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At least 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

DRIFT: Diffusivity Regulation of Isotopes by nanoconFinementT

Spontaneous isotope fractionation has been reported under nanoconfinement conditions in naturally occurring systems, but the origin of this phenomena is currently unknown. Two existing hypotheses have been proposed, one based on changes in the solvation environment of the isotopes that reduces the non-mass dependent hydrodynamics contribution to diffusion. The other is that isotopes have mass-dependent surface adsorption, varying their total diffusion through nanoconfined channels. To investigate these hypotheses, benchtop experiments, nuclear magnetic resonance (NMR) spectroscopy, and molecule scale modeling were applied. Classical molecular dynamics simulations identified that the Na + and Cl - hydration shells across the three different salt solutions ( 22 Na 35 Cl, 23 Na 35 Cl, 24 Na 35 Cl) did not vary as a function of the Na + isotope, but that there was a significant pore size effect, with larger hydration shells at larger pore sizes. Additionally, while total adsorption times did not vary as a function of the Na + isotope or pore size, the free ion concentration, or those adsorbed on the surface for <5% of the simulation time did exhibit isotope dependence. Experimentally, challenges occurred developing a repeatable experiment, but NMR characterization of water diffusion rates through ordered alumina membranes was able to identify the existence of two distinct water environments associated with water inside and outside the pore. Further NMR studies could be used to confirm variation in hydration shells and diffusion rates of dissolved ions in water. Ultimately, mass-dependence adsorption is a primary driver of variations in isotope diffusion rates, rather than variation in hydration shells that occur under nanoconfinement.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

The Relationship of Hydrology in the Green River to Colorado Pikeminnow Populations

The Federally listed Colorado Pikeminnow (CP) (Ptychocheilus Lucius) has been declining in the Green River Basin over the last 20 years. Muth et al. (2000) recommended flows and temperatures to benefit endangered fish species downstream of Flaming Gorge Dam on the Green River. The recommendations identified a range of flows during the base flow period (flows that occur after the annual snowmelt runoff period, usually from early summer to the following spring) that were intended to benefit CP. The recommendations indicated that the mean flow for the summer–winter period should be established each year on the basis of anticipated hydrologic conditions, but adjustments could be made if hydrologic conditions change. Flow should gradually decline from peak flow to base flow, with the base flow reached by early to middle summer (depending on hydrologic conditions) and maintained through February. The rate of decline should depend on rates of decline in Yampa River flows and the recommended rates of decline for dam releases. No specific recommendations were made for base flow variation in Reach 1, but variation around the annual mean base flow should be restricted to achieve recommended levels of variation in Reach 2 (middle Green River) (Table 5.5 in Muth et al. 2000). Implementation of the flow and temperature recommendations served as the proposed action for an EIS on Flaming Gorge Dam operations. A Biological Assessment of the impacts on endangered species of implementing the recommendations was prepared and a Biological Opinion that called for development of a study plan to examine the effects of implementation. Projects to address this evaluation were identified in the Green River Study Plan and have been conducted since then. The purpose of the Study Plan was to identify and recommend to the Recovery Program those monitoring or research projects necessary for implementation and evaluation of the flow and temperature recommendations. Those projects included studies to evaluate the anticipated effects of implementing the recommendations (including potential adverse effects identified in the 2006 Biological Opinion) and studies to examine recognized uncertainties of the recommendations. A new recovery program summer base flow study plan was approved in September of 2020 to evaluate stable and elevated summer base flows below Flaming Gorge Dam intended to benefit CP spawning and rearing success. Anecdotal observations suggest CP production may have been higher in years prior to flow restrictions for endangered fish. Based on long-term CP monitoring data in the Green River, Bestgen and Hill (2016) concluded that CP would benefit from higher summer baseflows (1,700-3,000 ft 3 /sec) with flows above or below associated with lower abundance of age-0 CP. Therefore, flexibility in the ROD is currently being utilized to establish higher stable summer base flows in an attempt create more advantageous conditions for spawning and rearing CP. These fish recovery flows are restrictive to WAPA in the summer months, therefore it is necessary to conduct an analysis of historic river data relationships to CP abundance to better understand if the recommended fish flows (elevated and stable base flows) are necessary for fish recovery.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Extinction of Laser Light Due to Arctic Haze Final Campaign Report

Recent changes in emission patterns may have altered the historical stability of light attenuation strengths within the Arctic and, more specifically, the polar dome. While there have been decades of past and ongoing research on how atmospheric constituents, such as aerosols, affect light absorption, the bulk of this work is focused on the visible region. In recent years, there has been renewed interest in understanding laser light propagation at wavelengths such as 1 and 2 µm in this area. There is a need to evaluate how specific environmental parameters affect the propagation of light in this wavelength region, in particular: the extinction, scattering, and absorption coefficients, and how they relate to particle concentration; cn 2 and refractive index variations. Seasonally dependent variations in particle concentrations and compositions introduce different absorption and scattering characteristics that, in conjunction with varying temperatures, index-of-refraction variations, and wind, can result in laser beam focus and irradiance degradation. Understanding the fundamental influence of these parameters with respect to the propagation of light across a wide spectral band could lead to new insights about the minimal required datastreams required to provide accurate light propagation forecasting.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Investigating Spatial Variability of Aerosol, Cloud Condensation Nuclei, and Ice Nucleating Particles in Mountainous Terrain Field Campaign Report

The U.S. Department of Energy Atmospheric System Research (ASR)-supported Surface Atmosphere Integrated Field Laboratory (SAIL) campaign in the East River Watershed (ERW) of the Upper Colorado River Basin in southwestern Colorado ran from fall 2021 to spring 2023. Two monitoring sites were deployed in the ERW as part of SAIL. The two sites were the Aerosol Observation System (AOS) located on Crested Butte Ski Mountain, and the second ARM Mobile Facility (AMF2), located at the Rocky Mountain Biological Laboratory in Gothic, Colorado. To gain a more comprehensive understanding of aerosols in complex, mountainous terrain, Handix Scientific deployed SAIL-Net, a distributed network of six measurement nodes spanning the domain of the SAIL research area from October 2021 to July 2023. Each node measured aerosol particles between 140 nm and 3.4 μm in diameter using a small portable optical particle spectrometer (POPS; Gao et al. 2016), cloud condensation nuclei (CNN) using a miniature CCN counter (CloudPuck), and ice nucleating particles (INP) using the time-resolved aerosol filter sampler (TRAPS; Creamean et al. 2018). Our approach was similar to other studies that aimed to better characterize and understand aerosols and gas-phase pollutants using networks of lower-cost sensors (Caubel et al. 2019, Kelly et al. 2021, Asher et al. 2022). Such studies have identified neighborhood-level variations in pollutant concentrations (Schneider et al. 2017, Popoola et al. 2018, Caubel et al. 2019). Small-scale variations such as this are poorly represented in models and poorly measured by a single monitoring system (Caubel et al. 2019). Previous work has shown the representation error (the ability of measurements to represent a larger area) increases with complex orography, leading to decreases in model accuracy (Schutgens et al. 2017). The overall goal of SAIL-Net was to improve our understanding of the variability of aerosol in the ERW, thus increasing our knowledge of aerosol-cloud interactions in this region and informing the usefulness of distributed networks of measurements for future studies. We met this goal by answering the following science questions: 1. What is the aerosol temporal variability, and how does aerosol inhomogeneity vary seasonally? Is there significant seasonal variability in sources, or are short-term meteorological conditions the most important determining factor in sources for cloud nuclei? 2. What is the aerosol spatial variability? What are the aerosol characteristics at cloud base, presumably the particles most representative of those acting as cloud nuclei? 3. How should measurement networks be designed to capture aerosol-cloud interactions, and what do they need to measure? Can a single measurement site accurately represent aerosol properties in regions of complex terrain? SAIL-Net consisted of six measurement nodes spread across the ERW near Crested Butte, Colorado. The primary objective in site placement was to select locations that captured the vertical variation in aerosol properties while also spanning the domain of the SAIL campaign. The elevation of the sites ranged from roughly 2750 m along the valley floor of the ERW to approximately 3500 m near the top of Crested Butte Mountain, which is one of the taller peaks in the ERW. The farthest distance between sites was 14 km, while the closest two sites were approximately 1 km apart. Two of the sites were collocated with the ARM SAIL sites; our instruments sat on top of one of the trailers at AOS and another one of our sites was located in a meadow just above AMF2.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Assessment of the Loss of Vacuum on the Local Metal Temperature in the TEX Experiment Assembly

A four-part assessment using analytical methods and semi-analytical simulation tools finds that the maximum temperature variation in the highly enriched uranium (HEU) Jemima plate assembly is less than ten Kelvin (< 10 K) in an abrupt loss of vacuum scenario. The temperature variation in the metals is likely to be one to four Kelvin (1 K – 4 K) based on the most realistic conditions in the assessment. The four assessment parts include: (1) the peak gas temperature bound for the initial influx of the ambient air; (2) the high-heat transfer limit during the high-speed forced convection period in an insulated HEU plate; (3) the high-heat transfer limit during the high-speed forced convection period with aluminum spacers; and (4) the longer-time thermal equilibration period between the air and metal stack. The four-part assessment serves as conservative upper bound on the temperature variation in the metal stack and remains well below the 40 Kelvin limit where the temperature-induced stresses could lead to permanent, plastic deformation.

42 ENGINEERING↗
DOE OSTI2026

Mechanical Characterization of the NIF Ignition Target TMPSA Bonding Flexure

The Thermo-Mechanical Package Sub-Assembly (TMPSA) provides a critical mechanical, thermal, and electrical interface between a silicon arm and a TMP aluminum can in a NIF ignition target. During assembly, sixteen silicon pads are bonded to the aluminum using a fixture that positions the components and applies a repeatable prescribed displacement through a compliant flexure. The flexure converts fixture interference into displacement and reaction force. Because bondline thickness variation must be maintained within +/-4 µm, consistent flexure behavior is important to the assembly process. With a recent string of TMPSAs exhibiting low bond strength, the flexures were inspected. Despite being manufactured to the same specifications, flexures were found to exhibit variation in measured stiffness. Additionally, the measured stiffness values did not always follow the presumed beam mechanics model. This work addresses two questions: whether the bonding fixture is working as intended, and whether the previously made stiffness measurements are accurate representations of the use case. The flexures are analyzed using Euler-Bernoulli beam theory, measured beam dimensions, finite element analysis, and tolerance stack-up calculations. The analysis shows that the fixed-guided beam mechanics model appropriately represents the flexure during TMPSA bonding, but the chisel-tip stiffness measurement method introduces a deformation to the inner ring of the flexure that is not represented during use. The measured stiffness values should therefore be interpreted as test-condition stiffness values rather than direct measurements of operational flexure stiffness. The discrepancy is therefore attributed primarily to the measurement boundary condition rather than to failure of the fixed-guided beam model. Recommendations are provided for GD&T, dimensional inspection, and a representative stiffness testing method to better control bondline variation.

42 ENGINEERING↗
DOE OSTI2026

Seeing values for LSST strategy simulations

The opsim4 operations simulation program for the LSST astronomical survey uses a database of seeing values covering the range of times to besimulated. Idescribethe creation of such a database using Dual Image Motion Monitor(DIMM)datacollected at Cerro Pachon from 2004-03-17 to 2019-10-07. In times during which the data overlap, I compare the distribution of DIMM seeing values to the seeing measured in DECamimages,takenatasite 10kmaway. Becauseinstrumentalproblemsinthe DIMMmay indicate unreliablemeasurements,cutsonimagequality(asindicatedby the measured Strehlratio)wereexplored. TheDIMMhassignificantgaps,soImodel thedata(withandwithoutcutsonStrehlratio)andgenerateartificialdatainthegaps according to the model. The model consists of a sinusoidal variation with a period of one year, an autoregressive (AR1) model for variations in mean seeing from one night to the next, and another AR1 model for variations on a 5 minute timescale. I create four databases according to thisprocedure, twobasedonDIMMdatastarting 2006-01-01 (with and without a Strehl ratio cut), and two starting 2009-01-01. I then run opsim simulations using each, and an otherwise identical simulation using the default seeing database, and explore the differences

Neilsen, Eric H. [Fermilab]↗
DOE OSTI2022

Diagnosing Barren Plateaus with Tools from Quantum Optimal Control

Variational Quantum Algorithms (VQAs) have received considerable attention due to their potential for achieving near-term quantum advantage. However, more work is needed to understand their scalability. One known scaling result for VQAs is barren plateaus, where certain circumstances lead to exponentially vanishing gradients. It is common folklore that problem-inspired ansatzes avoid barren plateaus, but in fact, very little is known about their gradient scaling. In this work we employ tools from quantum optimal control to develop a framework that can diagnose the presence or absence of barren plateaus for problem-inspired ansatzes. Such ansatzes include the Quantum Alternating Operator Ansatz (QAOA), the Hamiltonian Variational Ansatz (HVA), and others. With our framework, we prove that avoiding barren plateaus for these ansatzes is not always guaranteed. Specifically, we show that the gradient scaling of the VQA depends on the degree of controllability of the system, and hence can be diagnosed through the dynamical Lie algebra $\mathfrak{g}$ obtained from the generators of the ansatz. We analyze the existence of barren plateaus in QAOA and HVA ansatzes, and we highlight the role of the input state, as different initial states can lead to the presence or absence of barren plateaus. Taken together, our results provide a framework for trainability-aware ansatz design strategies that do not come at the cost of extra quantum resources. Moreover, we prove no-go results for obtaining ground states with variational ansatzes for controllable system such as spin glasses. Our work establishes a link between the existence of barren plateaus and the scaling of the dimension of $\mathfrak{g}$.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Individual Wave Detection and Tracking within a Rotating Detonation Engine through Computer Vision Object Detection applied to High-Speed Images

Known for their simplistic design and continuous detonation, rotating detonation engines (RDEs) constitute a majority of current pressure gain combustion (PGC) research efforts. Experimental RDE operation times have been continuously extended through the use of rig cooling techniques. As the window of observable behavior is expanded, and as the technology matures toward eventual integration within gas turbines, monitoring techniques must evolve to better match industrial diagnostics. High-speed image analysis techniques prove useful to capture and evaluate the unsteady detonation behavior within the RDE. Traditional image analysis techniques, however, require extensive processing times which prohibit simultaneous monitoring. To better address this problem, a computer vision object detection methodology is proposed to quickly detect individual detonation waves within a single down-axis image. Detonation waves are detected in individual images by the implemented computer vision method You Only Look Once (YOLO) object detection network. In order to detect detonation waves, the network must first be trained using RDE images of interest, for which each required phase of network development is outlined. Detection of waves is improved through proper treatment of the collected image set, variation of Intersection over Union (IoU) and confidence thresholding, and through a parametric study of annotation dimensions. Each detected wave is described by its location and rotational direction, and locations are tracked to calculate wave velocity across each frame, leading to a timestep resolution of 20 µs. Wave velocities are also calculated through a series of frames, leading to a suitable average velocity estimation using as few as 10 frames. Uncertainty analysis accounting for variation in camera framerate, pixel width and annotation centroid locations estimates a total uncertainty of ±4.3% for velocity calculations, using the smallest annotation boxes. This method offers great reductions in processing times, as a step toward real-time monitoring of detonation waves within an RDE. Improving on previous studies, this technique is impartial to wave modes not included in the original training set and calculates wave velocities independent of high-speed pressure data. The ability to isolate waves within predicted bounding boxes will likely facilitate analysis of pixel intensity variation as an estimation of wave strength in future work.

Johnson, Kristyn↗
DOE OSTI2025

Machine learning reveals genes impacting oxidative stress resistance across yeasts

Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection. Here, we characterized the variation in resistance to ROS across the ancient yeast subphylum Saccharomycotina and used machine learning (ML) to identify gene families whose sizes were predictive of ROS resistance.

AI↗
DOE OSTI2023

Red-green-bleached redox interfaces in the proximal Permian Cutler red beds: implications for regional fluid alteration

Siliciclastic strata of the Colorado Plateau attract attention for their striking red, green, bleached, and variegated colors that potentially record both early depositional and later diagenetic events. We investigated the proximal-most strata of the Paradox Basin, from their onlap contact with the Precambrian basement of the Uncompahgre Plateau to the younger Cutler strata exposed within 10 km of the Uncompahgre Plateau to attempt to understand the significance of the striking colors that occur here. These strata preserve a complex geology associated with buried paleorelief and sediment-related permeability variations at a major basin-uplift interface. Strata exposed within ~1.5 km of the onlap contact exhibit a pervasive drab color in contrast to the generally red colors that predominate farther from this front. In-between, strata commonly host variegated red/green/bleached intercalations. Thin-section petrography, SEM, XRD, Raman spectroscopy, Mössbauer spectroscopy, and whole-rock geochemistry of samples representing different color variations from demonstrate that water–rock interactions charged the rocks with Fe(II) that persists primarily in the phyllosilicate fraction. Color variations reflect grain-size differences that allowed the reduction of fluids from regional fault and basement/fill contacts to permeate coarser-grained Cutler sediments. Hematite and chlorite occur in both red and green sediments but are absent in the bleached sediments. Pervasive hematite in both red and green layers suggests that sediments were hematite-rich before later alteration. Chlorite and smectite are elevated in green samples and inversely correlated with biotite content. Green coloration is generally associated with 1) coarser grain sizes, 2) spatial association with basement contacts, 3) elevated smectite and/or chlorite, 4) less total Fe but greater Fe(II)/Fe(III) primarily in the phyllosilicate fraction, and 5) uranium enrichment. The bleached coloration reflects the removal of pigmentary Fe(III) oxide, while the green coloration is due to the removal of pigmentary hematite and the abundance of Fe(II)-bearing phyllosilicates. Abundant mixed-layer and swelling clays such as smectite, illite/smectite, and chlorite/smectite (including tosudite) dominate the mineralogy of the clay fraction. These results are consistent with other studies demonstrating fault-associated fluid alteration in the Paradox Basin region. However, the pervasive greening was not observed in many of these studies and appears to reflect the unique aspects of the paleovalley system and the importance of biotite alteration to Fe(II)-bearing phyllosilicates.

58 GEOSCIENCES↗
DOE OSTI2022

Image Analysis for Rapid Assessment and Quality-Based Sorting of Corn Stover

Imaging in the visible spectrum is a low-cost tool that can be readily deployed for in-field or over-belt monitoring of biomass quality for bio-refining operations. Rapid image analysis coupled with innovative preprocessing may reduce the impacts of feedstock variability through identification of contaminants or other material attributes to guide selective sorting and quality management. Image analysis was employed to evaluate the quality of corn stover in red-green-blue (RGB) chromatic space. This study used controlled, bench-scale imaging as a proof-of-concept for rapid quality assessment of corn stover based on variations in material attributes, including chemical and physical attributes, that relate to biological degradation and soil contamination. Additionally, logistic regression-based classification algorithms were used to develop a method for biomass screening as a function of biological degradation or soil contamination. This study demonstrated the use of image analysis to extract features from RGB color space to investigate variations in critical material attributes from chemical composition of corn stover. Fourier transform infrared (FT-IR) suggested a correlation between red band intensity and biological degradation, while detailed surface texture analysis was found to distinguish among variations in ash. These insights offer promise for development of a rapid screening tool that could be deployed by farmers for in-field assessment of biomass quality or biorefinery operators for in-line sorting and process optimization.

09 BIOMASS FUELS↗
DOE OSTI2022

Upscaling Methane Flux From Plot Level to Eddy Covariance Tower Domains in Five Alaskan Tundra Ecosystems

Spatial heterogeneity in methane (CH 4 ) flux requires a reliable upscaling approach to reach accurate regional CH 4 budgets in the Arctic tundra. In this study, we combined the CLM-Microbe model with three footprint algorithms to scale up CH 4 flux from a plot level to eddy covariance (EC) tower domains (200 m × 200 m) in the Alaska North Slope, for three sites in Utqiaġvik (US-Beo, US-Bes, and US-Brw), one in Atqasuk (US-Atq) and one in Ivotuk (US-Ivo), for a period of 2013–2015. Three footprint algorithms were the homogenous footprint (HF) that assumes even contribution of all grid cells, the gradient footprint (GF) that assumes gradually declining contribution from center grid cells to edges, and the dynamic footprint (DF) that considers the impacts of wind and heterogeneity of land surface. Simulated annual CH 4 flux was highly consistent with the EC measurements at US-Beo and US-Bes. In contrast, flux was overestimated at US-Brw, US-Atq, and US-Ivo due to the higher simulated CH 4 flux in early growing seasons. The simulated monthly CH 4 flux was consistent with EC measurements but with different accuracies among footprint algorithms. At US-Bes in September 2013, RMSE and NNSE were 0.002 μmol m −2 s −1 and 0.782 using the DF algorithm, but 0.007 μmol m −2 s −1 and 0.758 using HF and 0.007 μmol m −2 s −1 and 0.765 using GF, respectively. DF algorithm performed better than the HF and GF algorithms in capturing the temporal variation in daily CH 4 flux each month, while the model accuracy was similar among the three algorithms due to flat landscapes. Temporal variations in CH 4 flux during 2013–2015 were predominately explained by air temperature (67–74%), followed by precipitation (22–36%). Spatial heterogeneities in vegetation fraction and elevation dominated the spatial variations in CH 4 flux for all five tower domains despite relatively weak differences in simulated CH 4 flux among three footprint algorithms. The CLM-Microbe model can simulate CH 4 flux at both plot and landscape scales at a high temporal resolution, which should be applied to other landscapes. Integrating land surface models with an appropriate algorithm provides a powerful tool for upscaling CH 4 flux in terrestrial ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies

Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in P. trichocarpa germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.

Genetics & Heredity↗
DOE OSTI2022

Identification of a Fusarium ear rot resistance gene in maize by QTL mapping and RNA sequencing

Fusarium ear rot (FER) caused by Fusarium verticillioides is a prevalent maize disease. To comprehensively characterize the genetic basis of the natural variation in FER resistance, a recombinant inbred line (RIL) population was used to map quantitative trait loci (QTL) for FER resistance. A total of 17 QTL were identified by linkage mapping in eight environments. These QTL were located on six chromosomes and explained 3.88–15.62% of the total phenotypic variation. Moreover, qFER1.03 had the strongest effect and accounted for 4.98–15.62% of the phenotypic variation according to analyses of multiple environments involving best linear unbiased predictions. The chromosome segment substitution lines (CSSLs) derived from a cross between Qi319 (donor parent) and Ye478 (recurrent parent) were used to verify the contribution of qFER1.03 to FER resistance. The line CL171, which harbored an introgressed qFER1.03 , was significantly resistant to FER. Further fine mapping of qFER1.03 revealed that the resistance QTL was linked to insertion/deletion markers InDel 8 and InDel 2, with physical distances of 43.55 Mb and 43.76 Mb, respectively. Additionally, qFER1.03 differed from the previous resistance QTL on chromosome 1. There were three annotated genes in this region. On the basis of the RNA-seq data, which revealed the genes differentially expressed between the FER-resistant Qi319 and susceptible Ye478, GRMZM2G017792 (MPK3) was preliminarily identified as a candidate gene in the qFER1.03 region. The Pr-CMV-VIGS system was used to decrease the GRMZM2G017792 expression level in CL171 by 34–57%, which led to a significant decrease in FER resistance. Using RIL and CSSL populations combined with RNA-seq and Pr-CMV-VIGS, the candidate gene can be dissected effectively, which provided important gene resource for breeding FER-resistant varieties.

Xia, Yusheng↗
DOE OSTI2020

Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression in Populus Tomentosa

Cytokinins play important roles in the growth and development of plants. Physiological and photosynthetic characteristics are common indicators to measure the growth and development in plants. However, few reports have described the molecular mechanisms of physiological and photosynthetic changes in response to cytokinin, particularly in woody plants. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression in response to the external environment. In this study, we examined genome-wide DNA methylation variation and transcriptional variation in poplar (Populus tomentosa) after short-term treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 460 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 339 protein-coding genes, 262 long non-coding RNAs (lncRNAs), and 15,793 24-nt small interfering RNAs (siRNAs) were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa, and 102,819 allele-specific expression (ASE) loci in 19,200 genes were detected showing differences in ASE levels after 6-BA treatment. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 460 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa, and we identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions

Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus Vetrix are interesting for comparative studies of sex determination systems, yet genomic resources for these species are still quite limited. Only a few annotated reference genome assemblies are available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of 11 shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism, and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

In Situ Synchrotron X-ray Micro-Diffraction Investigation of Elastic Strains in Laminated Ti-Al Composites

Spatially resolved elastic strains in the bulk interior of a laminated Ti-Al metal composite were studied during in situ tensile loading at strains up to 1.66% by a synchrotron-based micro-diffraction technique, namely differential aperture X-ray microscopy (DAXM). For both Al and Ti grains, deviatoric elastic strains were estimated based on polychromatic X-ray microbeam diffraction, while lattice strains along the normal direction of the tensile sample were directly measured using monochromatic X-ray microbeam diffraction. The estimated deviatoric strains show large spatial variations, and the mean values are consistent with the external loading conditions, i.e., increasing tensile strain along the tensile direction and increasing compressive strain along the sample normal with increasing loading. The directly measured lattice strains also show large spatial variations, although the magnitude of this variation is smaller than that for the estimated deviatoric strain. The directly measured lattice strains in Ti grains are largely consistent with the external loading, whereas those in Al grains are in contradiction with the external loading. The causes of the experimental results are discussed and related to both the laminated microstructure of the composite material and the limitations of the techniques.

36 MATERIALS SCIENCE↗