therefore, to better understand leaf senescence in Z. japonica, we investigated the integrated analysis of chlorophyll fluorescence test (JIP-test) and RNA sequencing (RNA-seq) of mature and senescent leaves. First, we identified 22,049 genes, of which 4038 were differentially expressed genes (DEGs). The results for gene expression profiles were evaluated using quantitative real-time PCR. A total of 2515 genes have homologous genes in other plants. The matched known-function SAGs are mainly involved in chlorophyll degradation and plant hormone response. A total of 539 differentially expressed transcription factor genes, including AP2/ERF-ERF, NAC, WRKY, bHLH, and MYB, were identified to be associated with leaf senescence. Next, senescence represses chlorophyll biosynthesis while upregulating chlorophyll degradation. Senescence harms the integrity and functionality of PSII, PSI, and the intersystem electron transport chain. In addition, IAA biosynthesis was inhibited, whereas ABA and ET biosynthesis were activated in leaf senescence, and senescence activates signal transduction of IAA, ABA, and ET. These findings add to our understanding of the regulatory mechanism of leaf senescence. The senescence-associated genes are candidate targets for providing new insight into leaf senescence modeling in Z. japonica. They provided a theoretical foundation to reveal the functions of senescence-associated genes and chlorophyll catabolic genes involved in leaf senescence. [ABSTRACT FROM AUTHOR]

Drought is the major environmental stress that limits cotton (Gossypium hirsutum L.) production worldwide. LOS5/ABA3 (LOS5) encodes a molybdenum co-factor and is essential for activating aldehyde oxidase, which is involved in abscisic acid (ABA) biosynthesis. In this study, a LOS5 cDNA of Arabidopsis thaliana was overexpressed in cotton cultivar Zhongmiansuo35 (Z35) by Agrobacterium tumefaciens-mediated transformation. The transformation and overexpression of AtLOS5 were assessed by PCR and RT-PCR analysis. Detached shoots of transgenic cotton showed slower transpirational water loss than those of Z35. When pot-grown 6-week-old seedlings were withheld from watering for 3 d, transgenic cotton accumulated 25% more endogenous ABA and about 20% more proline than Z35 plants. The transgenic plants also showed increased expression of some drought-responding genes such as P5CS and RD22, and enhanced activity of antioxidant enzymes such as superoxide dismutase, peroxidase, and ascorbate peroxidase. Their membrane integrity was considerably improved under water stress, as indicated by reduced malondialdehyde content and electrolyte leakage relative to control plants. When the pot-grown plants were subjected to deficit irrigation for 8 weeks (watering to 50% of field capacity), transgenic plants showed a 13% increase in fresh weight than the wild type under the same drought condition. These results suggest that the AtLOS5 transgenic cotton plants acquired a better drought tolerance through enhanced ABA production and ABA-induced physiological regulations. [ABSTRACT FROM PUBLISHER]

Abstract: Crop productivity is greatly affected by soil salinity, so improvement in salinity tolerance of crops is a major objective of many studies. We overexpressed the Arabidopsis thaliana SOS1 gene, which encodes a plasma membrane Na+/H+ antiporter, in tobacco (Nicotiana tabacum cv. Xanthi-nc). Compared with nontransgenic plants, seeds from transgenic tobacco had better germination under 120mM (mmolL−1) NaCl stress; chlorophyll loss in the transgenic seedlings treated with 360mM NaCl was less; transgenic tobacco showed superior growth after irrigation with NaCl solutions; and transgenic seedlings with 150mM NaCl stress accumulated less Na+ and more K+. In addition, roots of SOS1-overexpressing seedlings lost less K+ instantaneously in response to 50mM NaCl than control plants. These results showed that the A. thaliana SOS1 gene potentially can improve the salt tolerance of other plant species. [Copyright &y& Elsevier]

Abstract: Drought is a major environmental stress factor that affects growth and development of plants. Abscisic acid (ABA), osmotically active compounds, and synthesis of specific proteins, such as proteins that scavenge oxygen radicals, are crucial for plants to adapt to water deficit. LOS5/ABA3 (LOS5) encodes molybdenum-cofactor sulfurase, which is a key regulator of ABA biosynthesis. We overexpressed LOS5 in tobacco using Agrobacterium-mediated transformation. Detached leaves of LOS5-overexpressing seedlings showed lower transpirational water loss than that of nontransgenic seedlings in the same period under normal conditions. When subjected to water-deficit stress, transgenic plants showed less wilting, maintained higher water content and better cellular membrane integrity, accumulated higher quantities of ABA and proline, and exhibited higher activities of antioxidant enzymes, i.e., superoxide dismutase, catalase, peroxidase and ascorbate peroxidase, as compared with control plants. Furthermore, LOS5-overexpressing plants treated with 30% polyethylene glycol showed similar performance in cellular membrane protection, ABA and proline accumulation, and activities of catalase and peroxidase to those under drought stress. Thus, overexpression of LOS5 in transgenic tobacco can enhance drought tolerance. [Copyright &y& Elsevier]

Key message: Through the histological, physiological, and transcriptome-level identification of the abscission zone of Pennisetum alopecuroides ‘Liqiu’, we explored the structure and the genes related to seed shattering, ultimately revealing the regulatory network of seed shattering in P. alopecuroides. Pennisetum alopecuroides is one of the most representative ornamental grass species of Pennisetum genus. It has unique inflorescence, elegant appearance, and strong stress tolerance. However, the shattering of seeds not only reduces the ornamental effect, but also hinders the seed production. In order to understand the potential mechanisms of seed shattering in P. alopecuroides, we conducted morphological, histological, physiological, and transcriptomic analyses on P. alopecuroides cv. ‘Liqiu’. According to histological findings, the seed shattering of ‘Liqiu’ was determined by the abscission zone at the base of the pedicel. Correlation analysis showed that seed shattering was significantly correlated with cellulase, lignin, auxin, gibberellin, cytokinin and jasmonic acid. Through a combination of histological and physiological analyses, we observed the accumulation of cellulase and lignin during ‘Liqiu’ seed abscission. We used PacBio full-length transcriptome sequencing (SMRT) combined with next-generation sequencing (NGS) transcriptome technology to improve the transcriptome data of ‘Liqiu’. Transcriptomics further identified many differential genes involved in cellulase, lignin and plant hormone-related pathways. This study will provide new insights into the research on the shattering mechanism of P. alopecuroides. [ABSTRACT FROM AUTHOR]

Pennisetum species have importance in foraging, agriculture, energy-production, the environment, and landscaping. To promote the preservation and utilization of ornamental Pennisetum resources, we developed simple sequence repeat (SSR) markers from the Pennisetum setaceum cv. 'Rubrum' transcriptome and verified their conservation in 38 sources. Our transcriptome sequencing efforts generated 58.91 Gb of clean data containing 55,627 unigenes. We functionally annotated 30,930 unigenes, with functions enriched in translation and ribosomal structure and biogenesis. Database comparisons indicated that the closest relative of P. setaceum cv. 'Rubrum' is Setaria italica. Over five thousand SSR markers were detected in the transcriptomic data. We selected 38 pairs of highly polymorphic SSR markers from 50 randomly selected SSR markers. Based on genetic diversity analysis of 38 ornamental Pennisetum sources, we obtained 312 polymorphic bands, with an average of 8.21 alleles per primer. Principal coordinate analyses and generation of a, which proved that Pennisetum has moderate genetic diversity. In addition, fingerprint maps were constructed to improve Pennisetum identification. The transcriptome data generated by our study enhances the transcriptional information available for P. setaceum. This study lays the foundation for the collection and utilization of ornamental Pennisetum resources and provides a basis for future breeding projects using this species. [ABSTRACT FROM AUTHOR]

Background: Zoysia japonica is an important warm-season turfgrass used worldwide. Although the draft genome sequence and a vast amount of next-generation sequencing data have been published, the current genome annotation and complete mRNA structure remain incomplete. Therefore, to analyze the full-length transcriptome of Z. japonica, we used the PacBio single-molecule long-read sequencing method in this study. Results: First, we generated 37,056 high-confidence non-redundant transcripts from 16,005 gene loci. Next, 32,948 novel transcripts, 913 novel gene loci, 8035 transcription factors, 89 long non-coding RNAs, and 254 fusion transcripts were identified. Furthermore, 15,675 alternative splicing events and 5325 alternative polyadenylation sites were detected. In addition, using bioinformatics analysis, the underlying transcriptional mechanism of senescence was explored based on the revised reference transcriptome. Conclusion: This study provides a full-length reference transcriptome of Z. japonica using PacBio single-molecule long-read sequencing for the first time. These results contribute to our knowledge of the transcriptome and improve the knowledge of the reference genome of Z. japonica. This will also facilitate genetic engineering projects using Z. japonica. [ABSTRACT FROM AUTHOR]

Background: Zoysia japonica is an important warm-season turfgrass used worldwide. Although the draft genome sequence and a vast amount of next-generation sequencing data have been published, the current genome annotation and complete mRNA structure remain incomplete. Therefore, to analyze the full-length transcriptome of Z. japonica, we used the PacBio single-molecule long-read sequencing method in this study. Results: First, we generated 37,056 high-confidence non-redundant transcripts from 16,005 gene loci. Next, 32,948 novel transcripts, 913 novel gene loci, 8035 transcription factors, 89 long non-coding RNAs, and 254 fusion transcripts were identified. Furthermore, 15,675 alternative splicing events and 5325 alternative polyadenylation sites were detected. In addition, using bioinformatics analysis, the underlying transcriptional mechanism of senescence was explored based on the revised reference transcriptome. Conclusion: This study provides a full-length reference transcriptome of Z. japonica using PacBio single-molecule long-read sequencing for the first time. These results contribute to our knowledge of the transcriptome and improve the knowledge of the reference genome of Z. japonica. This will also facilitate genetic engineering projects using Z. japonica. [ABSTRACT FROM AUTHOR]

Polyploidization is regularly regarded as an important tool for the generation of innovative germplasm resources and plant breeding. In this study, autopolyploid switchgrass lines were produced from calli derived from immature inflorescence of tetraploid switchgrass ( Panicum virgatum L.), both lowland cv. Alamo and Kanlow, and upland cv. Ranlow, through colchicine treatments. Ploidy levels of plantlets regenerated from the calli were screened by flow cytometry. Growth characteristics of the tetraploid and octoploid switchgrass cultivars were further investigated in a field experiment. Compared with the tetraploid plants of the three switchgrass cultivars, the corresponding octoploid plants showed significant reduction in plant height, number of tillers per plant and fresh matter, but an increase in leaf length and width. [ABSTRACT FROM AUTHOR]

Miscanthus spp. are increasingly cultivated in cropland worldwide due to their bioenergy potential and multiple ecological services. Effects of long‐term cropland‐to‐Miscanthus conversion without N fertilizer on soil microbiome and N cycling largely remain unknown. We aimed to explore the effects of Miscanthus conversion on soil microbiome and N cycling over a 15‐year period. We analyzed diversity, composition, and abundance of bacterial and archaeal communities using 16S rRNA amplicon sequencing, and abundances of N‐cycling‐related genes using quantitative polymerase chain reaction of 0–10 cm soils collected from bare land, cropland, 10‐year Miscanthus × giganteus, and 15‐year Miscanthussacchriflorus land in Beijing. Conversion decreased soil sand and micro‐aggregate proportion, nitrate N (NiN), available phosphorus levels, conductivity, temperature, and pH, while increasing proportion of soil clay and macro‐aggregate (MAA), soil organic C (SOC), available N (AN), exchangeable Mg2+ (EMg2+), and available potassium (AK) contents as well as microbial C/N. Consequently, diversity, composition, and abundance of soil bacterial community exhibited larger changes than those values of archaeal community after conversion. Soil AP, EMg2+, AK, and SOC were key factors in shifting microbiome from the cropland to Miscanthus pattern. Moreover, abundances of bacterial and archaeal communities and the N fixer gene nifH increased, whereas that of the bacterial ammonia monooxygenase gene decreased. The copies of other N‐cycling‐related genes in the two Miscanthus lands seemed similar to those values of cropland. The nifH copies negatively correlated with soil NiN and positively correlated with AN, EMg2+, ECa2+, SOC, AK, and MAA. We conclude that changes in soil microbiome pattern induced by the variation of soil properties enhance microbial N fixation potential, maintaining stable N levels and robust N cycling with lower N leakage risk after conversion. These results should inspire farmers and governments to large‐scale use Miscanthus on marginal cropland in Northern China. [ABSTRACT FROM AUTHOR]

Switchgrass is a photoperiod-sensitive energy grass suitable for growing in the marginal lands of China. We explored the effects of extended photoperiods of low-irradiance light (7 μmol·m-2·s-1, no effective photosynthesis) on the growth, the biomass dry weight, the biomass allocation, and, especially, the stem digestibility and cell wall characteristics of switchgrass. Two extended photoperiods (i.e., 18 and 24 h) were applied over Alamo. Extended light exposure (18 and 24 h) resulted in delayed heading and higher dry weights of vegetative organs (by 32.87 and 35.94%, respectively) at the expense of reducing the amount of sexual organs (by 40.05 and 50.87%, respectively). Compared to the control group (i.e., natural photoperiod), the yield of hexoses (% dry matter) in the stems after a direct enzymatic hydrolysis (DEH) treatment significantly increased (by 44.02 and 46.10%) for those groups irradiated during 18 and 24 h, respectively. Moreover, the yield of hexoses obtained via enzymatic hydrolysis increased after both basic (1% NaOH) and acid (1% H2SO4) pretreatments for the groups irradiated during 18 and 24 h. Additionally, low-irradiance light extension (LILE) significantly increased the content of non-structural carbohydrates (NSCs) while notably reducing the lignin content and the syringyl to guaiacyl (S/G) ratio. These structural changes were in part responsible for the observed improved stem digestibility. Remarkably, LILE significantly decreased the cellulose crystallinity index (CrI) of switchgrass by significantly increasing both the arabinose substitution degree in xylan and the content of ammonium oxalate-extractable uronic acids, both favoring cellulose digestibility. Despite this LILE technology is not applied to the cultivation of switchgrass on a large scale yet, we believe that the present work is important in that it reveals important relationships between extended day length irradiations and biomass production and quality. Additionally, this study paves the way for improving biomass production and digestibility via genetic modification of day length sensitive transcription factors or key structural genes in switchgrass leaves. [ABSTRACT FROM AUTHOR]

In this study, tassels of Cave-in-Rock (upland) and Alamo (lowland) were removed at or near tassel emergence to explore its effects on biomass production and quality. Tassel-removed (TR) Cave-in-Rock and Alamo both exhibited a significant (P<0.05) increase in plant heights (not including tassel length), tiller number, and aboveground biomass dry weight (10% and 12%, 30% and 13%, 13% and 18%, respectively by variety) compared to a control (CK) treatment. Notably, total sugar yields of TR Cave-in-Rock and Alamo stems increased significantly (P<0.05 or 0.01) by 19% and 19%, 21% and 14%, 52% and 18%, respectively by variety, compared to those of control switchgrass under 3 treatments by direct enzymatic hydrolysis (DEH), enzymatic hydrolysis after 1% NaOH pretreatment (EHAL) and enzymatic hydrolysis after 1% H2SO4 pretreatment (EHAC). These differences were mainly due to significantly (P<0.05 or 0.01) higher cellulose content, lower cellulose crystallinity indexes (CrI) caused by higher arabinose (Ara) substitution in xylans, and lower S/G ratio in lignin. However, the increases of nitrogen (N) and sulphur (S) concentration negatively affects the combustion quality of switchgrass aboveground biomass. This work provides information for increasing biomass production and quality in switchgrass and also facilitates the inhibition of gene dispersal of switchgrass in China. [ABSTRACT FROM AUTHOR]

Background: Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts. Results: In this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing. Conclusions: This study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis. [ABSTRACT FROM AUTHOR]

Background: Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts. Results: In this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing. Conclusions: This study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis. [ABSTRACT FROM AUTHOR]