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DOE OSTI2022

Identification of Critical Material Attributes in Lignin Streams Based on Pseudomonas putida Performance

Variability in chemical composition of corn stover feedstocks has been suggested to play a role in biocatalyst performance during the conversion of lignocellulosic biomass to value-added compounds. In previous studies, we investigated the performance of Pseudomonas putida CJ781 - an engineered bacterium that converts aromatic compounds to muconate - on various lignin streams produced from the deacetylation of corn stover, and we found significant differences on muconate production. To better understand the origin of these differences, we down selected twenty-two compounds from literature - that had previously been detected as extractives in lignin streams - and we analyzed their concentrations in 12 lignin streams generated from different feedstocks. P. putida CJ781 was then cultivated in mock lignin streams supplemented with various concentrations of these compounds. Bacterial growth was tracked in microtiter plates and the performance was measured by comparing maximum growth rates among conditions. At maximum concentrations that may be found in lignin streams, sodium was the material attribute that limited growth rate in a greater extent, with a reduction in growth rate by 8 to 37%, depending on the counter ion, with sodium nitrate being the most inhibitory, followed by sodium acetate, sodium chloride, and sodium sulfate. Ammonium acetate was also found to be inhibitory at average concentrations of ammonium in lignin streams, reducing maximum growth rate by 18%. Overall, the data from this study has allowed to down select critical material attributes in lignin streams and process parameters that significantly affect the performance of P. putida and will be used as input to predictive models that aim to reduce risks attributed to feedstock variability in lignocellulosic biorefineries.

biocatalyst↗
DOE OSTI2023

Flexible Gasification of Coal and Biomass to Generate Carbon Free Electric Power and Hydrogen

This paper describes the development of a coal and biomass-fed plant concept to co-produce electric power and hydrogen with net-negative CO2 emissions under the aegis of the 21st Century Power Plant initiative of the U.S. Department of Energy (DOE), whose goal is to advance innovative power plant concepts that are capable of flexible, net-zero carbon emission operations while producing cost-effective “blue” hydrogen to support economy-wide decarbonization goals. The proposed standalone plant will be in Nebraska, USA. The specified design feedstock is a hybrid blend of Powder River Basin (PRB) subbituminous coal from Wyoming and local Nebraska biomass (corn stover), 50 wt.% each (dry basis). Other potential feedstocks, including woody biomass (eastern red cedar) and waste plastic (auto shredder residue) were evaluated or reviewed as alternates. The proposed process block comprises a high-pressure, oxygen-blown fluidized bed gasifier (GTI Energy U-GAS® process) coupled with water gas shift, the Selexol process for acid gas (H2S and CO2) removal, and pressure-swing adsorption (PSA) to yield 8,500 kg/h of high-purity hydrogen. The off gas from the PSA unit is used in the power block (gas turbine combined cycle) to generate electric power to support the gasification process, hydrogen production, and 50 MWe net electric power to the grid. All major plant equipment including the gasifier, gas cleanup system, and power generation are commercially available and proven in other applications and considered at TRL 8-9. However, gasification of corn stover biomass is considered at TRL 6. Overall thermal efficiency of the plant is 50% (net HHV) with net atmospheric CO2 removal at a rate of 250-300,000 tpa. Design activities necessary to provide input to a FEED study (Phase II of the project), including the development of the Environmental Information Volume (EIV) for the host site, and an investment case, based on a pro-forma pre-FEED level cost estimate, have been completed and are described in detail in this paper.

Gülen, S. Can↗
DOE OSTI2024

A Step toward Process Electrification: Microwave-Assisted Co-Gasification of Waste Plastics and Biomass to Produce Clean Energy

Barely 9% of the 353 million metric tons of plastic waste produced worldwide over the last two decades has been recycled, with the majority of it being either landfilled or incinerated. Recycling and upcycling plastic waste is thus essential in mitigating environmental pollution. Gasification is the thermochemical conversion of solid carbon feedstock at high temperatures using a gasifying agent to produce hydrogen-rich syngas. Existing gasification technologies are energy-intensive and require high operating temperatures (>1000 °C), leaving them uncommercial. Microwave heating has sparked attention in a variety of chemical processes due to its specific advantages over traditional heating technologies, such as rapid and selective heating to improve process efficiency. NETL’s research team recently investigated the synergistic advantages of corn stover and mixed plastics in producing hydrogen-rich syngas via microwave heating. As a continuation of the research, this study provides an outlook over the non-catalytic versus catalytic effects of plastic-corn stover gasification via process electrification to enhance H2 production, minimize undesired tar, and improve process efficiency. Our aim is to provide complete electrification of the existing gasification process by using waste plastics as a starting block to produce valuable fuel and support the nation’s net zero goals.

Abedin, Ashraf↗
DOE OSTI2024

Herbaceous Feedstock 2022 State of Technology Report

The U.S. Department of Energy promotes production of advanced liquid transportation fuels from lignocellulosic biomass by funding fundamental and applied research that advances the state of technology (SOT). As part of its involvement in this mission, Idaho National Laboratory completes an annual SOT report for nth-plant and 1st-plant herbaceous biomass feedstock logistics. The purpose of the SOT is to provide the status of feedstock supply system technology development for herbaceous biomass to biofuels relative to technical targets and cost goals from specific design cases, based on data and experimental results. Although conventional feedstock supply systems form the backbone of the emerging biofuels industry, they have limitations that restrict widespread implementation on a national scale. To meet the demands of the future industry, the feedstock supply system must shift from the conventional system to what has been termed “advanced” supply systems. In advanced designs, a distributed network of aggregation and processing centers, termed “depots,” are employed near the points of biomass production (i.e., the field or forest) to reduce feedstock variability and produce feedstocks of a uniform format, moving toward biomass commoditization. The 2022 Herbaceous SOT is part of a vision of achieving an implemented advanced feedstock supply system, which produces a stable, tradable commodity at the decentralized distributed depot. It utilizes feedstock fractionation by incorporating technologies that can separate the biomass into its anatomical fractions (leaves, husks, stems and cobs) to reduce impurities and produce fractions that satisfy downstream quality considerations. By using a series of air classification steps, this strategy can reduce the extrinsic ash in corn stover and produce enriched tissue fractions that can be blended to a conversion specification or converted individually in optimized biochemical conversion campaigns. Additionally, a majority of the leaves (which do not meet the quality specification) are separated out early and can be supplied to alternate markets. The 2022 Herbaceous SOT incorporates an advanced biomass fractionation and processing system to produce pellets enriched tissues from three-pass corn stover. The resulting enriched pellets are delivered to the biorefinery individually where they can be blended to a specification or converted in campaigns where the conditions are optimized for each tissue. Unused fractions can be sent to a a midstream market or to a different conversion process that is better suited to their properties to offset the cost of the delivered feedstock. The main benefits from the proposed system can be summarized as: (1) $6.86/dry ton (2016$) lower cost for the air classification due to elimination of the requirement to discard the high ash lights fraction; (2) $1.56/dry ton lower delivered cost by selling the unsuitable leaf fraction into the feed market as a midstream co-product (assuming a selling price that is 11% higher than their cost of production); (3) 0.98% increase in carbohydrate content (from 60.16% to 61.14%); and (4) 0.97% decrease in ash content (from 6.00% to 5.03%) compared to the 2021 Herbaceous SOT. Overall, the 2022 nth-plant Herbaceous SOT predicts a modeled delivered feedstock cost of $78.64/dry ton (2016$) if it is assumed that the enriched leaf fraction is sold at its production cost; this is a slight increase of $0.43/dry ton increase from the 2021 Herbaceous SOT nth-Supply case cost. The increased cost derived from a $0.38/dry ton increase in transportation and handling cost to procure more biomass (to replace the enriched leaf fraction that was not delivered to the biorefinery. The total preprocessing cost was $0.27/dry ton higher than the 2021 result because of updates to energy consumption, purchasing price and dry matter loss data for the rotary shear ($3.00/dry ton increase) and the pelleting mill ($4.52/dry ton increase). The data utilized were generated in pilot-scale tests in the Biomass Feedstock National User Facility (BFNUF) at INL and at Forest Concepts, including tests for rotary shear and pelleting of the air classified fractions. A greenhouse gas emissions analysis was performed by Argonne National Laboratory using the most up to date version of the Greenhouse Gases, Regulated Emissions, and Energy use in Transportation model (GREET®). The analysis showed an increase of 17.34 kg CO2e/dry ton from the 2021 SOT (67.71 kg CO2e/ton in the 2021 Herbaceous SOT to 85.05 kg CO2e/ton in the 2022 Herbaceous SOT). The net increase is primarily attributed to increased energy consumption in pelleting mill.

09 BIOMASS FUELS↗
DOE OSTI2024

Decarbonizing Hydrogen Production: Assessing A Net-Negative Pathway

Hydrogen is gaining prominence as a key factor in the world's transition to a cleaner energy future. The International Energy Agency (IEA)'s Global Hydrogen Review 2023 reports that the number of low-emission hydrogen production projects is increasing rapidly. The potential for growth in new applications such as heavy industry, transportation, and power generation is significant. The IEA urges more decisive action to spur demand for low-emission hydrogen to achieve climate goals. While hydrogen is produced through various industrial methods, each with its own advantages and disadvantages, low-carbon hydrogen is critical for mitigating climate change and is incentivized by the Clean Hydrogen Production Tax Credit (45V). To this end, we have evaluated a commercial technology that can produce low- or negative-carbon hydrogen via ethanol catalytic oxidative reforming. This study assessed life cycle greenhouse gas emissions (carbon intensity or CI) associated with the hydrogen production technology. A total of 24 scenarios were evaluated, encompassing (a) Gen1 versus Gen2 ethanol inputs, (b) carbon capture and sequestration (CCS) of upstream fermentation CO2, and (c) oxygen sourcing via air separation unit (ASU) versus purchased or on-site production of oxygen as a byproduct of hydrogen electrolysis with a proton exchange membrane (PEM). Key findings include that the base case CI for hydrogen production using Gen2 ethanol from corn stover is lower than Gen1 dry mill corn ethanol. The study also points out that the CI for hydrogen production using PEM-O2 is lower than that using ASU-O2, whether the PEM-O2 is produced on-site or off-site (importing). When sourcing oxygen from on-site PEM-O2, the Gen1 and Gen2 ethanol-derived hydrogen exhibit favorable net-negative CI values for all evaluated scenarios, especially if the upstream ethanol CCS is included. As a reference, the 45V regulatory threshold for generating clean hydrogen tax credits is a CI below 0.45 kg CO2e/kg hydrogen.

BIOMASS FUELS,HYDROGEN↗
DOE OSTI2021

Screening of alkali-assisted storage conditions to define the operational window of deacetylation within storage systems in the bioenergy supply chain

Overcoming biomass heterogeneity and associated recalcitrance to thermal, chemical, and enzymatic depolymerization is a necessary but challenging aspect of valorizing lignocellulosic biomass to fuels and chemicals. Here, this study explores how this recalcitrance can be reduced during the supply chain unit operation of storage, which is required for seasonally harvested agricultural residues to maintain constant throughput at a biorefinery. In this work, partial alkali pretreatment was performed just prior to corn stover entering storage, which had the benefit of providing a high pH environment entering storage such that soluble sugars were preserved and saponified acetyl groups in hemicellulose. This work investigated a range of viable conditions where saponification and preservation occur simultaneously by varying the moisture content (40% and 60%) and concentrations of sodium hydroxide (low and high) during aerobic and anaerobic storage. Anaerobic conditions preserved overall dry matter below 5% in the three scenarios evaluated, and the highest alkali loading solubilized up to 15% lignin, 18% xylan, and 50% of acetate, meanwhile doubling the extractable components. Scanning electron microscopy images highlighted potential physical impacts including cell-wall disruption near vascular bundles, pitting within parenchyma cells, and cell-wall distortion. Techno-economic assessment indicated that this storage approach and associated logistics system is economically competitive with a conventional approach using low-moisture bales.

09 BIOMASS FUELS↗
DOE OSTI2022

Effect of biomass liquefaction on glucose and xylose prices predicted by National Renewable Energy Laboratory biochemical sugar model

Abstract The National Renewable Energy Laboratory (NREL) published a model in 2017 that enables the minimum selling price of lignocellulosic sugar to be calculated. The model can be modified to suit any biomass feedstock and operational design. In the present case, the model is used to understand the economics of a process configuration that incorporates liquefaction as a preprocessing step in corn‐stover‐fed biorefinery. This study demonstrates a quantitative approach utilizing an existing biorefinery setup to simulate the biomass liquefaction technique while estimating the price of the resulting sugar product. The objective is to understand whether the addition of liquefaction methodology – and the substitution of acid pretreatment – can reduce the cost of lignocellulosic sugars. The reason for setting up a liquefaction unit at the start is to reduce the yield stress of biomass slurry so that the flow remains unrestricted downstream. The liquefaction process is also unique because it uses no chemicals and saves the cost of pretreatment. The pretreatment step is bypassed because the output of liquefaction can be fed into enzyme hydrolysis just after simple cooking. The liquefaction process can be performed in three modes: enzyme, enzyme mimetic, and a combination of enzyme and enzyme mimetic. The results from the BC1707 model indicate the minimum cost for the enzyme liquefaction route. © 2022 The Authors. Biofuels, Bioproducts and Biorefining published by Society of Industrial Chemistry and John Wiley & Sons Ltd.

09 BIOMASS FUELS↗
DOE OSTI2022

MOF-Transformed In 2 O 3-x @C Nanocorn Electrocatalyst for Efficient CO 2 Reduction to HCOOH

For electrochemical CO 2 reduction to HCOOH, an ongoing challenge is to design energy efficient electrocatalysts that can deliver a high HCOOH current density (J HCOOH ) at a low overpotential. Indium oxide is good HCOOH production catalyst but with low conductivity. In this work, we report a unique corn design of In 2 O 3-x @C nanocatalyst, wherein In 2 O 3-x nanocube as the fine grains dispersed uniformly on the carbon nanorod cob, resulting in the enhanced conductivity. Excellent performance is achieved with 84% Faradaic efficiency (FE) and 11 mA cm –2 J HCOOH at a low potential of – 0.4 V versus RHE. At the current density of 100 mA cm –2 , the applied potential remained stable for more than 120 h with the FE above 90%. Density functional theory calculations reveal that the abundant oxygen vacancy in In 2 O 3-x has exposed more In 3+ sites with activated electroactivity, which facilitates the formation of HCOO* intermediate. Operando X-ray absorption spectroscopy also confirms In 3+ as the active site and the key intermediate of HCOO* during the process of CO 2 reduction to HCOOH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Solvent-free production of carbon materials with developed pore structure from biomass for high-performance supercapacitors

The study aimed at preparing porous carbon materials, with superhydrophilic characteristics and developed micro/mesoporous structure (CSB-800), from corn stover by a solvent-free method including pre-carbonization, ball milling, and activation. The effect of pre-carbonization, ball milling on the detailed structural composition and properties especially the hydrophilicity and porous structures were studied, and the potential application of CSB-800 as electrode in supercapacitors was also investigated. The results revealed that pre-carbonization increased the accessibility of raw materials as well as the efficiency of the ball milling with KOH, leading to small carbon particles with good dispersion behavior. Ball milling promoted the porosity, surface energy, hydrophilicity, crystallinity, and graphitization of the carbon materials. CSB-800 exhibited a high specific surface area of 2440.6 m 2 /g with developed micro and porous structures. The heteroatom nitrogen formed nitrogen-containing groups of N Q and N X, which provided faradaic pseudocapacitance when CSB-800 was used as an electrode material, and this material presented a specific capacitance of 398 F/g at 0.5 A/g in 1 M H 2 SO 4 electrolyte in a three-electrode system, while the value was 243 F/g in a two-electrode system, and the energy density reached 5.01 Wh/kg at a power density of 100 W/kg.

09 BIOMASS FUELS↗
DOE OSTI2024

Predicting biomass comminution: Physical experiment, population balance model, and deep learning

An extended population balance model (PBM) and a deep learning-based enhanced deep neural operator (DNO+) model are introduced for predicting particle size distribution (PSD) of comminuted biomass through a large knife mill. Experimental tests using corn stalks with varied moisture contents, mill blade speeds, and discharge screen sizes are conducted to support model development. A novel mechanism in the extended PBM allows for including additional input parameters such as moisture content, which is not possible in the original PBM. The DNO+ model can include influencing factors of different data types such as moisture content and discharge screen size, which significantly extends the engineering applicability of the standard DNO model that only admits feed PSD and outcome PSD. Test results show that both models are remarkably accurate in the calibration or training parameter space and can be used as surrogate models to provide effective guidance for biomass preprocessing design.

09 BIOMASS FUELS↗
DOE OSTI2024

A High-Performance Discrete-Element Framework for Simulating Flow and Jamming of Moisture Bearing Biomass Feedstocks

We developed and verified a high-performance open-source discrete element method (DEM) solver with simultaneously-supported feedstock-specific interaction models, including bonded-sphere, liquid bridge, cohesion, and non-linear contact models. Our solver uses parallel data structures on hybrid central and graphics processing unit (CPU/GPU) architectures, with favorable strong scaling performance observed for large problem sizes comprised of (100 M particles), and 4X single-node GPU speedup. The particles for corn stover feedstock were conceptualized and calibrated based on experimental measurements and results. Sensitivity analyses demonstrate that the mass flow rate from a wedge hopper is governed primarily by moisture content, friction coefficient, and cohesion energy density. The model is used to reproduce experimentally observed hopper jamming results, highlighting that the experimental no-flow trends can only be achieved by using non-spherical particles, liquid bridge and cohesion models, highlighting the importance of using concurrent feedstock specialized models for the effective representation of biomass material handling problems.

bioenergy↗
DOE OSTI2020

Composition-Preserving Extraction and Characterization of Biomass Extrinsic and Intrinsic Inorganic Compounds

The inorganic content of biomass impairs size reduction tool life and the conversion process. Conventional ash extraction relies on furnace combustion that inevitably alters the inorganic compounds due to oxidation and decomposition. This study developed composition-preserving methods for extracting and analyzing extrinsic and intrinsic inorganic compounds. Comprehensive characterization was carried out on selected biomass feedstocks, including corn stover, pine residue, and pine anatomical fractions, to reveal their inorganic species and morphology. The extrinsic inorganic compounds were found to be dominated by quartz, along with other minor minerals, such as albite, microcline, and gehlenite, and have particle sizes ranging from tens to hundreds of micrometers. Among the pine anatomical fractions, the needles contain the highest intrinsic silicon content while the bark trapped the most extrinsic minerals. By correlation of the total ash and extrinsic inorganic contents to the wear behavior, both the extrinsic and intrinsic inorganic compounds were concluded to have made significant contributions to the wear process. Finally, the results here validated a new approach to characterize inorganic compounds in biomass and provided fundamental insights for their potential impact on preprocessing tool wear.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Observational evidence for groundwater influence on crop yields in the United States

As climate change shifts crop exposure to dry and wet extremes, a better understanding of factors governing crop response is needed. Recent studies identified shallow groundwater—groundwater within or near the crop rooting zone—as influential, yet existing evidence is largely based on theoretical crop model simulations, indirect or static groundwater data, or small-scale field studies. Here, we use observational satellite yield data and dynamic water table simulations from 1999 to 2018 to provide field-scale evidence for shallow groundwater effects on maize yields across the United States Corn Belt. We identify three lines of evidence supporting groundwater influence: 1) crop model simulations better match observed yields after improvements in groundwater representation; 2) machine learning analysis of observed yields and modeled groundwater levels reveals a subsidy zone between 1.1 and 2.5 m depths, with yield penalties at shallower depths and no effect at deeper depths; and 3) locations with groundwater typically in the subsidy zone display higher yield stability across time. We estimate an average 3.4% yield increase when groundwater levels are at optimum depth, and this effect roughly doubles in dry conditions. Groundwater yield subsidies occur ~35% of years on average across locations, with 75% of the region benefitting in at least 10% of years. Overall, we estimate that groundwater-yield interactions had a net monetary contribution of approximately $10 billion from 1999 to 2018. This study provides empirical evidence for region-wide groundwater yield impacts and further underlines the need for better quantification of groundwater levels and their dynamic responses to short- and long-term weather conditions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Determination of fundamental mechanical properties of biomass using the cubical triaxial tester to model biomass flow

The flowability of biomass is an indicator of how amenable biomass is to handling. The flowability measurements are often determined with empirical or tertiary experiments. This status quo impedes employing engineering principles to advance the design and operation of biomass handling systems. It is imperative to establish an experimental protocol minimizing empirical aspects of flowability characterization to account for the variability of biomass. This study demonstrates the operational principles of the large chamber cubical triaxial tester and the procedure of triaxial tests to quantify bulk flow behaviors of two milled biomass feedstocks, namely corn stover 2 mm (CS) and Douglas fir 1 mm (DF). The Mohr-Coulomb (MC), Drucker-Prager (DP) and modified Cam Clay (mCC) models are calibrated for both biomasses. Analysis indicates that CS will exhibit a cohesive flow with a larger cohesion coefficient of MC (3.8 ± 3.5 kPa) than DF (0.42 ± 0.9 kPa) and a larger d value of DP (6.9 kPa) than DF (0.0 kPa), respectively. CS exhibits a higher spring-back index of mCC (0.39 ± 0.05) than DF (0.27 ± 0.05) also suggesting handling issues, which agrees with the experiences in the industry. This study demonstrates the capability of a CTT in a quantitative investigation of biomass handling characteristics.

09 BIOMASS FUELS↗
DOE OSTI2021

Planting miscanthus instead of row crops may increase the productivity and economic performance of farmed potholes

Abstract Climate change projections indicate that precipitation events in the central United States are expected to become more intense, more frequent in the spring, and less frequent in the summer. Such a precipitation shift could adversely impact crop yields, especially in subfield areas known as farmed potholes, which are highly susceptible to flooding and ponding, and crop death is more likely to occur, particularly early in the growing season. This suggests that planting alternative crops, such as more flood tolerant perennials, in these areas may be a more profitable option. Using observations of crop growth and yield along with ponding depth of a specific field and farmed pothole in the central United States, we developed a spatially explicit version of the agroecosystem model Agro‐IBIS to estimate water depth and crop yield. After evaluating the model, we conducted a case study for a specific farmed pothole with a range of future precipitation scenarios with Agro‐IBIS to simulate the effects of contemporary (2002–2016) and future precipitation on a conventional corn/soybean ( Zea mays L. and Glycine max Merr.) rotation and an alternative perennial miscanthus ( Miscanthus × giganteus Greef et Deu.) cropping system. The depth and frequency of ponding increased under most future precipitation scenarios. The corn/soybean rotation had greater total loss (i.e., no yield) on average (>30%) for all scenarios in comparison to miscanthus (<10%). Under one future precipitation scenario with increased spring precipitation, both the corn/soybean rotation and miscanthus simulations showed an increase in yield. A simple budget analysis indicated that it is more profitable to plant miscanthus instead of corn or soybeans where yields in farmed potholes are consistently poor. Our findings show that potholes can be individually modeled, and their influence on yield can be quantified for use in future management decisions dictated by change in climate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

T-Toxin Virulence Genes: Unconnected Dots in a Sea of Repeats

In 1970 a corn disease epidemic ravaged fields in the United States to great economic loss. The outbreak was caused by a never-before seen, supervirulent strain of the fungal pathogen Cochliobolus heterostrophus. This was a plant disease epidemic, however, the current COVID-19 pandemic of humans is a stark reminder that novel, highly virulent, pathogens evolve with devastating consequences, no matter what the host-animal, plant, or other organism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Conserved defense responses between maize and sorghum to Exserohilum turcicum

Abstract Background Exserohilum turcicum is an important pathogen of both sorghum and maize, causing sorghum leaf blight and northern corn leaf blight. Because the same pathogen can infect and cause major losses for two of the most important grain crops, it is an ideal pathosystem to study plant-pathogen evolution and investigate shared resistance mechanisms between the two plant species . To identify sorghum genes involved in the E. turcicum response, we conducted a genome-wide association study (GWAS). Results Using the sorghum conversion panel evaluated across three environments, we identified a total of 216 significant markers. Based on physical linkage with the significant markers, we detected a total of 113 unique candidate genes, some with known roles in plant defense. Also, we compared maize genes known to play a role in resistance to E. turcicum with the association mapping results and found evidence of genes conferring resistance in both crops, providing evidence of shared resistance between maize and sorghum . Conclusions Using a genetics approach, we identified shared genetic regions conferring resistance to E. turcicum in both maize and sorghum. We identified several promising candidate genes for resistance to leaf blight in sorghum, including genes related to R-gene mediated resistance. We present significant advancements in the understanding of host resistance to E. turcicum , which is crucial to reduce losses due to this important pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗