Transgenic woody plants for biofuel

Transgenic trees as a new source for biofuel have brought a great interest in tree biotechnology. Genetically modifying forest trees for ethanol production have advantages in technical challenges, costs, environmental concerns, and financial problems over some of crops. Genetic engineering of forest trees can be used to reduce the level of lignin, to produce the fast-growing trees, to develop trees with higher cellulose, and to allow the trees to be grown more widely. Trees can establish themselves in the field with less care of farmers, compared to most of crops. Transgenic crops as a new source for biofuel have been recently reviewed in several reviews. Here, we overview transgenic woody plants as a new source for biofuel including genetically modified woody plants and environment; main focus of woody plants genetic modifications; solar to chemical energy transfer; cellulose biosynthesis; lignin biosynthesis; and cellulosic ethanol as biofuel.

Overexpression of Arabidopsis thaliana malonyl-CoA synthetase gene enhances cold stress tolerance by activating mitogen-activated protein kinases in plant cells

Malonyl-CoA synthetases may modulate cell responses to abiotic stress by regulating stress-related signaling transduction pathways or activating expression of transcription factors.However,the molecular mechanism of cold stress tolerance enhanced by malonyl-CoA synthetase is not fully understood.Here,we report that overexpression of the Arabidopsis thaliana malonyl-CoA synthetase gene AAE13.1 resulted in increased cell viability and growth rate and decreased thiobarbituric acid reactive substances under cold stress in rice(Oryza sativa L.),tobacco(Nicotiana tabacum),and slash pine(Pinus elliottii Engelm.).AAE13.1 was associated with cold stress tolerance by increasing the activity of ascorbate peroxidase,catalase,polyphenol oxidase,and peroxidase and the accumulation of acid phosphatase and alkaline phosphatase.Among six rice mitogenactivated protein kinase(MAPK)genes examined,AAE13.1 overexpression increased the expression of OsMAPK genes during cold stress.AAE13.1 activated expression of stressresponse genes OsMAPK1,OsMAPK2,and OsMAPK3,indicating that AAE13.1 enhances cold stress tolerance by regulating expression of MAPK genes in plant cells.These results increase our understanding of cold stress tolerance in species of monocotyledons,dicotyledons,and gymnosperms.

MicroRNAs associated with molecular mechanisms for plant root formation and growth

Although roots are so important for plant growth and crop productivity, the molecular mecha- nism（s） of root formation and growth is not fully under- stood. To increase our understanding of the underlying molecular mechanisms, here we review microRNA regu- lation of processes related to root formation： the regulation of transcription factors, nutrient uptake, stress signaling, and growth signaling. We have summarized the interaction, expression, transport, and signaling events that involve microRNAs in ideal and stressed conditions in a number of model plants, highlighting the involvement of microRNAs in root formation. MicroRNAs are now known to be important players in root initiation, development, and growth; understanding the precise mechanisms involved will be valuable for plant molecular breeding to develop high-yielding crops with high stress resistance and low nutrient requirements.

Biological significance of RNA-seq and single-cell genomic research in woody plants

RNA-seq and single-cell genomic research emerge as an important research area in the recent years due to its ability to examine genetic information of any number of single cells in all living organisms.The knowledge gained from RNA-seq and single-cell genomic research will have a great impact in many aspects of plant biology.In this review,we summary and discuss the biological significance of RNA-seq and single-cell genomic research in plants including the single-cell DNA-sequencing,RNA-seq and single-cell RNA sequencing in woody plants,methods of RNA-seq and single-cell RNA-sequencing,single-cell RNA-sequencing for studying plant development,and single-cell RNA-sequencing for elucidating cell type composition.We will focus on RNA-seq and single-cell RNA sequencing in woody plants,understanding of plant development through single-cell RNAsequencing,and elucidation of cell type composition via single-cell RNA-sequencing.Information presented in this review will be helpful to increase our understanding of plant genomic research in a way with the power of plant single-cell RNA-sequencing analysis.

Transcriptional mechanisms regulating gene expression and determining cell fates in plant development

Transcriptional regulatory mechanisms that control transcriptional regulators, target genes, and their interactions provide new insights into general development processes throughout the life cycle of the plant. Although different molecular mechanisms that regulate plant growth and development have been identified, detailed transcriptional mechanisms that control gene expression, modulate developmental programmes, and determine cell fates in plant development are not fully understood. To increase our understanding on transcriptional mechanisms regulating diverse processes in plant development, we have reviewed the regulation of transcription during the process of development including transcriptional mechanisms regulating root, stem, leaf, flower, seed, embryo, endosperm, ovule, fruit, and chloroplast development. We have summarized the interaction, expression, transport, signaling events of transcriptional regulators and their targets in a number of model plants and highlighted the involvement of hormones and microRNAs in plant development. Understanding the precise transcriptional mechanisms regulating gene expression in plant development will be valuable for plant molecular breeding.

Overexpression of Arabidopsis thaliana cysteine2/histidine2-type transcription factor 6 gene enhances plant resistance to a bacterial pathogen

Transcription factors can be used to engineer plants for enhanced productivity.However,the mechanism(s)by which the C2H2-type zinc fi nger transcription factor enhances pathogen resistance in cells is not fully understood.Here,Agrobacterium tumefaciens carrying the gene for Arabidopsis thaliana cysteine2/histidine2-type transcription factor 6(ZAT6)was used to engineer rice(Oryza sativa L.),cotton(Gossypium hirsutum L.),and slash pine(Pinus elliottii Engelm.)to generate transgenic cell lines.Transgenic cells were then inoculated with the pathogenic bacterium Pseudomonas syringae.Compared to the control,cell viability of transgenic cells increased 39–47%and growth rate increased 9–15%by 7 days after inoculation in rice,cotton and slash pine.Acid phosphatase activity and alkaline phosphatase activity and transcript levels of Ca 2+-dependent protein kinase genes OsCPK1,OsCPK2,OsCPK6,and OsCPK8 and mitogen-activated protein kinase genes OsMAPK1,OsMAPK2,OsMAPK3,and OsMAPK8 increased signifi cantly in transgenic rice cells by 3 day after inoculation,and extracellular pH had decreased by 10–14%by 96 min after inoculation in transgenic rice,cotton and slash pine cells.These results suggest that ZAT6 enhances P.syringae resistance in plant cells by modulating transcription of CPK and MAPK and oxidase activity.

Applications and roles of the CRISPR system in genome editing of plants

Genome editing is a valuable tool to target specific DNA sequences for mutagenesis in the genomes of microbes, plants, and animals. Although different genome editing technologies are available, the clustered regularly interspaced short palindromic repeats/Cas9 （CRISPR/ Cas9） system, which utilizes engineered endonucleases to generate a double-stranded DNA break （DSB） in the target DNA region and subsequently stimulates site-specific mutagenesis through DNA repair machineries, is emerging as a powerful genome editing tool for elucidating mecha- nisms of protection from plant viruses, plant disease resistance, and gene functions in basic and applied research. In this review, we provide an overview of recent advances in the CRISPR system associated genome editing in plants by focusing on application of this technology in model plants, crop plants, fruit plants, woody plants and grasses and discuss how genome editing associated with the CRISPR system can provide insights into genome modifications and functional genomics in plants.