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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives

Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, “PolyHighResolution” (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain

The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Large Non‐Resonant Infrared Optical Second Harmonic Generation in Bulk Crystals of Van der Waals Semiconductor, SnP 2 Se 6

2D van der Waals (vdW) materials have emerged as a highly promising candidates for nonlinear optical (NLO) applications. This study presents the synthesis, comprehensive linear optical, and optical second harmonic generation (SHG) characterization of a novel 2D vdW semiconductor SnP2Se6 in its bulk single crystal form. It exhibits an indirect bandgap of ≈1.47 eV and an exceptional non-resonant SHG coefficient of d 33 ∼ −222 ± 30 pm V −1 at a fundamental wavelength of 2 µm, which is ≈7 times larger than that of the commercial AgGaSe 2 with a comparable bandgap. Density functional theory (DFT) calculations of the linear and nonlinear optical properties exhibit reasonable agreement with the experimental measurements, revealing the chemical origin of the enhanced properties. Moreover, SnP 2 Se 6 can exhibit both type-I and type-II phase matching over a wide spectral range, fulfilling one of the key criteria for an ideal NLO crystal. These exceptional properties position SnP 2 Se 6 as a highly promising candidate for NLO applications.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Accelerating SNP Development with Radiation Source Approximations for Far-Field Environment Modeling

The successful development and deployment of space nuclear power and propulsion technology requires a high-fidelity, efficient means of modeling ex-core radiation fields. Monte Carlo particle transport codes provide enable the highest level of fidelity in radiation field modeling but are inefficient for modeling ex-core radiation without modification. This paper details the development of an approach to ex-core radiation field modeling that maintains the fidelity of a Monte Carlo transport approach without sacrificing computational efficiency. This approach is based on recent improvements to an existing Monte Carlo transport acceleration technique known as surface source banking. As the transport of many particles is required to ensure adequate uncertainty in far field transport, analytical reconstruction techniques are employed to represent surface source banks as sampleable series of distributions in particle phase from which an arbitrarily large number of particles can be generated and simulated. All steps of this approach are incorporated into an AMA model to test both the underlying mathematics of the analytical source reconstruction process, as well as the relevance of the technique as a whole towards SNP applications. These tests demonstrated that this approach is capable of accelerating far-field radiation modeling in SNP-relevant scenarios by factors of at least nine over purely eigenvalue-based scenarios without significantly sacrificing simulation accuracy.

Surface Source Banking↗
DOE OSTI2020

Materials Data on SnP by Materials Project

SnP is Halite, Rock Salt structured and crystallizes in the cubic Fm-3m space group. The structure is three-dimensional. Sn3+ is bonded to six equivalent P3- atoms to form a mixture of edge and corner-sharing SnP6 octahedra. The corner-sharing octahedral tilt angles are 0°. All Sn–P bond lengths are 2.80 Å. P3- is bonded to six equivalent Sn3+ atoms to form a mixture of edge and corner-sharing PSn6 octahedra. The corner-sharing octahedral tilt angles are 0°.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on SnP by Materials Project

SnP is Halite, Rock Salt structured and crystallizes in the tetragonal I4mm space group. The structure is three-dimensional. Sn3+ is bonded to five equivalent P3- atoms to form a mixture of corner and edge-sharing SnP5 square pyramids. There are one shorter (2.64 Å) and four longer (2.76 Å) Sn–P bond lengths. P3- is bonded to five equivalent Sn3+ atoms to form a mixture of corner and edge-sharing PSn5 square pyramids.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

NASA Space Nuclear Propulsion (SNP) MBSE Initiatives

NASA’s Space Nuclear Propulsion (SNP) program is developing several MagicDraw SysML models to support the development of high performance Nuclear Thermal Rocket Engines (NTRE). Currently, the Demonstration Rocket for Agile Cislunar Operations (DRACO) project is aiming to perform the first ever flight demonstration of an NTRE, and NASA is developing a DRACO Insight Project Model Based Systems Engineering (MBSE) model to capture, define, analyze, and report on the flight and ground test system architecture, functional behavior, requirements, risks, and lessons learned. Additional models are in work for engine component trade trees, fault detection sensor coverage analysis using a Goal Function Tree (GFT) plugin, stakeholder engagement, and technology maturation projects. The GFT plugin is the Galois, Inc. Failure Recovery Instruction Generation using Automata derived from Traditional Engineering models (FRIGATE) tool. A new capability for Jira to MagicDraw data sharing using the OpenPDM collaboration platform is under development with partner Victory Solutions, Inc. to enhance risk impact analysis.

Space Nuclear Propulsion (SNP)↗
DOE OSTI2023

Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa

The image dataset consists of 11,791 images representing 1,219 genotypes of Populus trichocarpa undergoing in planta regeneration. Genotypes were imaged with a median of four weekly timepoints and a median of two replicates each. A representative and diverse subset of 249 images was annotated using the IDEAS annotation interface (ideas.eecs.oregonstate.edu) and these annotated images were used to train a deep semantic segmentation model (PSPNet), which was deployed for inference over the entire dataset. Annotated classes include specific stages of regeneration (callus and shoot) in addition to unregenerated plant material and background. Statistics of relative tissue area were extracted and used for downstream genetic association mapping in a genome-wide association study. The SNP dataset consists of over 40 million single-nucleotide polymorphisms across 1,323 wild accessions of Populus trichocarpa

09 BIOMASS FUELS↗
NASA NTRS2024

Space Nuclear Propulsion (SNP) Material Property Handbook

The National Aeronautics and Space Administration’s (NASA’s) Space Nuclear Propulsion (SNP) project aims to demonstrate the feasibility of nuclear thermal propulsion (NTP) as a thrust mechanism for spacecraft. An initial Demonstration Rocket for Agile Cislunar Operations (DRACO) launch will serve as a test of the technology in Earth’s orbit. Future work may involve the development of an NTP engine and spacecraft design with the capability to transport astronauts from Earth to Mars and back safely, though NTP has other potential uses too.

Nuclear Thermal Propulsion↗
DOE OSTI2024

Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1

The VCF dataset includes genetic variations found in 1,323 Populus trichocarpa genotypes, providing valuable information for scientists studying plant genetics. Researchers have generated this dataset using whole-genome DNA short-read sequencing on the Illumina Genome Analyzer, HiSeq 2000, and HiSeq 2500 platforms. This sequencing effort ensured a minimum expected sequencing depth of 15×. The dataset comprises more than 9.7 million single nucleotide polymorphisms (SNPs) and indel variants. The combined annotation files are derived from P. trichocarpa v3.0 and v3.1. We merged these files to create a comprehensive annotation file used for GWAS analysis. In total, 38,830 genes overlapped between the two versions. For overlapping genes, we defined the start as the smaller and the end as the larger among the two versions to increase the likelihood of locating candidate genetic loci. Additionally, we included 2,505 unique genes from v3.0 and 4,120 unique genes from v3.1, resulting in a total of 45,455 genes in the updated annotation file.

09 BIOMASS FUELS↗
NASA NTRS2021

Moisture and Temperature Influences on Nonlinear Vegetation Trends in Serengeti National Park

While long-term vegetation greening trends have appeared across large land areas over the late 20th century, uncertainty remains in identifying and attributing finer-scale vegetation changes and trends, particularly across protected areas. Serengeti National Park (SNP) is a critical East African protected area, where seasonal vegetation cycles support vast populations of grazing herbivores and a host of ecosystem dynamics. Previous work has shown how non-climate drivers (e.g. land use) shape the SNP ecosystem, but it is still unclear to what extent changing climate conditions influence SNP vegetation, particularly at finer spatial and temporal scales. We fill this research gap by evaluating long-term (1982–2016) changes in SNP leaf area index (LAI) in relation to both temperature and moisture availability using Ensemble Empirical Mode Decomposition and Principal Component Analysis with regression techniques. We find that SNP LAI trends are nonlinear, display high sub-seasonal variation, and are influenced by lagged changes in both moisture and temperature variables and their interactions. LAI during the long rains (e.g. March) exhibits a greening-to-browning trend reversal starting in the early 2000s, partly due to antecedent precipitation declines. In contrast, LAI during the short rains (e.g. November, December) displays browning-to-greening alongside increasing moisture availability. Rising temperature trends also have important, secondary interactions with moisture variables to shape these SNP vegetation trends. Our findings show complex vegetation-climate interactions occurring at important temporal and spatial scales of the SNP, and our rigorous statistical approaches detect these complex climate-vegetation trends and interactions, while guarding against spurious vegetation signals.

Moisture↗
DOE OSTI2021

Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut ( Arachis hypogaea L.)

Abstract The fatty acid composition of seed oil is a major determinant of the flavor, shelf-life, and nutritional quality of peanuts. Major QTLs controlling high oil content, high oleic content, and low linoleic content have been characterized in several seed oil crop species. Here, we employ genome-wide association approaches on a recently genotyped collection of 787 plant introduction accessions in the USDA peanut core collection, plus selected improved cultivars, to discover markers associated with the natural variation in fatty acid composition, and to explain the genetic control of fatty acid composition in seed oils. Overall, 251 single nucleotide polymorphisms (SNPs) had significant trait associations with the measured fatty acid components. Twelve SNPs were associated with two or three different traits. Of these loci with apparent pleiotropic effects, 10 were associated with both oleic (C18:1) and linoleic acid (C18:2) content at different positions in the genome. In all 10 cases, the favorable allele had an opposite effect—increasing and lowering the concentration, respectively, of oleic and linoleic acid. The other traits with pleiotropic variant control were palmitic (C16:0), behenic (C22:0), lignoceric (C24:0), gadoleic (C20:1), total saturated, and total unsaturated fatty acid content. One hundred (100) of the significantly associated SNPs were located within 1000 kbp of 55 genes with fatty acid biosynthesis functional annotations. These genes encoded, among others: ACCase carboxyl transferase subunits, and several fatty acid synthase II enzymes. With the exception of gadoleic (C20:1) and lignoceric (C24:0) acid content, which occur at relatively low abundance in cultivated peanuts, all traits had significant SNP interactions exceeding a stringent Bonferroni threshold (α = 1%). We detected 7682 pairwise SNP interactions affecting the relative abundance of fatty acid components in the seed oil. Of these, 627 SNP pairs had at least one SNP within 1000 kbp of a gene with fatty acid biosynthesis functional annotation. We evaluated 168 candidate genes underlying these SNP interactions. Functional enrichment and protein-to-protein interactions supported significant interactions (P-value < 1.0E−16) among the genes evaluated. These results show the complex nature of the biology and genes underlying the variation in seed oil fatty acid composition and contribute to an improved genotype-to-phenotype map for fatty acid variation in peanut seed oil.

Otyama, Paul I.↗
DOE OSTI2021

Whole Genome Sequencing Links Mycobacterium bovis From Cattle, Cheese and Humans in Baja California, Mexico

Mycobacterium bovis causes tuberculosis (TB) in cattle, which in turn can transmit the pathogen to humans. Tuberculosis in dairy cattle is of particular concern where the consumption of raw milk and dairy products is customary. Baja California (BCA), Mexico, presents high prevalence of TB in both cattle and humans, making it important to investigate the molecular epidemiology of the disease in the region. A long-term study was undertaken to fully characterize the diversity of M. bovis genotypes circulating in dairy cattle, cheese and humans in BCA by whole-genome sequencing (WGS). During a 2-year period, 412 granulomatous tissue samples were collected from local abattoirs and 314 cheese samples were purchased from local stores and vendors in BCA and sent to the laboratory for mycobacterial culture, histology, direct PCR and WGS. For tissue samples M. bovis was recovered from 86.8%, direct PCR detected 90% and histology confirmed 85.9% as mycobacteriosis-compatible. For cheese, M. bovis was recovered from 2.5% and direct PCR detected 6% of the samples. There was good agreement between diagnostic tests. Subsequently, a total of 345 whole-genome SNP sequences were obtained. Phylogenetic analysis grouped these isolates into 10 major clades. SNP analysis revealed putative transmission clusters where the pairwise SNP distance between isolates from different dairies was ≤3 SNP. Also, human and/or cheese isolates were within 8.45 (range 0–17) and 5.8 SNP (range 0–15), respectively, from cattle isolates. Finally, a comparison between the genotypes obtained in this study and those reported previously suggests that the genetic diversity of M. bovis in BCA is well-characterized, and can be used to determine if BCA is the likely source of M. bovis in humans and cattle in routine epidemiologic investigations and future studies. In conclusion, WGS provided evidence of ongoing local transmission of M. bovis among the dairies in this high-TB burden region of BCA, as well as show close relationships between isolates recovered from humans, cheese, and cattle. This confirms the need for a coordinated One Health approach in addressing the elimination of TB in animals and humans. Overall, the study contributes to the knowledge of the molecular epidemiology of M. bovis in BCA, providing insight into the pathogen's dynamics in a high prevalence setting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mapping crown rust resistance in the oat diploid accession PI 258731 ( Avena strigosa )

Oat crown rust, caused by Puccinia coronata Corda f. sp. avenae Eriks. (Pca), is a major biotic impediment to global oat production. Crown rust resistance has been described in oat diploid species A. strigosa accession PI 258731 and resistance from this accession has been successfully introgressed into hexaploid A. sativa germplasm. The current study focuses on 1) mapping the location of QTL containing resistance and evaluating the number of quantitative trait loci (QTL) conditioning resistance in PI 258731; 2) understanding the relationship between the original genomic location in A. strigosa and the location of the introgression in the A. sativa genome; 3) identifying molecular markers tightly linked with PI 258731 resistance loci that could be used for marker assisted selection and detection of this resistance in diverse A. strigosa accessions. To achieve this, A. strigosa accessions, PI 258731 and PI 573582 were crossed to produce 168 F5:6 recombinant inbred lines (RILs) through single seed descent. Parents and RILs were genotyped with the 6K Illumina SNP array which generated 168 segregating SNPs. Seedling reactions to two isolates of Pca (races TTTG, QTRG) were conditioned by two genes (0.6 cM apart) in this population. Linkage mapping placed these two resistant loci to 7.7 (QTRG) to 8 (TTTG) cM region on LG7. Field reaction data was used for QTL analysis and the results of interval mapping (MIM) revealed a major QTL (QPc.FD-AS-AA4) for field resistance. SNP marker assays were developed and tested in 125 diverse A. strigosa accessions that were rated for crown rust resistance in Baton Rouge, LA and Gainesville, FL and as seedlings against races TTTG and QTRG. Our data proposed SNP marker GMI_ES17_c6425_188 as a candidate for use in marker-assisted selection, in addition to the marker GMI_ES02_c37788_255 suggested by Rine’s group, which provides an additional tool in facilitating the utilization of this gene in oat breeding programs.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2008

Baroreflex Sensitivity Decreases During 90-Day Bed Rest

Baroreflex sensitivity (BRS) decreases during spaceflight and simulated spaceflight (head down bed rest [BR]). However, previous studies have only examined BRS in response to a limited blood pressure (BP) range or to a single sudden change in BP. PURPOSE: The purpose of this study was to examine BRS during 90 days of 6deg head-down tilt BR over a broad range of BP perturbations. METHODS: Nineteen normal volunteers (12M, 7F) were tested one day before BR, and then near BR days 30, 60 and 90. BP was pharmacologically altered by continuous infusions of phenylephrine (PE) and sodium nitroprusside (SNP). Electrocardiogram and continuous BP were collected during 10 min of normal saline (NS), followed by increasing concentrations of PE (10 min each of 0.4, 0.8 and 1.6 micro-g/kg/min). After a 20 min break, NS was infused again for 10 min, followed by increasing concentrations of SNP (10 min each of 0.4, 0.8, 1.2 micro-g/kg/min). Baroreceptor sensitivity was measured as the slope of a sequence of 3 or more beats in which the systolic BP and following R-R interval (RR) both increased or decreased. Spectral heart rate variability (HRV) and mean RR were analyzed using data from only the NS infusions. Two-way repeated-measures analysis of variance was performed to examine the effects of BR and gender. RESULTS: RR decreased (p<0.001) from pre- BR across BR days. High frequency in normalized units, a measure of parasympathetic activity, decreased with BR (p=0.027) and was lower (p=0.046) in men (0.39+/-0.02, mean+/-SEM) than women (0.48+/-0.02). The spontaneous baroreflex slope, our measure of BRS, increased with PE and decreased with SNP across BR (p<0.001). The percentage decrease in BRS from pre- to post-BR appeared to be larger in women (43.6+/-7.0%) than in men (31.3+/-3.9%, p=0.06). CONCLUSION: Parasympathetic activity and baroreflex sensitivity decrease during 90 days of BR, and BRS tends to diminish more in women than in men.

Stenger, M. B.↗