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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Data for The Stem Cell-Type Transcriptome of Bioenergy Sorghum Reveals the Spatial Regulation of Secondary Cell Wall Networks

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.

Software↗
DOE OSTI2024

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗
DOE OSTI2023

Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development

Bioenergy sorghum is a drought-tolerant high-biomass C4 grass targeted for production on annual cropland marginal for food crops due primarily to abiotic constraints. To better understand the overall contribution of stem wax to bioenergy sorghum’s resilience, the current study characterized sorghum stem cuticular wax loads, composition, morphometrics, wax pathway gene expression and regulation using vegetative phase Wray, R07020, and TX08001 genotypes. Wax loads on sorghum stems (~103-215 µg/cm 2 ) were much higher than Arabidopsis stem and leaf wax loads. Wax on developing sorghum stem internodes was enriched in C28/30 primary alcohols (~65%) while stem wax on fully developed stems was enriched in C28/30 aldehydes (~80%). Scanning Electron Microscopy showed minimal wax on internodes prior to the onset of elongation and that wax tubules first appear associated with cork-silica cell complexes when internode cell elongation is complete. Sorghum homologs of genes involved in wax biosynthesis/transport were differentially expressed in the stem epidermis. Expression of many wax pathway genes (i.e., SbKCS6, SbCER3-1, SbWSD1, SbABCG12, SbABCG11 ) is low in immature apical internodes then increases at the onset of stem wax accumulation. SbCER4 is expressed relatively early in stem development consistent with accumulation of C28/30 primary alcohols on developing apical internodes. High expression of two SbCER3 homologs in fully elongated internodes is consistent with a role in production of C28/30 aldehydes. Gene regulatory network analysis aided the identification of sorghum homologs of transcription factors that regulate wax biosynthesis (i.e., SbSHN1, SbWRI1/3, SbMYB94/96/30/60, MYS1 ) and other transcription factors that could regulate and specify expression of the wax pathway in epidermal cells during cuticle development.

09 BIOMASS FUELS↗
DOE OSTI2024

Bioenergy sorghum nodal root bud development: morphometric, transcriptomic and gene regulatory network analysis

Bioenergy sorghum’s large and deep nodal root system and associated microbiome enables uptake of water and nutrients from and deposition of soil organic carbon into soil profiles, key contributors to the crop’s resilience and sustainability. The goal of this study was to increase our understanding of bioenergy sorghum nodal root bud development. Sorghum nodal root bud initiation was first observed on the stem node of the 7 th phytomer below the shoot apex. Buds were initiated near the upper end of the stem node pulvinus on the side of the stem opposite the tiller bud, then additional buds were added over the next 6-8 days forming a ring of 10-15 nascent nodal root buds around the stem. Later in plant development, a second ring of nodal root buds began forming on the 17 th stem node immediately above the first ring of buds. Overall, nodal root bud development can take ~40 days from initiation to onset of nodal root outgrowth. Nodal root buds were initiated in close association with vascular bundles in the rind of the pulvinus. Stem tissue forming nascent nodal root buds expressed sorghum homologs of genes associated with root initiation (WOX4), auxin transport (LAX2, PIN4), meristem activation (NGAL2), and genes involved in cell proliferation. Expression of WOX11 and WOX5, genes involved in root stem niche formation, increased early in nodal root bud development followed by genes encoding PLTs, LBDs (LBD29), LRP1, SMB, RGF1 and root cap LEAs later in development. A nodal root bud gene regulatory network module expressed during nodal root bud initiation predicted connections linking PFA5, SPL9 and WOX4 to genes involved in hormone signaling, meristem activation, and cell proliferation. A network module expressed later in development predicted connections among SOMBRERO, a gene involved in root cap formation, and GATA19, BBM, LBD29 and RITF1/RGF1 signaling. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for understanding the regulation of sorghum nodal root bud formation and development.

09 BIOMASS FUELS↗
DOE OSTI2024

Optimizing bioenergy sorghum productivity and nutrient removal in Illinois: Impact of nitrogen fertilization under diverse marginal conditions

Bioenergy sorghum (Sorghum bicolor L. Moench) is a promising crop for contributing to the United States bioenergy supply. However, the varying limitations of the marginal lands targeted for its cultivation present a management challenge. This two-year study aimed to investigate how the limitations associated with marginal cropland impact the effects of nitrogen fertilization on the yield of bioenergy sorghum and the uptake of 11 macro- (N, P, K, Ca, Mg, and S) and micronutrients (Fe, Mn, Zn, Cu, and B). The study contrasted prime cropland in central Illinois (Urbana) with three marginal cropland sites in southern (Ewing) and central Illinois (Fairbury and Pesotum). These marginal cropland sites are characterized by varying limitations, including low soil fertility (P and K limitations), leaching and erosion, and flooding, respectively. Four nitrogen rates (0, 56, 112, and 168 kg N ha –1 ) were tested under eight environments. The average yields and ranges of sorghum biomass were 20.2 (17.0–23.2) Mg ha –1 in Urbana, 18.1 (13.1–19.8) Mg ha –1 in Ewing, 13.8 (9.0–17.3) Mg ha –1 in Fairbury, and 23.3 (14.6–33.0) Mg ha –1 in Pesotum. Optimal N rates were 56 N in Pesotum and 112 N in Urbana, Ewing, and Fairbury. Tissue macronutrient contents in Urbana were generally higher than in the marginal croplands, while micronutrient contents did not show discernible trends. Increasing N rate generally correlated with the macronutrient removal except in Ewing. Comparable sorghum biomass yields were observed between prime and marginal croplands (averaging 18.3 Mg ha –1 ), but optimal N rates varied between 56 N and 112 N. This suggests that yield gaps can be narrowed by applying the optimal N rates for the respective locations. However, increased removals of macronutrients, especially P and K, with increasing yields indicate the need to revise fertilizer recommendations, particularly for soils deficient in these nutrients.

09 BIOMASS FUELS↗
DOE OSTI2024

Data for Optimizing Bioenergy Sorghum Productivity and Nutrient Removal in Illinois: Impact of Nitrogen Fertilization Under Diverse Marginal Conditions

Bioenergy sorghum ( Sorghum bicolor L. Moench) is a promising crop for contributing to the United States bioenergy supply. However, the varying limitations of the marginal lands targeted for its cultivation present a management challenge. This two-year study aimed to investigate how the limitations associated with marginal cropland impact the effects of nitrogen fertilization on the yield of bioenergy sorghum and the uptake of 11 macro- (N, P, K, Ca, Mg, and S) and micronutrients (Fe, Mn, Zn, Cu, and B). The study contrasted prime cropland in central Illinois (Urbana) with three marginal cropland sites in southern (Ewing) and central Illinois (Fairbury and Pesotum). These marginal cropland sites are characterized by varying limitations, including low soil fertility (P and K limitations), leaching and erosion, and flooding, respectively. Four nitrogen rates (0, 56, 112, and 168 kg N ha−1) were tested under eight environments. The average yields and ranges of sorghum biomass were 20.2 (17.0–23.2) Mg ha−1 in Urbana, 18.1 (13.1–19.8) Mg ha−1 in Ewing, 13.8 (9.0–17.3) Mg ha−1 in Fairbury, and 23.3 (14.6–33.0) Mg ha−1 in Pesotum. Optimal N rates were 56 N in Pesotum and 112 N in Urbana, Ewing, and Fairbury. Tissue macronutrient contents in Urbana were generally higher than in the marginal croplands, while micronutrient contents did not show discernible trends. Increasing N rate generally correlated with the macronutrient removal except in Ewing. Comparable sorghum biomass yields were observed between prime and marginal croplands (averaging 18.3 Mg ha−1), but optimal N rates varied between 56 N and 112 N. This suggests that yield gaps can be narrowed by applying the optimal N rates for the respective locations. However, increased removals of macronutrients, especially P and K, with increasing yields indicate the need to revise fertilizer recommendations, particularly for soils deficient in these nutrients. Our study suggests that while sorghum production on marginal cropland is feasible, N management needs to be adapted to the unique limitations associated with various types of marginal cropland.

Biomass Analytics↗
DOE OSTI2022

Evaluation of UAV-derived multimodal remote sensing data for biomass prediction and drought tolerance assessment in bioenergy sorghum

Screening for drought tolerance is critical to ensure high biomass production of bioenergy sorghum in arid or semi-arid environments. The bottleneck in drought tolerance selection is the challenge of accurately predicting biomass for a large number of genotypes. Although biomass prediction by low-altitude remote sensing has been widely investigated on various crops, the performance of the predictions are not consistent, especially when applied in a breeding context with hundreds of genotypes. In some cases, biomass prediction of a large group of genotypes benefited from multimodal remote sensing data; while in other cases, the benefits were not obvious. In this study, we evaluated the performance of single and multimodal data (thermal, RGB, and multispectral) derived from an unmanned aerial vehicle (UAV) for biomass prediction for drought tolerance assessments within a context of bioenergy sorghum breeding. The biomass of 360 sorghum genotypes grown under well-watered and water-stressed regimes was predicted with a series of UAV-derived canopy features, including canopy structure, spectral reflectance, and thermal radiation features. Biomass predictions using canopy features derived from the multimodal data showed comparable performance with the best results obtained with the single modal data with coefficients of determination (R 2 ) ranging from 0.40 to 0.53 under water-stressed environment and 0.11 to 0.35 under well-watered environment. The significance in biomass prediction was highest with multispectral followed by RGB and lowest with the thermal sensor. Finally, two well-recognized yield-based drought tolerance indices were calculated from ground truth biomass data and UAV predicted biomass, respectively. Results showed that the geometric mean productivity index outperformed the yield stability index in terms of the potential for reliable predictions by the remotely sensed data. Collectively, this study demonstrated a promising strategy for the use of different UAV-based imaging sensors to quantify yield-based drought tolerance.

09 BIOMASS FUELS↗
DOE OSTI2022

Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis

SUMMARY Bioenergy sorghum is a highly productive drought tolerant C 4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES ( SbLOB ), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM ( dw2 ) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non‐meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin‐dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bioenergy sorghum stem density increases threefold following internode elongation due to continued accumulation of lignified cell walls and complex regulation of genes involved in cell wall biosynthesis

Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates ~ 80% of its harvested biomass in ~ 4 m long stems comprised of > 40 internodes that develop sequentially during an extended vegetative growth phase. Following elongation of each internode, internode density increases ~ threefold to fourfold primarily due to the accumulation of cell walls composed of cellulose, glucuronoarabinoxylan and lignin. Lignin accumulates initially on cell walls of sclerenchyma cells surrounding vascular bundles and later on cell walls of the stem rind and stem core pith parenchyma. Many genes involved in cell wall biosynthesis were expressed continuously during the stem internode densification process whereas others showed dynamic patterns of expression (high to low, low to high). Several CESA genes involved in primary cell wall cellulose synthesis were expressed in the stem rind and core throughout the stem densification phase. In contrast, CESA genes involved in secondary cell wall biogenesis were expressed continuously in the stem rind but downregulated in the stem core shortly after completion of internode elongation. Overall, accumulation of cell wall biomass in elongated internodes during stem densification increases stem mechanical strength and biomass bulk density while modifying biomass composition in ways that could impact the amount and release of cellulosic sugars and lignin-derived bioproducts.

09 BIOMASS FUELS↗
DOE OSTI2026

Draft Genome Sequences of 14 Bacterial Isolates from the Rhizosphere of Bioenergy Sorghum

We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.

Black, Grace S.↗
DOE OSTI2023

Production of Designer Xylose-Acetic Acid Enriched Hydrolysate from Bioenergy Sorghum, Oilcane, and Energycane Bagasses

Xylan accounts for up to 40% of the structural carbohydrates in lignocellulosic feedstocks. Along with xylan, acetic acid in sources of hemicellulose can be recovered and marketed as a commodity chemical. Through vibrant bioprocessing innovations, converting xylose and acetic acid into high-value bioproducts via microbial cultures improves the feasibility of lignocellulosic biorefineries. Enzymatic hydrolysis using xylanase supplemented with acetylxylan esterase (AXE) was applied to prepare xylose-acetic acid enriched hydrolysates from bioenergy sorghum, oilcane, or energycane using sequential hydrothermal-mechanical pretreatment. Various biomass solids contents (15 to 25%, w/v) and xylanase loadings (140 to 280 FXU/g biomass) were tested to maximize xylose and acetic acid titers. The xylose and acetic acid yields were significantly improved by supplementing with AXE. The optimal yields of xylose and acetic acid were 92.29% and 62.26% obtained from hydrolyzing energycane and oilcane at 25% and 15% w/v biomass solids using 280 FXU xylanase/g biomass and AXE, respectively.

09 BIOMASS FUELS↗
DOE OSTI2023

Data for Production of Designer Xylose-Acetic Acid Enriched Hydrolysate from Bioenergy Sorghum, Oilcane, and Energycane Bagasses

Xylan accounts for up to 40% of the structural carbohydrates in lignocellulosic feedstocks. Along with xylan, acetic acid in sources of hemicellulose can be recovered and marketed as a commodity chemical. Through vibrant bioprocessing innovations, converting xylose and acetic acid into high-value bioproducts via microbial cultures improves the feasibility of lignocellulosic biorefineries. Enzymatic hydrolysis using xylanase supplemented with acetylxylan esterase (AXE) was applied to prepare xylose-acetic acid enriched hydrolysates from bioenergy sorghum, oilcane, or energycane using sequential hydrothermal-mechanical pretreatment. Various biomass solids contents (15 to 25%, w/v) and xylanase loadings (140 to 280 FXU/g biomass) were tested to maximize xylose and acetic acid titers. The xylose and acetic acid yields were significantly improved by supplementing with AXE. The optimal yields of xylose and acetic acid were 92.29% and 62.26% obtained from hydrolyzing energycane and oilcane at 25% and 15% w/v biomass solids using 280 FXU xylanase/g biomass and AXE, respectively.

Biomass Analytics↗
DOE OSTI2025

Combining biotechnology with sustainability: feasibility of bioenergy sorghum in generating high-value bioproducts

Biofuels generated through fermentation of plant-derived lignocellulosic biomass are currently not competitive with fossil fuels. Here, a framework is described for the engineering of valuable coproducts to improve the economic feasibility of biofuel production. To accomplish this goal, the desirable traits of the bioenergy crop Sorghum bicolor are harnessed via modern engineering approaches. A robust analysis is provided to highlight the scientific basis, costs, regulatory challenges, and lucrative nature of coproduct development. Sustainable biofuel production could also have far-reaching societal impacts, especially in the context of our rapidly changing global climate. This perspective suggests that the path to profitable biofuel production is attainable and encourages consideration of similar approaches by the biotechnology industry.

09 BIOMASS FUELS↗
DOE OSTI2024

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [ Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink’s yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height ( Dw1 and Dw2 ) and the YELLOW SEED1 locus ( Y1 ) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.

bioenergy association panel↗
DOE OSTI2024

The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks

Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type.

cell specificity↗
DOE OSTI2022

Elucidation of Triacylglycerol Overproduction in the C4 Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis

Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C 4 biomass crop Sorghum bicolor ( iTJC1414 ) along with a minimal model for photosynthetic CO 2 assimilation, sucrose and TAG biosynthesis in C 3 plants. Extending iTJC1414 to a four-cell diel model we simulate C 4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO 2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.

59 BASIC BIOLOGICAL SCIENCES↗