Poplar transformation with variable explant sources to maximize transformation efficiency.

For decades, Agrobacterium tumefaciens-mediated plant transformation has played an integral role in advancing fundamental and applied plant biology. The recent omnipresent emergence of synthetic biology, which relies on plant transformation to manipulate plant DNA and gene expression for novel product biosynthesis, has further propelled basic as well as applied interests in plant transformation technologies. The strong demand for a faster design-build-test-learn cycle, the essence of synthetic biology, is, however, still ill-matched with the long-standing issues of high tissue culture recalcitrance and low transformation efficiency of a wide range of plant species especially food, fiber and energy crops.

Intraspecific variability in plant and soil chemical properties in a common garden plantation of the energy crop Populus.

Optimizing crops for synergistic soil carbon (C) sequestration can enhance CO2 removal in food and bioenergy production systems. Yet, in bioenergy systems, we lack an understanding of how intraspecies variation in plant traits correlates with variation in soil biogeochemistry. This knowledge gap is exacerbated by both the heterogeneity and difficulty of measuring belowground traits.

Validation of a metabolite-GWAS network for family 1 UDP-glycosyltransferases.

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as , a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships.

Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop .

For plants, distinguishing between mutualistic and pathogenic microbes is a matter of survival. All microbes contain microbe-associated molecular patterns (MAMPs) that are perceived by plant pattern recognition receptors (PRRs). Lysin motif receptor-like kinases (LysM-RLKs) are PRRs attuned for binding and triggering a response to specific MAMPs, including chitin oligomers (COs) in fungi, lipo-chitooligosaccharides (LCOs), which are produced by mycorrhizal fungi and nitrogen-fixing rhizobial bacteria, and peptidoglycan in bacteria.

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal.

A grand challenge facing society is climate change caused mainly by rising CO concentration in Earth's atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy.

Cultivating the Bacterial Microbiota of Roots.

The integral role of microbial communities in plant growth and health is now widely recognized, and, increasingly, the constituents of the microbiome are being defined. While phylogenetic surveys have revealed the taxa present in a microbiome and show that this composition can depend on, and respond to, environmental perturbations, the challenge shifts to determining why particular microbes are selected and how they collectively function in concert with their host. In this study, we targeted the isolation of representative bacterial strains from environmental samples of roots using a direct plating approach and compared them to amplicon-based sequencing analysis of root samples.

Importance of suberin biopolymer in plant function, contributions to soil organic carbon and in the production of bio-derived energy and materials.

Suberin is a hydrophobic biopolymer of significance in the production of biomass-derived materials and in biogeochemical cycling in terrestrial ecosystems. Here, we describe suberin structure and biosynthesis, and its importance in biological (i.e.

Plant Biosystems Design Research Roadmap 1.0.

Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches.

Molecular Remodeling in Populus PdKOR RNAi Roots Profiled Using LC-MS/MS Proteomics.

Plant endo-β-1,4-glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)-β-d-glucosidic linkages. Modification of cell wall chemistry via RNA interference (RNAi)-mediated downregulation of Populus deltoides KORRIGAN (PdKOR), an endo-β-1,4-glucanase familygene was shown to have functional consequences on the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood.

Plant Biosystems Design for a Carbon-Neutral Bioeconomy.

Our society faces multiple daunting challenges including finding sustainable solutions towards climate change mitigation; efficient production of food, biofuels, and biomaterials; maximizing land-use efficiency; and enabling a sustainable bioeconomy. Plants can provide environmentally and economically sustainable solutions to these challenges due to their inherent capabilities for photosynthetic capture of atmospheric CO, allocation of carbon to various organs and partitioning into various chemical forms, including contributions to total soil carbon. In order to enhance crop productivity and optimize chemistry simultaneously in the above- and belowground plant tissues, transformative biosystems design strategies are needed.

Transgenic Poplar Designed for Biofuels.

Members of the genus Populus (i.e., cottonwood, hybrid poplar) represent a promising source of lignocellulosic biomass for biofuels.

Draft Genome Sequence of sp. Strain BK434, Isolated from the Roots of Eastern Cottonwood.

A Gram-positive bacterium was isolated from the root of an eastern cottonwood tree () in Georgia and identified as a species with 99% 16S rRNA nucleotide identity to The genome is 4.6 Mbp and encodes 4,072 proteins and 251 RNAs.

Draft Genome Sequence of sp. Strain BK230, Isolated from Roots.

sp. strain BK230, a heterotrophic bacterium of the phylum , was isolated from the roots of a field-grown eastern cottonwood tree () located in Georgia. The draft 7.

Nanomechanics and Raman Spectroscopy of in Situ Native Carbohydrate Storage Granules for Enhancing Starch Quality and Lignocellulosic Biomass Production.

Alternative energy strategies based on plant biomass-derived bioenergy and biofuels rely on understanding and optimization of plant structure, chemistry, and performance. Starch, a constitutive element of all green plants, is important to food, biofuels, and industrial applications. Models of carbohydrate storage granules are highly heterogeneous in representing morphology and structure, though a deeper understanding of the role of structure in functional behavior is emerging.

A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in .

A greater understanding of biosynthesis, signaling and regulatory pathways involved in determining stem growth and secondary cell wall chemistry is important for enabling pathway engineering and genetic optimization of biomass properties. The present study describes a new functional role of , a gene belonging to the IQ67-Domain1 family of genes, in impacting biomass formation and chemistry. Expression studies showed that has enhanced expression in developing xylem and tension-stressed tissues in .

Perspectives on the basic and applied aspects of crassulacean acid metabolism (CAM) research.

Due to public concerns about the decreasing supply of blue water and increasing heat and drought stress on plant growth caused by urbanization, increasing human population and climate change, interest in crassulacean acid metabolism (CAM), a specialized type of photosynthesis enhancing water-use efficiency (WUE) and drought tolerance, has increased markedly. Significant progress has been achieved in both basic and applied research in CAM plants since the beginning of this century. Here we provide a brief overview of the current status of CAM research, and discuss future needs and opportunities in a wide range of areas including systems biology, synthetic biology, and utilization of CAM crops for human benefit, with a focus on the following aspects: 1) application of genome-editing technology and high-throughput phenotyping to functional genomics research in model CAM species and genetic improvement of CAM crops, 2) challenges for multi-scale metabolic modeling of CAM systems, 3) opportunities and new strategies for CAM pathway engineering to enhance WUE and drought tolerance in C (and C) photosynthesis crops, 4) potential of CAM species as resources for food, feed, natural products, pharmaceuticals and biofuels, and 5) development of CAM crops for ecological and aesthetic benefits.

Tension wood structure and morphology conducive for better enzymatic digestion.

Background: Tension wood is a type of reaction wood in response to bending or leaning stem as a corrective growth process. Tension wood is formed by both natural and man-made processes. Most attractively, tension wood contains higher glucan content and undergoes higher enzymatic conversion to fermentable sugars.

Agronomic performance of trees engineered for biofuel production.

Background: One of the major barriers to the development of lignocellulosic feedstocks is the recalcitrance of plant cell walls to deconstruction and saccharification. Recalcitrance can be reduced by targeting genes involved in cell wall biosynthesis, but this can have unintended consequences that compromise the agronomic performance of the trees under field conditions. Here we report the results of a field trial of fourteen distinct transgenic lines that had previously demonstrated reduced recalcitrance without yield penalties under greenhouse conditions.

Down-Regulation of -Like Endo-β-1,4-Glucanase Genes Impacts Carbon Partitioning, Mycorrhizal Colonization and Biomass Production in .

A greater understanding of the genetic regulation of plant cell wall remodeling and the impact of modified cell walls on plant performance is important for the development of sustainable biofuel crops. Here, we studied the impact of down-regulating KORRIGAN-like cell wall biosynthesis genes, belonging to the endo-β-1,4-glucanase gene family, on growth, metabolism and the ability to interact with symbiotic microbes. The reductions in cellulose content and lignin syringyl-to-guaiacyl unit ratio, and increase in cellulose crystallinity of cell walls of RNAi plants corroborated the functional role of PdKOR in cell wall biosynthesis.

Carbon Nanofiber Arrays: A Novel Tool for Microdelivery of Biomolecules to Plants.

Effective methods for delivering bioprobes into the cells of intact plants are essential for investigating diverse biological processes. Increasing research on trees, such as Populus spp., for bioenergy applications is driving the need for techniques that work well with tree species.

Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance.

Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls.

Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus.

Background: UDP-glucose pyrophosphorylase (UGPase) is a sugar-metabolizing enzyme (E.C. 2.

Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions.

A wide variety of microorganisms known to produce auxin and auxin precursors form beneficial relationships with plants and alter host root development. Moreover, other signals produced by microorganisms affect auxin pathways in host plants. However, the precise role of auxin and auxin-signalling pathways in modulating plant-microbe interactions is unknown.