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NASA NTRS1986

High-temperature, high-pressure optical cell

The invention is an optical cell for containment of chemicals under conditions of high temperature and high pressure. The cell is formed of a vitreous silica tube, two optical windows comprising a vitreous silica rod inserted into the ends of a tube, and fused into position in the tube ends. Windows are spaced apart to form a cavity enclosed by the tube and the windows. A hole is drilled radially through the tube and into the cavity. Another vitreous silica tube is fused to the silica tube around the hole to form the stem, which is perpendicular to the long axis of the tube. The open end of the stem is used to load chemicals into the cavity. Then the stem may be sealed, and if desired, it may be shortened in order to reduce the volume of the cavity, which extends into the stem.

Harris, R. P.↗

NASA NTRS1992

Synergistic action of the benzene metabolite hydroquinone on myelopoietic stimulating activity of granulocyte/macrophage colony-stimulating factor in vitro

The effects of in vitro pretreatment with benzene metabolites on colony-forming response of murine bone marrow cells stimulated with recombinant granulocyte/macrophage colony-stimulating factor (rGM-CSF) were examined. Pretreatment with hydroquinone (HQ) at concentrations ranging from picomolar to micromolar for 30 min resulted in a 1.5- to 4.6-fold enhancement in colonies formed in response to rGM-CSF that was due to an increase in granulocyte/macrophage colonies. The synergism equaled or exceeded that reported for the effects of interleukin 1, interleukin 3, or interleukin 6 with GM-CSF. Optimal enhancement was obtained with 1 microM HQ and was largely independent of the concentration of rGM-CSF. Pretreatment with other authentic benzene metabolites, phenol and catechol, and the putative metabolite trans, trans-muconaldehyde did not enhance growth factor response. Coadministration of phenol and HQ did not enhance the maximal rGM-CSF response obtained with HQ alone but shifted the optimal concentration to 100 pM. Synergism between HQ and rGM-CSF was observed with nonadherent bone marrow cells and lineage-depleted bone marrow cells, suggesting an intrinsic effect on recruitment of myeloid progenitor cells not normally responsive to rGM-CSF. Alterations in differentiation in a myeloid progenitor cell population may be of relevance in the pathogenesis of acute myelogenous leukemia secondary to drug or chemical exposure.

NASA Discipline Environmental Health↗

DOE OSTI2021

Cytokinin signaling localized in phloem noncell‐autonomously regulates cambial activity during secondary growth of Populus stems

Summary The regulation of cytokinin on secondary vascular development has been uncovered by modulating cytokinin content. However, it remains unclear how cytokinin enriched in developing secondary phloem regulates cambium activity in poplar. Here, we visualized the gradient distribution of cytokinin with a peak in the secondary phloem of poplar stem via immunohistochemical imaging, and determined the role of phloem‐located cytokinin signaling during wood formation. We generated transgenic poplar harboring cytokinin oxidase/dehydrogenase ( CKX)2 , a gene encoding a cytokinin degrading enzyme, driven by the phloem‐specific CLE41b promoter, indicating that the disruption of the cytokinin gradient pattern restricts the cambial activity. The RNA interference‐based knockdown of the histidine kinase ( HK ) genes encoding cytokinin receptors specifically in secondary phloem significantly compromised the division activity of cambial cells, whereas the phloem‐specific expression of a type‐B response regulator (RR) transcription factor stimulated cambial proliferation, providing evidence for the noncell‐autonomous regulation of local cytokinin signaling on the cambial activity. Moreover, the cambium‐specific knockdown of HK s also led to restricted cambial activity, and the defects were aggravated by the reduced cytokinin accumulation. Our results showed that local cytokinin signaling in secondary phloem regulates cambial activity noncell‐autonomously, and coordinately with its local signaling in cambium.

Fu, Xiaokang↗

DOE OSTI2021

Inside out: Measuring the effect of wood anatomy on the efflux and assimilation of xylem–transported CO 2

Carbon dioxide concentrations (including aqueous CO 2 , carbonic acid, bicarbonate, and carbonate) in woody tissues can be up to 750 times higher than atmospheric CO 2 concentrations, ranging from <1% to >26% vs atmospheric ~0.04% (Fig. 1) (Teskey et al. 2008). CO 2 formed through respiration is generally assumed to diffuse to the atmosphere from tissues adjacent to where it is produced. Here, this CO 2 buildups in the stem due to the diffusional barriers in woody and bark tissues. CO 2 in the stem has three fates: 1) it can be refixed for photosynthesis, 2) it can be used for anaplerotic reactions, or 3) it can exit the plant either adjacent to where it was produced (radial diffusion) or in an area remote from its point of origin (xylem-transported CO 2 ). Not accounting for assimilation of xylem-transported CO 2 may result in underestimating total plant photosynthesis. Alternatively, overlooking the transport of CO 2 away from its point of origin complicates the estimation of respiration in stems, branches, or even leaves. For example, CO 2 efflux from the stem may not solely represent stem respiration, but it may represent CO 2 generated through respiration in areas remote from the point of efflux (Stutz et al., 2017). Additionally, wood anatomy and branching architecture likely influence how much and how far xylem-transported CO 2 travels (Fig. 2). Few studies have combined measurements of both the efflux of xylem-transported CO 2 from trees together and the assimilation of xylem-transported CO 2 . Excitingly in this issue of Plant, Cell & Environment, Salomón et al. (pp. ) demonstrate the importance of xylem-transported CO 2 in plants with different wood anatomies by comparing the amount of xylem-transported CO 2 used for photosynthesis to the amount effluxed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Single Atomic Iron Site Catalysts via Benign Aqueous Synthesis for Durability Improvement in Proton Exchange Membrane Fuel Cells

Atomically-dispersed iron-nitrogen-carbon (Fe–N–C) catalysts have arisen as promising candidates for replacing the costly precious metal catalysts in fuel cells but still face some grand challenges, such as insufficient site density and durability. Herein, we report a self-assembly method in an aqueous solution to develop an atomically-dispersed iron catalyst with high oxygen reduction reaction (ORR) activity and stability in acidic electrolytes. As determined by high-resolution transmission electron microscopy (HR-TEM), X-ray absorption spectroscopy (XAS), and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), this benign aqueous synthesis strategy facilitates the formation of homogeneous atomic nitrogen-coordinated iron sites embedded in a popcorn-like porous graphitic carbon matrix. These catalyst properties contribute to the improved ORR kinetic current density and mass transport. By controlling synthesis chemistry, the correlation between structure and property is systematically investigated. In this work, the iron content is the most critical material property and can regulate site density and graphitic carbon structures in the catalyst, impacting catalytic activity and stability. The enhanced performance and durability were examined in both acidic aqueous electrolytes and membrane electrode assemblies.

25 ENERGY STORAGE↗

DOE OSTI2022

Electrochemical characterization of evolving ionomer/electrocatalyst interactions throughout accelerated stress tests

Here, the degradation of polymer electrolyte membrane fuel cells (PEMFCs) catalyst layers used for heavy-duty vehicles was examined using a catalyst-specific accelerated stress test (AST). High surface area carbon supported dispersed Pt (Pt/HSC), annealed Pt (a-Pt/HSC) and PtCo (PtCo/HSC) alloy catalysts were examined over the course of 90,000 cycles by measuring changes in mass activity, O 2 transport resistance, electrochemical active surface area (ECSA), catalyst accessibility and ionomer-electrocatalyst interactions. Compared to a-Pt/HSC and Pt/HSC catalyst, the PtCo/HSC showed better initial mass activity, a larger initial mass transport loss, and faster degradation after the first 30k AST cycles, as a large portion of Co leached out during potential cycling. Pt/HSC showed higher initial performance relative to a-Pt/HSC but had faster degradation. STEM characterizations show that the ECSA losses are largely related to Pt dissolution resulting in either catalyst particle growth via the Ostwald ripening mechanism or redeposition in the membrane. Catalyst accessibility measurements showed decreased RH sensitivity for all three samples, while CO impedance measurements revealed a decrease in both Pt-water and carbon-water interactions. This implies that, Pt is either preferentially redepositing on the exterior of the carbon support, or that the ionomer is undergoing morphological changes enabling the enhanced intrusion of mesopores.

25 ENERGY STORAGE↗

DOE OSTI2023

Light-trapping structures fabricated in situ for ultrathin III-V solar cells

Here, we describe a fully in situ method of fabricating light-scattering structures on III-V materials that generates a rough morphology via vapor phase etching and redeposition. Fully in situ methods support higher industrial throughput by utilizing the growth reactor to generate the light-trapping structures after device growth without removal from the reactor. We use HCl and PH 3 to etch and redeposit scattering morphologies on Ga 0.5 In 0.5 P in a dynamic hydride vapor phase epitaxy (D-HVPE) reactor. We show that the addition of PH 3 leads to redeposition during the vapor phase HCl etching of Ga 0.5 In 0.5 P and that HCl flow rate and time exposed to HCl-PH 3 each independently cause a linear increase in the redeposited feature size, indicating that redeposition proceeds by island growth in a III-Cl-limited, hydride-enhanced HVPE regime. Auger electron spectroscopy and scanning transmission electron microscopy with energy dispersive spectroscopy (STEM-EDS) reveal redeposition to be highly Ga-rich GaInP, i.e., Ga(In)P. The Ga-rich nature of the redeposition results from the higher thermodynamic driving force for Ga incorporation than for In during HVPE growth and the difference in the volatility of the III-Cl etch products. The resulting morphologies have high broadband scattering, as determined by normal specular reflectance and integrating sphere measurements, indicating effectiveness as light-scattering structures. In a 270-nm-thick GaAs photovoltaic device with a textured back surface, we achieve a 4.9% increase in short circuit current density (J SC ) without any loss in open-circuit voltage (V OC ) relative to a planar control using only a 60 s in situ texturing treatment.

14 SOLAR ENERGY↗

DOE OSTI2025

Revealing structure and shaping priorities in plant and fungal cell wall architecture via solid-state NMR

Plant and fungal cell walls are essential for growth, adaptation, and survival, with their intricate architectures dictating both resistance to stress and susceptibility to antifungal or biomass-degrading strategies. Understanding how these walls are built, remodeled, and function at the molecular level is therefore central to both clinical and biotechnological applications. Solid-state nuclear magnetic resonance (ssNMR) has emerged as a uniquely powerful tool for this purpose, as it reveals the structure, dynamics, and interactions of intact biopolymers without disrupting their native organization. Using this approach, recent studies have shown how structural polymorphism, polymer-polymer interactions, and species-specific remodeling govern mechanical integrity, drug resistance, and stress adaptation. Applications highlighted here include lignin-carbohydrate packing during plant stem maturation, fungal wall reorganization under treatment by wall-targeting antifungals such as echinocandin and nikkomycin, and the functional diversity of glucans, chitins, and mannans. Together, these insights uncover conserved principles of polymer assembly across kingdoms while informing new opportunities for antifungal development and biomass utilization. Ongoing advances in sensitivity and resolution are expected to broaden the reach of ssNMR and further accelerate its role in linking structural heterogeneity to biosynthetic complexity and biological function.

Antifungal↗

DOE OSTI2021

Nitrogen Fertilizer, Arbuscular Mycorrhizal Fungi, and Soil Nematodes Affect Lignin Quality and Quantity in Switchgrass (Panicum virgatum L.)

Plant lignin content and composition, which limit cell wall digestibility and efficiency of cellulose conversion to bioethanol, can be influenced by belowground biotic and abiotic factors. Switchgrass (Panicum virgatum L.) is a leading lignocellulosic biofuel crop and forms strong belowground associations with arbuscular mycorrhizal fungi (AMF), is susceptible to belowground plant-parasitic nematodes (PPN), and when grown in monoculture generally requires nitrogen (N) fertilization. The main objectives of the study were to investigate the effects of N fertilizer and belowground organisms on lignin content and composition of switchgrass. Here, leaf, stem, and root tissues were evaluated separately to test whether these factors had varying belowground (local) or aboveground (systemic) effects on plants. These factors were manipulated in a field study in 2017 using biocide applications to reduce soil fungi and nematodes. Combined biocide application reduced p-hydroxyphenyl (H) unit abundance in the leaves by 14% and increased the syringyl:guaiacyl (S:G) ratio in stems by 2%. Application of fungicide alone increased stem syringyl (S) unit by 12.4% as compared with control plots, and 11.1% as compared with nematicide plots. Overall, fertilizer increased total stem lignin by 3%, stem S unit by 6.7%, and stem S:G ratio by 10%, whereas it reduced the amount of H-unit in the roots by 11%. While the effects of N fertilizer were more pronounced in this study, changes to soil organisms had similar magnitudes of effect for some measures of lignin, indicating that these belowground interactions may be important for growers to consider in the future.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1996

Light-modulated abundance of an mRNA encoding a calmodulin-regulated, chromatin-associated NTPase in pea

A CDNA encoding a 47 kDa nucleoside triphosphatase (NTPase) that is associated with the chromatin of pea nuclei has been cloned and sequenced. The translated sequence of the cDNA includes several domains predicted by known biochemical properties of the enzyme, including five motifs characteristic of the ATP-binding domain of many proteins, several potential casein kinase II phosphorylation sites, a helix-turn-helix region characteristic of DNA-binding proteins, and a potential calmodulin-binding domain. The deduced primary structure also includes an N-terminal sequence that is a predicted signal peptide and an internal sequence that could serve as a bipartite-type nuclear localization signal. Both in situ immunocytochemistry of pea plumules and immunoblots of purified cell fractions indicate that most of the immunodetectable NTPase is within the nucleus, a compartment proteins typically reach through nuclear pores rather than through the endoplasmic reticulum pathway. The translated sequence has some similarity to that of human lamin C, but not high enough to account for the earlier observation that IgG against human lamin C binds to the NTPase in immunoblots. Northern blot analysis shows that the NTPase MRNA is strongly expressed in etiolated plumules, but only poorly or not at all in the leaf and stem tissues of light-grown plants. Accumulation of NTPase mRNA in etiolated seedlings is stimulated by brief treatments with both red and far-red light, as is characteristic of very low-fluence phytochrome responses. Southern blotting with pea genomic DNA indicates the NTPase is likely to be encoded by a single gene.

NASA Discipline Number 40-50↗

DOE OSTI2023

Unraveling Anisotropic and Pulsating Etching of ZnO Nanorods in Hydrochloric Acid via Correlative Electron Microscopy

Despite much technical progress achieved so far, the exact surface and shape evolution during wet chemical etching is less unraveled, especially in ionically bonded ceramics. Herein, by using in situ liquid cell transmission electron microscopy, a repeated two-stage anisotropic and pulsating periodic etching dynamic is discovered during the pencil shape evolution of a single crystal ZnO nanorod in aqueous hydrochloric acid. Specifically, the nanopencil tip shrinks at a slower rate along [0001̅] than that along the $\langle$101̅0$\rangle$ directions, resulting in a sharper ZnO pencil tip. Afterward, rapid tip dissolution happens due to accelerated etching rates along various crystal directions. Concurrently, the vicinal base region of the original nanopencil tip emerges as a new tip followed by the repeated sequence of tip shrinking and removal. The high-index surfaces, such as {101̅m} (m = 0, 1, 2, or 3) and {21̅1̅n} (n = 0, 1, 2, or 3), are found to preferentially expose in different ratios. Our 3D electron tomography, convergent beam electron diffraction, middle-angle bright-field STEM, and XPS results indicate the dissociative Cl – species were bound to the Zn-terminated tip surfaces. Furthermore, DFT calculation suggests the preferential Cl – passivation over the {101̅1} and (0001) surfaces of lower energy than others, leading to preferential surface exposures and the oscillatory variation of different facet etching rates. The boosted reactivity due to high-index nanoscale surface exposures is confirmed by comparatively enhanced chemical sensing and CO 2 hydrogenation activity. In conclusion, these findings provide an in-depth understanding of anisotropic wet chemical etching of ionic nanocrystals and offer a design strategy for advanced functional materials.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Garnet solid electrolyte blended LiNi 0.6 Mn 0.2 Co 0.2 O 2 as high-voltage stable cathodes for advanced lithium-ion batteries

Ni-rich LiNi 1-x Co x/2 Mn x/2 O 2 layered materials have been widely adopted as cathodes for current electric vehicles (EVs) due to their high gravimetric and volumetric energy densities. However, their high-voltage instability (e.g., > 4.3 V vsLi ) limited their usable capacities corresponding to about 60 – 70 % of theoretical capacities. The major problems of high-voltage operation stem from instability of Ni 3+/4+ at cathode-electrolyte interphase (CEI) in contact with electrolytes. Here we propose garnet-type Li 6.7 La 3 Zr 1.7 Ta 0.3 O 12 (LLZT) solid-electrolyte-blended LiNi 0.6 Mn 0.2 Co 0.2 O 2 (NMC) as high-voltage stable cathodes. The LLZT not only passivates the CEI but scavenges protons and moisture in electrolytes. From well-balanced ionic and electronic transport properties, 5 wt% LLZT blended NMC cathodes delivered enhanced electrochemical performances in full-cells. Unlike other complicated coating processes, our proposed solid-electrolyte blending approach can be readily implementable in commercial Li-ion batteries due to its manufacturing friendliness, energy saving, and cost effectiveness.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain

Abstract SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5′-TCGGAT-3′) of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

Biochemistry & Molecular Biology↗

NASA NTRS1996

A Potato cDNA Encoding a Homologue of Mammalian Multidrug Resistant P-Glycoprotein

A homologue of the multidrug resistance (MDR) gene was obtained while screening a potato stolon tip cDNA expression library with S-15-labeled calmodulin. The mammalian MDR gene codes for a membrane-bound P-glycoprotein (170-180 kDa) which imparts multidrug resistance to cancerous cells. The potato cDNA (PMDR1) codes for a polypeptide of 1313 amino acid residues (ca. 144 kDa) and its structural features are very similar to the MDR P-glycoprotein. The N-terminal half of the PMDR1-encoded protein shares striking homology with its C-terminal half, and each half contains a conserved ATP-binding site and six putative transmembrane domains. Southern blot analysis indicated that potato has one or two MDR-like genes. PMDR1 mRNA is constitutively expressed in all organs studied with higher expression in the stem and stolon tip. The PMDR1 expression was highest during tuber initiation and decreased during tuber development.

Wang, W.↗

NASA NTRS2022

The Puzzling Structure of Solar Convection: Window into the Dynamo

The operation of the solar dynamo, with all of its remarkable spatio-temporal ordering, remains an outstanding problem of modern solar physics. A number of mechanisms that might plausibly contribute to its operation have been proposed, but the relative role played by each remains unclear. This uncertainty stems from continuing questions concerning the speed and structure of deep-seated convective flows. Those flows are in-turn thought to sustain both the Sun’s turbulent EMF and the large-scale flows of differential rotation and meridional circulation suspected of influencing the dynamo’s organization and timing. Ultimately, the convective and large-scale flow structure derive from the Coriolis force. When the Coriolis effect is weak (rapid convective flow), convection exhibits little organization in its spatial structure, and the meridional flow is expected to assume a single-celled profile within each hemisphere. Convection subject to strong Coriolis forces instead organizes into compact, spiraling columnar structures and sustains meridional flows that possess multiple cells in latitude and radius. The implications for the dynamo in these two regimes are substantial, impacting the flux-transport properties of any assumed meridional flow and the convectively-driven EMF. Continued progress in this area is complicated by (i) inconsistencies between helioseismic measurements of convective and meridional flow made with different techniques and instruments, and (ii) a lack of high-latitude data for convection, differential rotation, and meridional flow. We suggest that the path forward to resolving these difficulties is twofold. First, the acquisition of long-term helioseismic and emissivity measurements obtained from a polar vantage point is vital to complete our picture of the Sun’s outer convection zone. Second, sustained and expanded investment in theory-oriented and combined theory/observational research initiatives will be crucial to fully exploit these new observations and to resolve inconsistencies between existing measurements.

SMD↗

DOE OSTI2026

Multiscale Cryo Electron Microscopy Reveals Interfacial Degradation and Stabilization in Battery Electrodes

Electrochemical interfaces are dynamic systems, evolving based on their local environment and reactant surface structures. The electrode-electrolyte interface in Li-ion batteries can be protective, limiting parasitic reactions with the electrolyte to passivate the surface [1]. Additionally, this interphase has an impact on the Li-ion transport through that layer based on its composition, bonding environment, and thickness. These parameters are challenging to collect and may vary depending on the electrode surface site investigated relative to its spatial position in a coin cell. This study will detail a multiscale cryogenic electron microscopy approach where millimeter-scale cross-sections through the coin cell batteries were made using a cryogenic stage within a fs-laser plasma focused ion beam (laser PFIB) with complementary energy dispersive X-ray spectroscopy able to detect variations in the composition at electrode interfaces [2]. Microscale cross-sectioning and lamella sample preparation of battery electrodes was conducted at the Center for Integrated Nanotechnologies using a Ga-ion focused ion beam (FIB) with air-free and cryo-transfer [3], followed by nanoscale mapping of composition and bonding within the CEI through cryo-scanning transmission electron microscopy (cryo-STEM) electron energy loss spectroscopy [4]. This multiscale approach enabled identification of millimeter-scale features of a battery stack with visualization of degradation in electrodes such as cracks in cathode particles, gas evolution, and SEI evolution; microscale interfacial characteristics, such as heterogeneity in the SEI or barrier layer and identification of electrolyte networks to the electrode surfaces; and nanoscale measurement of the CEI thickness, mapping of transition metal bonding within the cathode particles to identify loss of active materials, and identification of beneficial electrolyte additives incorporated into the CEI structure. This multiscale approach allows for a statistical understanding of the primary mechanisms and parasitic degradation pathways that impact performance by limiting the ion transport pathways within Li+ batteries.

36 MATERIALS SCIENCE↗

DOE OSTI2020

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

Abstract Background Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials. Results Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions. Conclusion Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

RNA-seq↗