Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

Relationship between DHX15 expression and survival in colorectal cancer.

OBJECTIVE: to explore the relationship between the expression of DEAH-box RNA helicase 15 (DHX15) in colorectal cancer (CRC), its clinical pathological features and survival. METHOD: DHX15 expression data with clinical pathological features from the Cancer Gene Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) were statistically analyzed for the association between DHX15 expression and overall survival in CRC. The expression of DHX15 was performed by immunohistochemical staining (IHC) using tumor and the adjacent normal tissue, mounted in tissue microarrays. The significance of DHX15 expression to predict survival and prognosis of CRC were analyzed using the Kaplan-Meier method, univariate and multivariate Cox regression analysis. RESULTS: low expression of DHX15 mRNA and DHX15 protein in CRC were both negative factors for survival. Overall survival of patients with low-expression of DHX15 was significantly lower (χ2 = 8.452, p = 0.004) by Kaplan-Meier evaluation. Low expression of DHX15 in CRC tissues correlated with distal lymph node metastasis (χ² = 7.120, p = 0.008), TNM stage (χ² = 3.935, p = 0.047) and disease recurrence (χ² = 9.524, p = 0.002) in CRC. Low expression of DHX15 (HR = 4.012, 95 % CI: 1.462-11.013, p = 0.007), late TNM stage (HR = 0.067, 95 % CI: 0.029-0.156, p < 0.001) and recurrence (HR = 0.008, 95 % CI: 0.002-0.034, p < 0.001) were risk factors related to the prognosis of CRC patients by univariate Cox regression analysis. CONCLUSION: our findings reveal a key role for DHX15 in the progress of CRC metastasis and recurrence. DHX15 may be a potential biomarker for CRC targeted therapy.

Identification and overexpression of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance.

Gibberellin 2-oxidases (GA2oxs) are a group of 2-oxoglutarate-dependent dioxygenases that catalyse the deactivation of bioactive GA or its precursors through 2ß-hydroxylation reaction. In this study, putatively novel switchgrass C20 GA2ox genes were identified with the aim of genetically engineering switchgrass for improved architecture and reduced biomass recalcitrance for biofuel. Three C20 GA2ox genes showed differential regulation patterns among tissues including roots, seedlings and reproductive parts. Using a transgenic approach, we showed that overexpression of two C20 GA2ox genes, that is PvGA2ox5 and PvGA2ox9, resulted in characteristic GA-deficient phenotypes with dark-green leaves and modified plant architecture. The changes in plant morphology appeared to be associated with GA2ox transcript abundance. Exogenous application of GA rescued the GA-deficient phenotypes in transgenic lines. Transgenic semi-dwarf lines displayed increased tillering and reduced lignin content, and the syringyl/guaiacyl lignin monomer ratio accompanied by the reduced expression of lignin biosynthetic genes compared to nontransgenic plants. A moderate increase in the level of glucose release in these transgenic lines might be attributed to reduced biomass recalcitrance as a result of reduced lignin content and lignin composition. Our results suggest that overexpression of GA2ox genes in switchgrass is a feasible strategy to improve plant architecture and reduce biomass recalcitrance for biofuel.

Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN.

Improvement and year-to-year stabilization of biomass yields are primary objectives for the development of a low-input switchgrass feedstock production system using microbial endophytes. An earlier investigation of the effect of Burkholderia phytofirmans strain PsJN on switchgrass germplasm demonstrated differential responses between genotypes. PsJN inoculation of cv. Alamo (lowland ecotype) increased the plant root system, shoot length, and biomass yields, whereas it had no beneficial effect on cv. Cave-in-Rock (upland ecotype). To understand the gene networks governing plant growth promotion responses triggered by PsJN, the gene expression profiles were analysed in these two hosts, following seedling inoculation. The Affymetrix platform switchgrass expressed sequence tag (EST) microarray chip representing 122 972 probe sets, developed by the DOE BioEnergy Science Center, was employed to assess transcript abundance at 0.5, 2, 4, and 8 DAI (days after PsJN inoculation). Approximately 20 000 switchgrass probe sets showed significant responses in either cultivar. Switchgrass identifiers were used to map 19 421 genes in MapMan software. There were apparent differences in gene expression profiling between responsive and non-responsive cultivars after PsJN inoculation. Overall, there were 14 984 and 9691 genes affected by PsJN inoculation in Alamo and Cave-in-Rock, respectively. Of these, 394 are annotated as pathogenesis-related genes. In the responsive cv. Alamo, 68 pathogenesis-related genes were affected, compared with only 10 in the non-responsive cv. Cave-in-Rock. At the very early stage at 0.5 DAI, both cultivars exhibited similar recognition and defence responses, such as genes in signalling and proteolysis, after which the defence reaction in the responsive cv. Alamo became weaker while it was sustained in non-responsive cv. Cave-in-Rock.

Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.).

Switchgrass (Panicum virgatum L.) is a perennial C4 grass with the potential to become a major bioenergy crop. To help realize this potential, a set of RNA-based resources were developed. Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high-quality ESTs were generated with 454 sequencing technology, and an additional 169 079 Sanger sequences were obtained from the 5' and 3' ends of 93 312 clones from normalized, full-length-enriched cDNA libraries. AP13 and VS16 ESTs were assembled into 77 854 and 30 524 unique transcripts (unitranscripts), respectively, using the Newbler and pave programs. Published Sanger-ESTs (544 225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128 058 unitranscripts, which were annotated for function. An Affymetrix cDNA microarray chip (Pvi_cDNAa520831) containing 122 973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA). The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data. The PviGEA was used to identify representatives of all known genes in the phenylpropanoid-monolignol biosynthesis pathway.

Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after rewatering.

Medicago truncatula is a model legume forage crop native to the arid and semi-arid environments of the Mediterranean. Given its drought-adapted nature, it is an ideal candidate to study the molecular and biochemical mechanisms conferring drought resistance in plants. Medicago plants were subjected to a progressive drought stress over 14 d of water withholding followed by rewatering under controlled environmental conditions. Based on physiological measurements of plant water status and changes in morphology, plants experienced mild, moderate and severe water stress before rehydration. Transcriptome analysis of roots and shoots from control, mildly, moderately and severely stressed, and rewatered plants, identified many thousands of genes that were altered in expression in response to drought. Many genes with expression tightly coupled to the plant water potential (i.e. drought intensity) were identified suggesting an involvement in Medicago drought adaptation responses. Metabolite profiling of drought-stressed plants revealed the presence of 135 polar and 165 non-polar compounds in roots and shoots. Combining Medicago metabolomic data with transcriptomic data yielded insight into the regulation of metabolic pathways operating under drought stress. Among the metabolites detected in drought-stressed Medicago plants, myo-inositol and proline had striking regulatory profiles indicating involvement in Medicago drought tolerance.

Protective Effect of Deer Heart Peptide on Cardiac Injury in Mice.

Peptides are widely used as natural bio-small molecules because of their various pharmacological activities such as enhancing immunity, promoting wound healing, and improving inflammation. Alcoholic heart injury has become one of the major health problems worldwide, and alcohol consumption is now the main cause of alcoholic cardiomyopathy. In this study, deer heart peptides were extracted from deer hearts by enzymatic digestion and the antioxidant activity of deer heart peptides extracted at different times was evaluated by three in vitro antioxidant methods, and the active peptide with the best enzymatic effect has been selected for in vivo animal experiments. The anti-inflammatory and antioxidant properties of deer heart enzymatic extracts were evaluated in in vivo experiments in mice. In this study, mice were orally gavaged with white wine (12 mL/kg body weight) to induce a mouse model of cardiac injury, while mice were orally administered a single dose of 100 mg/kg/bw and 200 mg/kg/bw of deer heart enzyme digest and were examined for body weight, dietary intake, water intake, and coat gloss, as well as for general behaviors, adverse effects, and mortality. Histology, serum, anti-inflammatory factors, and oxidative stress parameters were subsequently assessed. In all modeled mice, no four-way or any significant behavioral changes were observed in all groups, but in the modeled group, mice showed weight loss, decreased diet and water intake, and decreased cardiac index. For in vivo tests, the extract inhibited the anti-inflammatory activity with a significant decrease in inflammatory factors of TNF-α, IL-6, and IL-1ß in cardiac tissues, a significant increase in serum levels of both CAT and SOD, an increase in MDA content, and a remarkable increase in the level of the marker CK in the cardiac myocardial enzyme profile. Significant improvement in myocardial disorders by deer heart peptide could be observed from heart tissue sections. The present study emphasizes the anti-inflammatory and antioxidant activity of deer heart peptide, an enzymatic digest of deer heart, which provides empirical as well as supportive role for the anti-inflammatory properties of traditional medicine.

Jinmaitong alleviates diabetic neuropathic pain by inhibiting JAK2/STAT3 signaling in microglia of diabetic rats.

ETHNOPHARMACOLOGICAL RELEVANCE: Jinmaitong (JMT) is a prescription of Traditional Chinese Medicine that is composed of 12 crude drugs. It has been used in the treatment of diabetic neuropathic pain (DNP) for more than 30 years. AIM OF STUDY: Microglia are thought to play an important role in neuropathic pain. This study aimed to evaluate the protective effect of JMT against DNP and to investigate the underlying mechanisms in which the microglia and JAK2/STAT3 signaling pathway were mainly involved. MATERIALS AND METHODS: The chemical composition of JMT was analyzed using liquid chromatography tandem mass spectrometry. The diabetes model was constructed using 11 to 12-week-old male Zucker diabetic fatty (ZDF) rat (fa/fa). The model rats were divided into 5 groups and were given JMT at three dosages (11.6, 23.2, and 46.4 g/kg, respectively, calculated as the crude drug materials), JAK inhibitor AG490 (positive drug, 10 µg/day), and placebo (deionized water), respectively, for eight weeks (n = 6). Meanwhile, Zucker lean controls (fa/+) were given a placebo (n = 6). Body weight was tested weekly and blood glucose was monitored every 2 weeks. The mechanical allodynia and heat hyperalgesia were assessed using mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL) tests. After treatment, the microglia activation marker Iba-1, CD11B, CD68, neuroinflammatory mediators, and mediators of the JAK2/STAT3 signaling pathway were compared between different groups. The mRNA and protein levels of target genes were assessed by quantitative real-time PCR and Western Blot, respectively. RESULTS: We found that JMT significantly inhibited the overactivation of microglia in spinal cords, and suppressed neuroinflammation of DNP model rats, thereby ameliorating neurological dysfunction and injuries. Furthermore, these effects of JMT could be attributed to the inhibition of the JAK2/STAT3 signaling pathway. CONCLUSIONS: Our findings suggested that JMT effectively ameliorated DNP by modulating microglia activation via inhibition of the JAK2/STAT3 signaling pathway. The present study provided a basis for further research on the therapeutic strategies of DNP.

Core-shell CoCuOx@MOx (MNb, Ti and Ce) catalysts with outstanding durability and resistance to H2O for the catalytic combustion of o-dichlorobenzene.

Configuring Co-based catalysts with excellent activity, durability, anti-H2O capability and superior chlorine resistance is an effective strategy for catalytic combustion of CVOCs. In this work, we elaborated a CoCuOx catalysts with the same core but different shell. The CoCuOx dodecahedron surface was successfully coated with shells of Nb2O5, TiO2, and CeO2 using a range of conventional synthesis methods. The prepared core-shell catalysts (CoCuOx@TiO2 and CoCuOx@Nb2O5) were found to generate plentiful acid sites and abundant lattice oxygen species, indicating a strong interaction between the core and shell layers that resulted in a significant enhancement of catalytic activity. Additionally, by-products generation was successfully controlled by acid sites and lattice oxygen species. More importantly, the core-shell structure design significantly improved the thermal stability and anti-H2O capability of the catalysts. Furthermore, the possible formation pathways and reaction mechanisms were proposed based on in-situ FTIR and selectivity analysis.

Significant Enhanced SO2 Resistance of Pt/SiO2 Catalysts by Building the Ultrathin Metal Oxide Shell for Benzene Catalytic Combustion.

A noble metal catalyst shows excellent low-temperature oxidation activity in the catalytic combustion of benzene but has the problem of SO2 poisoning. We all know that SO2 easily competes with the reactant molecules for adsorption of the active site and has electronic effects on the active site to deactivate the catalyst. Therefore, the sulfur resistance of catalysts is the key problem to be solved in the process of catalytic combustion of benzene. Herein, the Pt/SiO2 catalyst with an ordered mesoporous structure was prepared by a one-step hydrothermal method, and MgO, ZnO, and MnOx were, respectively, coated on the surface of Pt/SiO2 as ultrathin shells to improve the sulfur resistance of Pt/SiO2. We observed that the sulfur resistance of the Pt/SiO2 catalyst was significantly improved due to the protective effect of the metal oxide shell. By comparing the three core-shell catalysts, it was found that the Pt/SiO2@MnOx catalyst coated with a MnOx shell had the best performance. The reason was that the MnOx shell not only protected the Pt active site but also had a good electron transfer effect on the core Pt, so it could effectively avoid the rapid adsorption poisoning of SO2 on the active Pt0 site. In addition, it was verified that the excellent redispersion of MnOx species in a SO2 atmosphere could increase the low-temperature oxidation activity of the Pt/SiO2@MnOx catalyst. Meanwhile, in situ DRIFT results also confirmed that the MnOx shell could significantly promote the oxidation of benzene molecules in the SO2 atmosphere.

Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production.

Switchgrass (Panicum virgatum L.) has been developed into a dedicated herbaceous bioenergy crop. Biomass yield is a major target trait for genetic improvement of switchgrass. microRNAs have emerged as a prominent class of gene regulatory factors that has the potential to improve complex traits such as biomass yield. A miR156b precursor was overexpressed in switchgrass. The effects of miR156 overexpression on SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes were revealed by microarray and quantitative RT-PCR analyses. Morphological alterations, biomass yield, saccharification efficiency and forage digestibility of the transgenic plants were characterized. miR156 controls apical dominance and floral transition in switchgrass by suppressing its target SPL genes. Relatively low levels of miR156 overexpression were sufficient to increase biomass yield while producing plants with normal flowering time. Moderate levels of miR156 led to improved biomass but the plants were non-flowering. These two groups of plants produced 58%-101% more biomass yield compared with the control. However, high miR156 levels resulted in severely stunted growth. The degree of morphological alterations of the transgenic switchgrass depends on miR156 level. Compared with floral transition, a lower miR156 level is required to disrupt apical dominance. The improvement in biomass yield was mainly because of the increase in tiller number. Targeted overexpression of miR156 also improved solubilized sugar yield and forage digestibility, and offered an effective approach for transgene containment.

Extracting Wetland Type Information with a Deep Convolutional Neural Network.

Wetlands have important ecological value. The application of wetland remote sensing is essential for the timely and accurate analysis of the current situation in wetlands and dynamic changes in wetland resources, but high-resolution remote sensing images display nonobvious boundaries between wetland types. However, high classification accuracy and time efficiency cannot be guaranteed simultaneously. Extraction of wetland type information based on high-spatial-resolution remote sensing images is a bottleneck that has hindered wetland development research and change detection. This paper proposes an automatic and efficient method for extracting wetland type information. First, the object-oriented multiscale segmentation method is used to realize the fine segmentation of high-resolution remote sensing images, and then the deep convolutional neural network model AlexNet is used to classify automatically the types of wetland images. The method is verified in a case study involving field-measured data, and the classification results are compared with those of traditional classification methods. The results show that the proposed method can more accurately and efficiently extract different wetland types in high-resolution remote sensing images than the traditional classification methods. The proposed method will be helpful in the extension and application of wetland remote sensing technology and will provide technical support for the protection, development, and utilization of wetland resources.

Engineering yolk-shell MnFe@CeOx@TiOx nanocages as a highly efficient catalyst for selective catalytic reduction of NO with NH3 at low temperatures.

To broaden the reaction temperature range and improve the H2O-resistance of manganese-based catalysts, yolk-shell structured MnFe@CeOx@TiOx nanocages were prepared. The CeO2 shell could effectively increase the oxygen vacancy defect sites, and the TiO2 shell could remarkably improve the surface acid sites. Combining the advantages of the two shells could effectively solve the above questions. The catalytic efficiency of the yolk-shell MnFe@CeOx@TiOx-40 nanocages could reach above 90% in the range of 120-240 °C, and the water resistance could reach 90% at 240 °C. On the one hand, the construction of double shells could significantly increase the proportion of active species (Mn4+, Fe3+, Ce3+ and Oads) and the interface effect between the shell layers could effectively enhance the interaction between metal oxides. On the other hand, the construction of double shells could achieve an appropriate balance between the redox capacity of the catalyst and surface acidity. Simultaneously, in situ DRIFT spectroscopy indicated that the yolk-shell MnFe@CeOx@TiOx-40 nanocages mainly followed the L-H mechanism during the NH3-SCR reaction. Finally, this double-shell structure strategy provided a new idea for constructing a Mn-based catalyst with a wide temperature window and better low-temperature water resistance.

Construction of Superhydrophobic Ru/TiCeOx Catalysts for the Enhanced Water Resistance of o-Dichlorobenzene Catalytic Combustion.

In this paper, a simple method to enhance the H2O resistance of Ru/TiCeOx catalysts for o-DCB catalytic combustion by constructing superhydrophobic coating of phenyltriethoxysilane (PhTES) was proposed. The effect of PhTES content on the pore structure, specific surface area, H2O resistance, contact angle (CA) value, and catalytic activity of the catalyst was studied. When water was added, the pristine Ru/TiCeOx catalytic activity decreased by about 26%, while the Ru/TiCeOx-16Ph activity hardly decreased. According to the analysis results of XRD, FT-IR, SEM, and CA, PhTES was closely coated on the surface of Ru/TiCeOx to produce a more hydrophobic surface. The Ru/TiCeOx-16Ph catalyst had strong hydrophobicity, and the contact angle was 159.8°, which not only significantly enhanced the water resistance and self-cleaning activity but also showed a good elimination temperature (T90 = 341 °C) for the o-DCB. The enhanced water resistance of Ru/TiCeOx-XPh catalysts resulted from the reduction of the active centers consumed (water occupying oxygen vacancy sites). The reaction mechanism of the Ru/TiCeOx-16Ph catalyst based on surface oxygen species and the Deacon reaction was proposed. This method provided new idea for the design of a new water-resistant composite catalyst and promoted the practical application of the composite catalyst in the catalytic oxidation of o-DCB.

Precise design and synthesis of Pd/InOx@CoOx core-shell nanofibers for the highly efficient catalytic combustion of toluene.

In this work, Pd/InOx@CoOx core-shell nanofibers, CoOx@Pd/InOx core-shell nanofibers and Pd/InOx/CoOx nanofibers with different morphologies have been successfully synthesized for the catalytic combustion of toluene. Among them, the Pd/InOx@CoOx core-shell sample is novel and composed of Pd/InOx nanotube cores, CoOx nanocubes and CoOx nanoparticle shells derived from ZIF-67. On the contrary, the CoOx@Pd/InOx core-shell catalyst is assembled by CoOx nanocube cores and Pd/InOx nanotube shells. Finally, the Pd/InOx/CoOx nanofibers as references are synthesized by a method similar to the synthesis of the CoOx@Pd/InOx core-shell sample. Interestingly, the Pd/InOx@CoOx core-shell sample displayed the best activity for toluene oxidation with T90 = 253 °C, good thermal stability and good cyclic stability during three runs. Through some characterizations, it was verified that the Pd/InOx@CoOx core-shell sample exhibited the best performance for toluene oxidation reactions due to a larger specific surface area, higher reducibility, more abundant structural defects and oxygen vacancies, higher proportion of Pd0 and Co3+ species and higher lattice oxygen species than others. Simultaneously, the Pd/InOx@CoOx core-shell sample exhibited good thermal stability and cyclic stability, which might be due to the layer of the CoOx shell to protect the stability of the Pd nanoparticle core.

Expression and protease characterization of a conserved protein YgjD in Vibrio harveyi.

The glycopeptidase GCP and its homologue proteins are conserved and essential for survival of bacteria. The ygjD gene (Glycopeptidase homologue) was cloned from Vibrio harveyi strain SF-1. The gene consisted of 1,017 bp, which encodes a 338 amino acid polypeptide. The nucleotide sequence similarity of the ygjD gene with that of V. harveyi FDAARGOS 107 was 95%. The ygjD gene also showed similarities of 68%, 67% and 50% with those of Salmonella enterica, Escherichia coli and Bacillus cereus. The ygjD gene was expressed in E. coli BL21 (DE3) and the recombinant YgjD was purified by Ni2+ affinity chromatography column. The purified YgjD showed a specific 37 kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and exhibited protease activities of 59,000 units/mg, 53,700 units/mg and 8,100 units/mg, respectively, on N-Acetyl-L-tyrosine ethyl ester monohydrate (ATEE), N-Benzoyl-L-tyrosine ethyl ester (BTEE) and N-Benzoyl-DL-arginine-4-nitroanilide hydrochloride (BAPNA) substrates. When the conserved amino acids of His111, Glu113 and His115 in the YgjD were replaced with alanine, respectively, the protease activities of the mutants were partly decreased. The two conserved His111 and His115 of YgjD were mutated and the protein lost the protease activity, which implied that the two amino acid played very important roles in maintaining its protease activity. The addition of the purified YgjD to the culture medium of V. harveyi strain SF-1 can effectively promote the bacteria growth. These results indicated that the protease activities may be involved in the survival of bacteria.

Silencing Folylpolyglutamate Synthetase1 (FPGS1) in Switchgrass (Panicum virgatum L.) Improves Lignocellulosic Biofuel Production.

Switchgrass (Panicum virgatum L.) is a lignocellulosic perennial grass with great potential in bioenergy field. Lignocellulosic bioenergy crops are mostly resistant to cell wall deconstruction, and therefore yield suboptimal levels of biofuel. The one-carbon pathway (also known as C1 metabolism) is critical for polymer methylation, including that of lignin and hemicelluloses in cell walls. Folylpolyglutamate synthetase (FPGS) catalyzes a biochemical reaction that leads to the formation of folylpolyglutamate, an important cofactor for many enzymes in the C1 pathway. In this study, the putatively novel switchgrass PvFPGS1 gene was identified and its functional role in cell wall composition and biofuel production was examined by RNAi knockdown analysis. The PvFPGS1-downregulated plants were analyzed in the field over three growing seasons. Transgenic plants with the highest reduction in PvFPGS1 expression grew slower and produced lower end-of-season biomass. Transgenic plants with low-to-moderate reduction in PvFPGS1 transcript levels produced equivalent biomass as controls. There were no significant differences observed for lignin content and syringyl/guaiacyl lignin monomer ratio in the low-to-moderately reduced PvFPGS1 transgenic lines compared with the controls. Similarly, sugar release efficiency was also not significantly different in these transgenic lines compared with the control lines. However, transgenic plants produced up to 18% more ethanol while maintaining congruent growth and biomass as non-transgenic controls. Severity of rust disease among transgenic and control lines were not different during the time course of the field experiments. Altogether, the unchanged lignin content and composition in the low-to-moderate PvFPGS1-downregulated lines may suggest that partial downregulation of PvFPGS1 expression did not impact lignin biosynthesis in switchgrass. In conclusion, the manipulation of PvFPGS1 expression in bioenergy crops may be useful to increase biofuel potential with no growth penalty or increased susceptibility to rust in feedstock.

Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages.

BACKGROUND: Tall fescue (Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence tag (EST) database developed from nine cDNA libraries representing tissues from different plant organs, developmental stages, and abiotic stress factors. The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported. RESULTS: A total of 41,516 ESTs were generated from nine cDNA libraries of tall fescue representing tissues from different plant organs, developmental stages, and abiotic stress conditions. The Festuca Gene Index (FaGI) has been established. To date, this represents the first publicly available tall fescue EST database. In silico gene expression studies using these ESTs were performed to understand stress responses in tall fescue. A large number of ESTs of known stress response gene were identified from stressed tissue libraries. These ESTs represent gene homologues of heat-shock and oxidative stress proteins, and various transcription factor protein families. Highly expressed ESTs representing genes of unknown functions were also identified in the stressed tissue libraries. CONCLUSION: FaGI provides a useful resource for genomics studies of tall fescue and other closely related forage and turf grass species. Comparative genomic analyses between tall fescue and other grass species, including ryegrasses (Lolium sp.), meadow fescue (F. pratensis) and tetraploid fescue (F. arundinacea var glaucescens) will benefit from this database. These ESTs are an excellent resource for the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) PCR-based molecular markers.

Functional Analysis of Cellulose Synthase CesA4 and CesA6 Genes in Switchgrass (Panicum virgatum) by Overexpression and RNAi-Mediated Gene Silencing.

Switchgrass (Panicum virgatum L.) is a leading lignocellulosic bioenergy feedstock. Cellulose is a major component of the plant cell walls and the primary substrate for saccharification. Accessibility of cellulose to enzymatic breakdown into fermentable sugars is limited by the presence of lignin in the plant cell wall. In this study, putatively novel switchgrass secondary cell wall cellulose synthase PvCesA4 and primary cell wall PvCesA6 genes were identified and their functional role in cellulose synthesis and cell wall composition was examined by overexpression and knockdown of the individual genes in switchgrass. The endogenous expression of PvCesA4 and PvCesA6 genes varied among including roots, leaves, stem, and reproductive tissues. Increasing or decreasing PvCesA4 and PvCesA6 expression to extreme levels in the transgenic lines resulted in decreased biomass production. PvCesA6-overexpressing lines had reduced lignin content and syringyl/guaiacyl lignin monomer ratio accompanied by increased sugar release efficiency, suggesting an impact of PvCesA6 expression levels on lignin biosynthesis. Cellulose content and cellulose crystallinity were decreased, while xylan content was increased in PvCesA4 and PvCesA6 overexpression or knockdown lines. The increase in xylan content suggests that the amount of non-cellulosic cell wall polysaccharide was modified in these plants. Taken together, the results show that the manipulation of the cellulose synthase genes alters the cell wall composition and availability of cellulose as a bioprocessing substrate.

Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis.

Cell walls in crops and trees have been engineered for production of biofuels and commodity chemicals, but engineered varieties often fail multi-year field trials and are not commercialized. We engineered reduced expression of a pectin biosynthesis gene (Galacturonosyltransferase 4, GAUT4) in switchgrass and poplar, and find that this improves biomass yields and sugar release from biomass processing. Both traits were maintained in a 3-year field trial of GAUT4-knockdown switchgrass, with up to sevenfold increased saccharification and ethanol production and sixfold increased biomass yield compared with control plants. We show that GAUT4 is an α-1,4-galacturonosyltransferase that synthesizes homogalacturonan (HG). Downregulation of GAUT4 reduces HG and rhamnogalacturonan II (RGII), reduces wall calcium and boron, and increases extractability of cell wall sugars. Decreased recalcitrance in biomass processing and increased growth are likely due to reduced HG and RGII cross-linking in the cell wall.