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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Sharing the Sun: Community Solar Deployment and Subscriptions (As of January 2026)

The community solar market analysis presented here is based primarily on data collected through Sharing the Sun, an initiative of the National Community Solar Partnership+ (NCSP+). Sharing the Sun data collection and analysis are conducted by the National Laboratory of the Rockies (NLR) as part of its support for implementation of NCSP+. NLR first released a dataset of community solar projects in 2018 and updates it biannually. The January 2026 dataset, data collection methodology, and all the previous datasets are available from NLR's Data Catalog: https://data.nlr.gov/submissions/244. The dataset presents project-level information including location, capacity, operating utility, and year of interconnection. The dataset is created from multiple data sources such as utility data, public utility commissions, project developer websites, media releases, primary data collection by NLR, and data provided by developers under nondisclosure agreements. This presentation builds on a previous analysis of the community solar project dataset, Sharing the Sun: Community Solar Deployment and Subscriptions (as of June 2024). Dr. Gabriel Chan and his team at the University of Minnesota contribute to this effort. NCSP+ is led and funded by U.S. Department of Energy's Integrated Energy Systems Office (IESO).

14 SOLAR ENERGY↗
DOE OSTI2020

Tight-Binding-Based Method for Simulations of Complex Materials with Accompanying Database

The NRL-Tight-Binding (NRL-TB) method has been applied successfully to many monatomic, binary, and a few ternary systems. The method consists of a fit to Density Functional Theory (DFT) results and has transferability beyond the fitted DFT database including performing tight-binding molecular dynamics simulations. We are working on a new website with a detailed guide of how to use the method in performing the fit to DFT results (Fitting Code) and obtaining non-orthogonal TB parameters expressed in a polynomial form as environment-dependent Slater-Koster parameters (on-site terms), and neighbor distance-dependent Hamiltonian and Overlap terms. These parameters are then used in a Static Code to verify or make predictions for large systems often beyond the computational capabilities of standard DFT codes. Our starting point was a website developed at NRL some years ago which NRL no longer supports. We have now been augmenting that website with new examples of expanding the original capabilities of the method such as incorporating in the codes f-electron states. Our website (esd.cos.gmu.edu/tb) contains two separate branches: One named NRL-TB with the full documentation of the method including source codes and examples. The other branch, named ESD-dB, is a library of electronic structure calculations for all the monatomic elements (a subset of the elements also found in a recent book by the author of this proposal. See reference 22) and an approximately 700 hundred compounds in specific crystal structures. We discuss below the progress made so far in improving and expanding the capabilities of our TB method and the plans for further extensions of our approach.

36 MATERIALS SCIENCE↗
DOE OSTI2020

cdat.github.io

This is the repository for the CDAT website developed at Lawrence Livermore National Laboratory (LLNL).

Harris, Matthew↗
DOE OSTI2023

University Coalition for Fossil Fuel Energy Research

Following a nationwide open competition, the University Coalition for Fossil Energy Research (UCFER) was established in October 2015 through a cooperative agreement between Penn State and the Department of Energy (DOE) National Energy Technology Laboratory (NETL). Penn State lead UCFER with the objective of advancing basic and applied research for clean and low-carbon energy based on fossil fuels in support of the DOE’s mission. UCFER focused on research that improves the efficiency of production and use of fossil energy resources, while minimizing the environmental impacts and reducing greenhouse gas emissions. Penn State lead a team of nine universities (Massachusetts Institute of Technology, The Pennsylvania State University, Princeton University, Texas A&M University, University of Kentucky, University of Southern California, The University of Tulsa, University of Wyoming, and Virginia Polytechnic and State University) during the competition stage, adding seven more universities in 2017 (Carnegie Mellon University, Louisiana State University, The Ohio State University, University of North Dakota, University of Pittsburgh, University of Utah, and West Virginia University). This Coalition exhibited a wide geographical distribution across the U.S. bringing a wide variety of fossil energy expertise. This national university alliance was a major collaborative effort with NETL to address specific topics of R&D in NETL’s mission area, which involved one or more of NETL’s five core competencies (Geologic and Environmental Systems, Materials Engineering and Manufacturing, Energy Conversion Engineering, Systems Engineering and Analysis, and Computational Science and Engineering). The first five to six months of the project was the definitization stage. During this period, Penn State worked closely with NETL to finalize the Coalition organizational structure and By- Laws, prepare a statement of substantial involvement and a statement of project objectives, and develop operations and membership plans. A major component of this stage included preparing an execution plan to solicit research, evaluate proposals, recommend selected projects to NETL, and award projects. In addition, a plan was prepared to monitor projects, review projects, disseminate knowledge from research projects and develop an online system for Coalition research portfolio management. This included developing a website and several databases. The first of six rounds of solicitations started in mid-2016. Projects from the sixth solicitation started February 1, 2021, and ended January 31, 2023. Projects that were selected represented twelve technology lines. Approximately $16.6 million in funding was available for the six solicitations. Most of the funding was provided by DOE, Office of Fossil Energy (DOEFE) with the DOE Fuel Cells Technologies Office (DOE-FCTO) providing funding for a few projects. Coalition universities submitted 259 proposals in response to the solicitations, requesting approximately $67.0 million in funding, and forty-three projects were selected. However, one project withdrew after the principal investigator left the university. The management of the Coalition projects was a major activity by Penn State. Managing the Coalition projects consisted of monitoring the projects, reviewing the projects through annual technical review meetings, disseminating knowledge from the research projects, and developing an online system for Coalition research portfolio management. Penn State’s OMT monitored projects to ensure that all milestones (technical, schedule, budget) were met, expenditures were allowable, cost share (when applicable) were reported, and all technical reports were submitted. The OMT also posted the technical reports electronically on a secure members-only website for access and review by the Coalition members. Disseminating knowledge from the research projects was done through a website, newsletters, various meetings, conferences, journal articles, publicity/press releases, and project summaries that were prepared after each project was completed. Penn State kept NETL apprised of UCFER progress through quarterly reports (thirtyone were submitted by Penn State), verbal and written communications, yearly updates at the annual technical review meetings, and cost accrual reports. The UCFER project had a significant impacty. The UCFER program established the first national university alliance in fossil energy research with a major collaboration effort with DOE NETL that addressed specific topics in NETL’s research and development mission areas. It generated inter-university collaborations, which was another program interest. Twenty-two out of 259 proposals contained collaborations (≈8.5%) and three of forty-two funded projects involved inter-university collaborations (≈7.0%). The forty-two funded projects provided support at fourteen universities involving 269 personnel. Research was conducted by 106 faculty, 115 graduate and undergraduate students, forty-six research staff and post-doctoral scholars, and two visiting scholars. Students and post-doctoral scholars were also on-site at NETL through CRADAs. In addition, non-Coalition participants included six universities and sixteen companies and national laboratories. The non-Coalition participants were involved as subcontractors, providers of cost share, performed unpaid consultation and sample analysis, served as advisory board members, or were providers of samples and materials for testing. UCFER also produced visibility in that fifty-six refereed journal articles were published, fifty-seven conference papers and twenty-three posters were prepared, 190 presentations were given, eight patent applications were filed, two books/book chapters were written, and ten software codes were developed. Collaboration between NETL and the individual projects was a major requirement for all funded projects. This included NETL staff time to support collaboration, consultation, technical guidance, sample preparation and analysis, internships at NETL, on-site testing and equipment usage by Coalition participants at NETL, co-mentoring students, and coauthoring journal articles and conference papers. Collaboration was impacted by COVID-19 in that not all on-site activities could be performed. NETL personnel were coauthors on eight of the conference papers (fourteen percent of the conference papers that were prepared) and seventeen of the journal articles (thirty percent of the journal articles that were prepared). A website was developed for an online proposal solicitation and review process and to provide exposure to UCFER. A website analysis highlighted the large amount of member and general public interest in UCFER by interpreting access statistics from March 2016 through June 2023. Visitors to the site originated from many different organizations, businesses, and countries. The website provided a means to disseminate information to both the general public and the UCFER members and was successfully used for outreach activities. In addition, NETL required that RFP release, proposal submission, and proposal reviews all be performed online. Penn State successfully developed these capabilities in a secure section of the website, which were used throughout the UCFER project. It is recognized that each project had its technical successes. In addition, highlighted successes were compiled and summarized from the research projects. Information was requested from the PIs of completed projects. In addition, Penn State’s Operations Management Team reviewed subcontract reports to identify project successes. Examples of information requested from PIs included (not all-inclusive): new projects that have been funded as a result of UCFER funding; new commercial products; establishment of a new center; new patent; new software; best paper awards; highly-cited work; and graduate student successes. A total of forty-eight highlighted successes were reported.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2019

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

U.S. Efforts in Support of Examinations at Fukushima Daiichi: 2019 Evaluations

Much is still not known about the end-state of core materials in each unit that was operating on March 11, 2011 at the Fukushima Daiichi Nuclear Power Station (Daiichi). Information obtained from Daiichi is required to inform Decontamination and Decommissioning (D&D) activities, improving the ability of the Tokyo Electric Power Company Holdings, Incorporated (TEPCO Holdings) to characterize potential hazards and to ensure the safety of workers involved with cleanup activities. This document, which has been updated to include Fiscal Year 2019 (FY2019) information, summarizes results from a U.S. effort to review Daiichi information and extract insights to enhance the safety of existing and future nuclear power plant designs. This U.S. effort, which was initiated in 2014 by the Department of Energy Office of Nuclear Energy (DOE-NE), is completed by a group of experts in reactor safety and plant operations that identify examination needs and evaluate recent Daiichi examination data to address these needs. Each year, annual reports are issued that document significant safety insights being obtained in areas of special emphasis. For FY2019, the areas emphasized by the expert panel include component performance, radionuclide surveys and sampling, debris end-state location, combustible gas effects, and plant operations and maintenance. In addition to reducing uncertainties related to severe accident modeling progression, these insights have and continue to be used to update guidance for severe accident prevention, mitigation, and emergency planning. Reduced uncertainties in modeling the events at Daiichi improve the realism of reactor safety evaluations that inform future D&D activities. In addition, the process established by this U.S. effort provides an example that Japan may wish to implement in future international efforts to support D&D. As emphasized in this FY2019 report, important insights are being gained from examinations of the affected units at Daiichi. Although many results from prior years have been moved to appendices, key areas of interest are highlighted in the main document. For example, larger intact components and fuel containing materials observed on the floor of the primary containment and retained on ex-vessel structures continue to be emphasized because of insights that may be gained with respect to vessel failure and ex-vessel interactions with structures and concrete. In addition, the main report presents insights gained by focused evaluations of plant data because of potential use of systems and components during severe accident conditions and alternate perspectives regarding accident progression that may be inferred from such data. The report also illustrates how systems analysis codes can be applied to reduce uncertainties about the progression of events at Daiichi and how practical insights obtained from Daiichi can be used to enhance radiation safety for the existing fleet. Recent and planned updates to systems analysis codes are also discussed. As in prior years, this report contains an appendix with a list of examination needs that was updated after U.S. experts reviewed recently obtained information from Daiichi. Additional details for higher priority, near-term, examination activities are also provided. This report also includes an appendix with a description of a website that was developed to assist U.S. experts by providing information in an archived retrievable location.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

A Framework for Effective Science Communication and Outreach Strategies and Dissemination of Research Findings for Marine Energy Projects

Marine energy is an emerging renewable energy industry with the potential to produce 2300 terawatt-hours per year from resources within the United States. As development and testing of marine energy devices advance, regulatory and permitting decision-makers are concerned about the uncertainty surrounding the potential environmental effects resulting from the introduction of these novel devices in coastal and riverine environments. The Triton Initiative researches and provides recommendations for environmental monitoring technologies and methods to inform industry stakeholders with the data necessary to permit the testing of marine energy systems. Effective dissemination of the research findings is essential for improving the accessibility of data to stakeholders who may use the results to inform policy decisions, yet few frameworks for conducting science communications for marine energy projects exist. In this paper, we present tools, channels, and tactics for developing a science communication framework for marine energy projects, or similar areas of study, using the Triton Initiative’s pilot science communication program as a case study. By leveraging existing bodies of work in disciplines such as communications theory, marketing, public relations, and social science, the presented framework includes audience identification and analysis; channel development, including a website, blog, newsletter, social media, and webinars and presentations; and metrics for determining success. Outcomes from one year of Triton’s case study are presented, including the most effective tactics and lessons learned.

communication framework↗
DOE OSTI2024

Latest Development to the Mass Tracking System (MTG)

This poster informs about the ongoing development project of the Mass Tracking System (MTG) taking place in Fuels Conditioning Complex at MFC. The information is about the MTG utilization, the possible complications in the future with the system and the solution for those complication. Furthermore, the poster reports about the progress and the future plans of the project after brief insight on how the MTG operates in the facility. Essentially, the project is separated in three different phases starting with the back-end development focusing on conversion and migration phases and finalizing with the front-end development of the website phase to provide FCF with versatile and efficient system.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research

ABSTRACT The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a ‘big data’ resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Efficient computational design of two-dimensional van der Waals heterostructures: Band alignment, lattice mismatch, and machine learning

Here, we develop a computational database, website applications (web-apps), and machine-learning (ML) models to accelerate the design and discovery of two-dimensional (2D) heterostructures. Using density functional theory (DFT) based lattice parameters and electronic band energies for 674 nonmetallic exfoliable 2D materials, we generate 226 779 possible bilayer heterostructures. We classify these heterostructures into type-I, -II, and -III systems according to Anderson’s rule, which is based on the relative band alignments of the noninteracting monolayers. We find that type II is the most common and type III the least common heterostructure type. We subsequently analyze the chemical trends for each heterostructure type in terms of the Periodic Table of constituent elements. The band alignment data can also be used for identifying photocatalysts and high-work-function 2D metals for contacts. We validate our results by comparing them to experimental data as well as hybrid-functional predictions. Additionally, we carry out DFT calculations of a few selected systems (MoS 2 /WSe 2 , MoS 2 /h-BN, and MoSe 2 /CrI 3 ), to compare the band-alignment description with the predictions from Anderson’s rule. We develop web-apps to enable users to virtually create combinations of 2D materials and predict their properties. Additionally, we use ML tools to predict band-alignment information for 2D materials. The web-apps, tools, and associated data will be distributed through the JARVIS-HETEROSTRUCTURE website. Our analysis, results, and the developed web-apps can be applied to the screening and design applications, such as finding alternative photocatalysts, photodetectors, and high-work-function (WF) 2D-metal contacts.

2-dimensional systems↗
DOE OSTI2025

Standardizing UI/UX across accelerator labs

During February 26–28, 2025, the first-ever particle accelerator user interface/user experience (UI/UX) workshop was held at SLAC. Attendees had backgrounds ranging from software development to control systems management and human factors (HF) science. The workshop began with participants discussing the current state of UI/UX procedures and practices at their respective laboratories to share experiences and learn from one another. Additional discussions focused on how to effectively integrate UI/UX best practices into actionable goals for developers, managers, and operators when working on new or existing interfaces. The goal of the working group is to create a website that will guide developers, managers, scientists, and end users at accelerator laboratories in incorporating UI/UX best practices into software development. The working group continues to meet virtually toward this goal, and is planning a second workshop for next year.

Tran, Tiffany [SLAC]↗
DOE OSTI2023

NREL 25-cm2 High-Pressure Low-Temperature Electrolysis Cell Hardware (Open Source)

This data resource describes an open-source cell hardware that enables low temperature electrolysis (LTE) testing at elevated pressures. Existing commercial options have several downsides when it comes to R&D testing. They are often not designed for repeated reassembly, may not be able to accommodate porous transport layers with different thicknesses, and do not give state-of-the-art performance. Therefore, this hardware was developed specifically with LTE R&D in mind and its design is being made available to the global LTE community. This work was planned and funded by the U.S. Department of Energy's H2NEW consortium (https://h2new.energy.gov/). The hardware design package (.zip file) details the drawings, auxiliary materials, and procedures required to fabricate, assemble, and operate the National Renewable Energy Laboratory's (NREL's) high-pressure low-temperature electrolysis cells. While the hardware itself—end plates, current collectors, flow fields, bolts and washers, tube fittings—is always the same, the assembly and operating procedures may change depending on the active materials being tested, especially for the membrane. Material-specific assembly and operating procedures will be posted to the H2NEW website as they are developed and validated. Disclaimer: The documents and drawings included in this download package describe a design for a low temperature electrolysis hardware that is intended to comply with leak testing according to ASME B31.1. Safe operation at ambient and elevated pressures is the sole responsibility of the end user, which should be evaluated on a case-by-case basis for each individual cell. Factors affecting the sealing capability may depend on, for example, machining quality, cell assembly components, operating conditions, and operating history. Operation at pressure should only be performed on qualified test stands by qualified operators. NREL/ALLIANCE FOR SUSTAINABLE ENERGY, LLC/DOE DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING THE WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, AND MAKES NO WARRANTY AS TO THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION PROVIDED HEREIN. USE OF THIS PACKAGE IS AT THE USER’S OWN RISK.

08 HYDROGEN↗
DOE OSTI2023

SAM Software Quality Assurance Plan Implementation and NQA-1 Assessment

The System Analysis Module (SAM) is an advanced and modern system analysis tool being developed at Argonne National Laboratory under the U.S. DOE Office of Nuclear Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. As a modern-day software, SAM development included efforts to follow best practices in software development. These best practices include version control using git, independent reviews of development activities, and detailed descriptions of developments and bug fixes using the GitLab issue and merge request system. In Fiscal Year 2023 (FY23), the SAM development team set out to formalize a Software Quality Assurance (SQA) program that allowed industry partners to credit the informal steps being taken by the SAM development team to ensure the quality of the software. As part of formalizing an SQA program, a SQA Plan (SQAP) was developed, implemented, and assessed. The SAM SQAP targets compliance with NQA-1-2008/2009 Addenda. The SQAP builds on the MOOSE SQAP and the Argonne SSQAPP while accounting for the needs of the multi-organization SAM development team. Modifications to the SAM repository structure, including a new testing system, updated test cases, and the development of an internal website, facilitate the implementation of the SAM SQAP. The initial assessment of the SAM SQAP indicated that the SAM SQAP was adequately and effectively implemented and additional work was required to improve the compliance of the SAM SQAP with NQA-1 2008/2009 Addenda. Several improvements to the SQAP have already been drafted to address these assessments and future work is planned to further improve the SAM SQAP in support of end-user needs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Alternative Fuels Data Center

This presentation provides an overview of the Alternative Fuels Data Center for the 2026 Transportation Technologies Annual Merit Review, including project objectives, milestone, approach to developing and maintaining the website, project accomplishments and progress, and collaboration with other national labs and external partners.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Educational Consortium for Energy-related Data Science & Computation in Building Engineering Programs

The project spearheaded by Pennsylvania State University aims to address the growing need for integrating energy-focused computation and data science into building engineering education. As the demand for energy-efficient building designs and operations increases, the educational sector must adapt to equip future engineers with the necessary skills. This initiative responds to this need by developing a consortium that unites multiple institutions to enhance curriculum development, dataset curation, and resource sharing, thereby ensuring students are well-prepared for the evolving energy sector. The primary goal of the project is to establish a consortium that will develop and disseminate educational materials and training programs focused on energy-related data science and computation. Key accomplishments include the creation of a beta website for resource sharing, the development of training programs and standalone modules, and the curation of datasets accessible to the public. This effort will culminate in a curriculum that incorporates advanced modeling technologies and data science skills into building engineering programs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

ComStock™ 2024 Release 1 [SWR-19-33 and SWR-20-32]

ComStock™ is an NREL model of the U.S. commercial building stock. The model takes some building characteristics from the U.S. Department of Energy's (DOE's) Commercial Prototype Building Models and Commercial Reference Building. However, unlike many other building stock models, ComStock also combines these with a variety of additional public- and private-sector data sets. Collectively, this information provides high-fidelity building stock representation with a realistic diversity of building characteristics. This repository contains the source code used to build and execute ComStock models, including upgrade scenarios. In addition, the sampling of buildings characteristics used for the initial ComStock (V1.0) release is provided. The ComStock model is under active calibration and development, which is publicly visible on this repository. Execution of the ComStock workflow is managed through the buildstockbatch repository, a shared asset of ResStock™ and ComStock™ , specifically developed to scale to execution of tens of millions of simulations through multiple infrastructure providers. The dataset output from the initial ComStock (V1.0) release can be found at the accompanying ComStock data viewer website and additional information about ComStock found on the NREL Buildings Website. For more details about ongoing model development please consult the End Use Load Profiles website. ComStock is a direct result of the NREL residential stock modeling tool ResStock™ (recipient of a R&D100 award) and was inspired by the high-fidelity solar & storage adoption model dGen™. Additionally, this tool would not be possible without the decades of work undertaken by the OpenStudio® and EnergyPlus® visionaries and contributors, significant funding, feedback and support from the Los Angeles Department of Water and Power, and the Department of Energy's Building Technology Office ongoing support of and investment in building energy modeling software. is an analytic methodology for modeling the energy usage of the commercial building stock within the United States of America. The commercial building stock is represented through a sampling of complex probabilistic distributions of various features of interest for modeling energy usage within commercial buildings. Each sample from these distributions is converted into a building energy model based on the features of that specific sample. Each building energy model can be simulated as is, but additional changes can be made to the model through addition of energy conservation measures, component faults, or other desired alterations. The results of the simulations are then processed to provide insights for various stakeholders, including but not limited to policy makers, engineers, and marketers.

Horsey, Henry↗
DOE OSTI2018

An updated gene atlas for maize reveals organ-specific and stress-induced genes

Maize (Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ-specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co-expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co-expression patterns. Presence–absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ-specific and stress-induced DE genes suggesting that PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co-expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. Here, to facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data-mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes

Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36,207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4,154 organ‐specific and 7,704 differentially expressed genes following stress treatment. Gene co‐expression network analyses revealed 12 modules associated with distinct biological processes containing 13,590 genes providing a resource for further association of gene function based on co‐expression patterns. Presence/absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ‐specific and stress‐induced differentially expressed genes, suggesting PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average, have significantly fewer co‐expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website(maize.plantbiology.msu.edu) for viewing and data‐mining these resources and deployed two new views on the Maize electronic Fluorescent Pictograph Browser (bar.utoronto. ca/efp_maize)

59 BASIC BIOLOGICAL SCIENCES↗