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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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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Application of Analytical Hierarchy Process for Narrowing Down Nep Candidate Reactor Designs

NASA is currently studying the possibility of human exploration of Mars in the late 2030s timeframe using a hybrid nuclear electric propulsion (NEP)/chemical propulsion system. Present analyses indicate such a mission could require a reactor power system in the range of 2 to 6 MWe operating for approximately 3 years. At present, the Technology Readiness Levels (TRL) of key NEP technologies are still low, implying that significant technology development activities must be undertaken prior to making informed design selections for an integrated propulsion system. NASA’s Space Nuclear Propulsion (SNP) project has recently undertaken an in-depth effort to identify NEP candidate technologies and determine the required developmental work to mature these technologies to the point where they could realistically support the design and assembly of a full NEP system. A version of the Analytical Hierarchy Process is being employed to narrow the technology candidates for SNP investment planning. This multi-attribute decision-making process relies on quantified technical inputs and the judgement of Subject Matter Experts (SMEs) to evaluate technology options against key technical and programmatic Figures-of-Merit (FOM) at the subsystem and optimized system level. The process and an example evaluation of nuclear fuel/moderator combinations in a sodium heat pipe honeycomb-geometry reactor concept are described. The evaluation and analysis methodology described in this paper can be employed for pairwise comparisons between reactor concepts and technology choices as new data become available.

Dasari V Rao↗
NASA NTRSDate not supplied

A Technology Maturation Plan for the Development of Nuclear Electric Propulsion

Over the last two years NASA’s Space Nuclear Propulsion (SNP) Project formulated a Technology Maturation Plan (TMP) for development of the sub-systems needed for a MW-class Nuclear Electric Propulsion (NEP) system which, combined with a high thrust chemical propulsion stage, would be suitable for human missions to Mars. Two recent assessments, independently conducted by the National Academies for Science, Engineering, and Medicine and the NASA Engineering & Safety Center, concluded that the technologies required for a high-power NEP system are immature and the attendant risks insufficiently quantified to justify initiating a flight project. For NEP to be available as a viable option to meet flight opportunities in the late 2030s / 2040s time frame, development of the key sub-systems must begin now. SNP has subdivided the NEP system into five Critical Technology Elements (CTE): the nuclear reactor, power conversion, power management and distribution, electric propulsion sub-system, and the primary heat rejection system. Development plans for each of these CTEs have been drafted which will serve as the template for a focused milestone-driven research and development campaign intended to advance each CTE to Technology Readiness Level (TRL) 5. This will be accomplished by building and testing hardware at relevant power levels (~ 1 MW) and for relevant durations (2,500 hours, ~10% of the required operational lifetime) and conducting numerical modeling of the CTEs anchored by the accumulated test data to predict system performance and reliability. Concurrent with this work, high-level coupled system/mission modeling will be carried out to refine the key performance parameters that the various CTEs must achieve. Non-advocate reviews will be held at milestone points to assess progress and inform down-select decisions. The strategy for formulating the TMP was described previously; this paper describes ongoing progress on the drafting and baselining of the plan, including key specific details.

Space Nuclear Propulsion↗
NASA NTRSDate not supplied

A Technology Maturation Plan for the Development of Nuclear Electric Propulsion

Over the last two years NASA’s Space Nuclear Propulsion (SNP) Project formulated a Technology Maturation Plan (TMP) for development of the sub-systems needed for a MW-class Nuclear Electric Propulsion (NEP) system which, combined with a high thrust chemical propulsion stage, would be suitable for human missions to Mars. Two recent assessments, independently conducted by the National Academies for Science, Engineering, and Medicine and the NASA Engineering & Safety Center, concluded that the technologies required for a high-power NEP system are immature and the attendant risks insufficiently quantified to justify initiating a flight project. For NEP to be available as a viable option to meet flight opportunities in the late 2030s / 2040s time frame, development of the key sub-systems must begin now. SNP has subdivided the NEP system into five Critical Technology Elements (CTE): the nuclear reactor, power conversion, power management and distribution, electric propulsion sub-system, and the primary heat rejection system. Development plans for each of these CTEs have been drafted which will serve as the template for a focused milestone-driven research and development campaign intended to advance each CTE to Technology Readiness Level (TRL) 5. This will be accomplished by building and testing hardware at relevant power levels (~ 1 MW) and for relevant durations (2,500 hours, ~10% of the required operational lifetime) and conducting numerical modeling of the CTEs anchored by the accumulated test data to predict system performance and reliability. Concurrent with this work, high-level coupled system/mission modeling will be carried out to refine the key performance parameters that the various CTEs must achieve. Non-advocate reviews will be held at milestone points to assess progress and inform down-select decisions. The strategy for formulating the TMP was described previously*; this paper describes ongoing progress on the drafting and baselining of the plan, including key specific details. * “Strategy for Developing Technologies for Megawatt-class Nuclear Electric Propulsion Systems”, K.A. Polzin, et. al., International Electric Propulsion Conference IEPC 2022, IEPC-2022-155

Nuclear Electric Propulsion↗
NASA NTRSDate not supplied

A Dominant Arabidopsis Thaliana ACTIN7 Mutant for Studies of Cytoskeletal-Mediated Root Gravity and Spaceflight Stress Responses

A forward genetic screen for Arabidopsis thaliana mutants that exhibited differential sensitivity to the actin-disrupting compound, latrunculin B (LatB), was conducted to uncover new players involved in actin-mediated root gravity responses. This to the isolation of a mutant that exhibited robust primary root growth at 100 nM LatB, which is a concentration that severely inhibits wild-type root elongation. Phenotypic analysis revealed that hypocotyl elongation in the dark and root hair tip growth in the mutant could tolerate LatB concentrations that impaired these processes in wild type. A cross between the mutant and wild type resulted in progeny resistance to LatB, which indicated that the mutant is dominant (hereafter referred to as LBR1 for LatB Resistant1). Filamentous-actin (F-actin) organization in LBR1 primary roots remained intact at 100 nM LatB, while that of wild type exhibited fragmented F-actin. Next generation sequencing revealed that LBR1 had a single nucleotide polymorphism (SNP) in the AT5G09810 gene that changed cytosine to a thiamine at the first exon. AT5G09810 encodes ACTIN7 (ACT7), which is one of three vegetative actin isoforms in A. thaliana. The SNP in the ACT7 gene led to a change in a single amino acid from proline at position 32 to a serine. Transgenic complementation of LBR1 plants with wild-type ACT7 under the control of the ACT7 promoter (pACT7:ACT7) and wild-type plants with LBR1, which contained the proline to serine mutation, also under the ACT7 promoter (pACT7:LBR1) confirmed that LBR1 is ACT7. The pACT7:LBR1 construct was also able to confer LatB resistance to the act7-5 and act2-3 vegetative ACT mutants. Moreover, LBR1 exhibited partial tolerance to salt and low phosphate, and enhanced root skewing on a clinostat, suggesting that site-directed engineering of vegetative ACT presents a strategy for generating stress-tolerant plants for spaceflight applications and studies of actin-mediated gravity responses.

Plant Space Biology↗
NASA NTRSDate not supplied

A Dominant Arabidopsis Thaliana ACTIN7 Mutant for Studies of Cytoskeletal-Mediated Root Gravity and Spaceflight Stress Responses

A forward genetic screen for Arabidopsis thaliana mutants that exhibited differential sensitivity to the actin-disrupting compound, latrunculin B (LatB), was conducted to uncover new players involved in actin-mediated root gravity responses. This led to the isolation of a mutant that exhibited robust primary root growth at 100 nM LatB, which is a concentration that severely inhibits wild-type root elongation. Phenotypic analysis revealed that hypocotyl elongation in the dark and root hair tip growth in the mutant could tolerate LatB concentrations that impaired these processes in wild type. A cross between the mutant and wild type resulted in progeny resistance to LatB, which indicated that the mutant is dominant (hereafter referred to as LBR1 for LatB Resistant1). Filamentous-actin (F-actin) organization in LBR1 primary roots remained intact at 100 nM LatB, while that of wild type exhibited fragmented F-actin. Next generation sequencing revealed that LBR1 had a single nucleotide polymorphism (SNP) in the AT5G09810 gene that changed cytosine to a thiamine at the first exon. AT5G09810 encodes ACTIN7 (ACT7), which is one of three vegetative actin isoforms in A. thaliana. The SNP in the ACT7 gene led to a change in a single amino acid from proline at position 32 to a serine. Transgenic complementation of LBR1 plants with wild-type ACT7 under the control of the ACT7 promoter (pACT7:ACT7) and wild-type plants with LBR1, which contained the proline to serine mutation, also under the ACT7 promoter (pACT7:LBR1) confirmed that LBR1 is ACT7. The pACT7:LBR1 construct was also able to confer LatB resistance to the act7-5 and act2-3 vegetative ACT mutants. Moreover, LBR1 exhibited partial tolerance to salt and low phosphate, and enhanced root skewing on a clinostat, suggesting that site-directed engineering of vegetative ACT presents a strategy for generating stress-tolerant plants for spaceflight applications and studies of actin-mediated gravity responses.

Plant Space Biology↗
NASA NTRSDate not supplied

Sensitivity Analysis of Heat Rejection and Propellant Management Technologies for Nuclear Thermal Propulsion Architectures

Cryogenic fluid management (CFM) technologies are very important for enabling a wider range of missions to utilize space nuclear propulsion (SNP) concepts such as nuclear thermal propulsion (NTP). Technologies for thermal and cryogenic propellant management allow for vehicles to take full advantage of the higher efficiency NTP systems for longer duration human interplanetary and deep space robotic missions. Currently, the CFM Portfolio Project at NASA’s Marshall Space Flight Center (MSFC) is developing thermal and propellant management technologies needed for SNP. When developing these technologies, it is important to understand the sensitivities of key performance parameters (KPPs) at the system and overall mission level due to the ways the technologies interact with each other, other subsystems, and influence the overall vehicle. The Advanced Concepts Office (ACO) at NASA-MSFC was tasked with building an integrated system model of a human Mars NTP mission to evaluate the impacts and sensitivities of CFM technologies on the overall vehicle and mission. This paper will cover the buildup of the model and highlight major sensitivities and breakpoints encountered, as well as future work in improving the existing models and sensitivities being evaluated.

Robert J. Hetterich↗
NASA NTRSDate not supplied

Sensitivity Analysis of Heat Rejection and Propellant Management Technologies for Nuclear Thermal Propulsion Architectures

Cryogenic fluid management (CFM) technologies are very important for enabling a wider range of missions to utilize space nuclear propulsion (SNP) concepts such as nuclear thermal propulsion (NTP). Technologies for thermal and cryogenic propellant management allow for vehicles to take full advantage of the higher efficiency NTP systems for longer duration human interplanetary and deep space robotic missions. Currently, the CFM Portfolio Project at NASA’s Marshall Space Flight Center (MSFC) is developing thermal and propellant management technologies needed for SNP. When developing these technologies, it is important to understand the sensitivities of key performance parameters (KPPs) at the system and overall mission level due to the ways the technologies interact with each other, other subsystems, and influence the overall vehicle. The Advanced Concepts Office (ACO) at NASA-MSFC was tasked with building an integrated system model of a human Mars NTP mission to evaluate the impacts and sensitivities of CFM technologies on the overall vehicle and mission. This paper will cover the buildup of the model and highlight major sensitivities and breakpoints encountered, as well as future work in improving the existing models and sensitivities being evaluated.

Robert J Hetterich↗
NASA NTRS2026

Space Nuclear Propulsion for Space Applications: Multi-Mission Nuclear Thermal Propulsion Vehicle Design

This NASA Technical Memorandum (TM) is intended to capture design work that the Advanced Concepts Office (ACO) at NASA’s Marshall Space Flight Center (MSFC) performed on behalf of the Space Nuclear Propulsion (SNP) Project during an SNP-driven design and mission analysis initiative in FY2025. Specifically, this TM focuses on several spacecraft design concepts intended to explore the feasibility of nuclear thermal propulsion (NTP) for use in a selection of notional, unmanned space missions. While references to the missions will be made in this TM, the primary focus will be on the spacecraft design concepts themselves, the ground rules and assumptions used for designing the spacecraft, a description of the various subsystems and their performance parameters, and the methodologies used to design them. The TM will also highlight areas of future work and additional considerations that may need to be taken into account when evaluating the feasibility of NTP space systems for other applications. The report will discuss the results from ACO’s analysis as they pertain to the different vehicle concepts that were evaluated. Each discipline section in this report will discuss the discipline-specific ground rules and assumptions, the methodology and design approaches employed, and present the results along with any relevant discussion, and highlight areas of future work where applicable.

Mitchell A Rodriguez↗
DOE OSTI2026

Populus_trichocarpa_Breeding_Population_SNPs

These data are from the manuscript “Application of Genomic Prediction in a Populus trichocarpa Breeding Program”, by Brian J. Stanton, David Macaya-Sanz, Chanaka Roshan Abeyratne, David Kainer, Kathy Haiby, Austin Himes, Carlos Gantz, Gerald A. Tuskan, and Stephen P. DiFazio. The data are based on genome resequencing to approximately 10X depth on two collections of Populus trichocarpa trees from Oregon, Washington, California, and British Columbia. The first collection consists of 293 genets collected by Poplar Innovations LLC for a breeding program. The second collection consists of 961 trees collected for the purpose of genome-wide association studies. These genets were sequenced using short, paired-end Illumina sequence reads (Chhetri et al. 2019). Reads were aligned to the P. trichocarpa ′Stettler-14′ reference (Hofmeister et al. 2020), with minor modifications to correct mis-assemblies (Zhou et al. 2020), and variants were called as per methods described in (Abeyratne et al. 2023). Identified variants were filtered using GATK’s VariantFiltration tool (DePristo et al. 2011), with filter expression flag set to “AF < 0.01 || AF > 0.99 || QD < 10.0 || ExcessHet > 20.0 || FS > 10.0 || MQ < 58.0”. SNPs with severe departures from Hardy−Weinberg expectations (exact-test p< 0.01) were also removed using vcftools --hwe flag (Danecek et al. 2011), resulting in 15,627,211 bi-allelic SNPs. The data included here consist of 141,903 high quality bi-allelic genome-wide SNPs obtained by further filtering the original SNP dataset using vcftools with flags --maf 0.05, --max-maf 0.95, --max-missing 0.95, --min-meanDP 10.75, --max-meanDP 43.00, --thin 2000. Collectively, these filtering parameters removed SNPs with 1) a minor allele frequency ≤ 0.05; 2) proportion of missing data for individual loci exceeding 5%; 3) sequencing depth more than 2X mean-depth or less than 0.5X mean-depth; or 4) a distance of

09 BIOMASS FUELS↗
DOE OSTI2022

Genetic mapping of sugarcane aphid resistance in sorghum line SC112-14

Sugarcane aphid [Melanaphis sacchari (Zehntner)] is a destructive pest that has had an economic effect on sorghum in North America since 2013. The identification, development, and use of resistant sorghum germplasm is the most feasible strategy to control the pest. Nevertheless, the genetic control of sugarcane aphid (SCA) resistance is unknown for most sorghum resistant lines. To identify the genetic regions that confer SCA resistance in sorghum line SC112-14, 103 recombinant inbred lines (RILs) derived by its cross with the susceptible line PI 609251 were evaluated for their SCA resistance response in Georgia during two consecutive years. The resistance response was determined based on two ratings (2 wk apart) for aphid population size (APS) and aphid-induced plant damage (APD) each year. Segregation for SCA resistance was observed for the first APS and both APD ratings, and the broad-sense heritability estimate ranged from .71 to .76, respectively. A quantitative trait locus analysis using a high-density linkage map of 3,852 single nucleotide polymorphisms (SNPs) detected an 81-kb genomic region on chromosome 6 that explained 50–55% of the phenotypic variation. Comparative mapping analysis found that the resistance locus in SC112-14 is located 8- and 10-cM upstream of the Henong 16 (RMES1) and Tx2783 resistance loci, respectively, and encloses the SNP Sbv3.1_06_2316351 associated in Haitian resistant lines. Therefore, the line SC112-14 is an additional SCA resistance source that can be combined or strategically used with other resistance sources to assure a more robust host plant resistance to the SCA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping

Abstract Camelina [ Camelina sativa (L.) Crantz] is an oilseed crop in the Brassicaceae family that is currently being developed as a source of bioenergy and healthy fatty acids. To facilitate modern breeding efforts through marker‐assisted selection and biotechnology, we evaluated genetic variation among a worldwide collection of 222 camelina accessions. We performed whole‐genome resequencing to obtain single nucleotide polymorphism (SNP) markers and to analyze genomic diversity. We also conducted phenotypic field evaluations in two consecutive seasons for variations in key agronomic traits related to oilseed production such as seed size, oil content (OC), fatty acid composition, and flowering time. We determined the population structure of the camelina accessions using 161,301 SNPs. Further, we identified quantitative trait loci (QTL) and candidate genes controlling the above field‐evaluated traits by genome‐wide association studies (GWAS) complemented with linkage mapping using a recombinant inbred line (RIL) population. Characterization of the natural variation at the genome and phenotypic levels provides valuable resources to camelina genetic studies and crop improvement. The QTL and candidate genes should assist in breeding of advanced camelina varieties that can be integrated into the cropping systems for the production of high yield of oils of desired fatty acid composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Linkage map construction using limited parental genotypic information

Abstract Genetic linkage maps based on single nucleotide polymorphisms (SNPs) represent an essential tool for a variety of genomic analyses. Today, next-generation sequencing (NGS) enables rapid genotyping of different mapping populations based on thousands of SNPs and the construction of highly saturated linkage maps. Nevertheless, missing data in the genotyping of the parental lines creates a bottleneck that determines the number of SNPs that can be used for the linkage map. As a proof of concept, a highly saturated genetic linkage map was constructed using the imputed genotypic data of a recombinant inbred line (RIL) population and the limited genotypic information of its parental lines. Two ABH genotype files were created from a pseudo-parental genotypic data set that includes all the SNPs present in the RIL population. In the first ABH file pseudo-parental 1 was considered parental A, while in the second pseudo-parental 1 was considered parental B. These two duplicate ABH genotype files were merged by chromosome and subjected to linkage map analysis. Since the ABH data were duplicated, two mirrored linkage groups were generated per chromosome. The correct linkage map was identified and selected based on the partial genotypic data of the parental lines. This strategy was effective for constructing a highly saturated linkage map of 33,421 SNPs based on the genotyping of 205 RILs and a limited number of 100 SNPs present in the parental lines. This strategy enables the use of all the NGS SNP data obtained from a low-coverage sequencing experiment in the mapping population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genetic architecture of leaf morphological and physiological traits in a Populus deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ pedigree revealed by quantitative trait locus analysis

Understanding the genetic architecture of leaf morphological and physiological traits will help plant breeders develop high biomass poplar genotypes. Quantitative trait locus (QTL) studies combining next-generation sequencing techniques can advance our understanding of the genetic basis of complex traits. In this study, we measured 13 leaf morphological and physiological traits and identified quantitative trait loci (QTLs) in a Populus deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ F1 population (500 progenies) using a high-density genetic map constructed by whole genome re-sequencing. This linkage map consisted of 5796 single nucleotide polymorphism (SNP) markers assigned to 19 linkage groups (LGs), spanning 2683.80 centimorgans (cM) of genetic length, with an average marker density of 0.46 cM. We identified 109 QTLs on 18 LGs for leaf morphological traits and 55 QTLs on 14 LGs for leaf physiological traits. One-hundred eight putative candidate genes were identified within the candidate genomic region. Co-expression network and gene ontology enrichment analyses suggested that these candidate genes were involved in the photosynthetic process. The differential expression patterns of the CYCLIN (Potri.015G112200) and RED CHLOROPHYLL REDUCTASE (Potri.007G043600) genes between two parents indicated their potential roles in leaf morphological and physiological traits. These findings decipher the genetic architecture of leaf morphological and physiological traits in the P. deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ pedigree and provide candidate genes for future poplar genetic improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A compact electromagnetic neutron nutator for precise neutron spin manipulation

A superconducting electromagnetic nutator (EMN) capable of generating a magnetic field vector along an arbitrary direction on a 2D plane has been designed. Its performance in precisely manipulating the neutron polarization vector has been tested at the HB2-D polarized development beamline at the High Flux Isotope Reactor. Unlike mechanical nutators that require physical handling or motor-driven actuation to rotate the magnetic field, the magnitude and orientation of the magnetic field produced by the EMN can be controlled electromagnetically. Further, the compact design (~15 mm depth, not including cryogenic housing) of this device ensures ease of coupling within existing superconducting neutron spin manipulation devices, such as magnetic Wollaston prisms (MWP), resonant radio frequency (RF) flippers, spherical neutron polarimetry (SNP) devices, etc.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Unraveling plant phenotype to genotype associations with daily hyperspectral traits in Populus trichocarpa

Hyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales. In this study, we combined tower-based continuous hyperspectral sensing with genome-wide association studies to analyze 1423 wavebands (400-900 nm) and derivative vegetation indices across 505 genotypes and the genetic architecture of hyperspectral phenotypes over time in Populus trichocarpa Torr. & Gray grown under field conditions. Wavelengths related to chlorophyll and carotenoid absorption spectra exhibited the strongest genetic variation resulting in 98 significant SNP associations. Notably, we found substantial overlap in genetic association between the blue and red spectral regions, indicative of carotenoids and chlorophyll, respectively, and identified more than 10 candidate genes associated with chloroplast function, underpinning photosynthetic activity. Furthermore, fluctuations in associations for vegetative indices, such as the chlorophyll:carotenoid index (CCI), across the growing season reveal a temporally dynamic genetic architecture of physiological traits associated with fall senescence of this temperate tree species. Finally, we also observed correlations (spearman rho = 0.3, p < 1x10 −8 ) between individual wavebands or vegetative indices and growth rate, assessed as the relative change of tree height over the growing season. The growth rate prediction was substantially improved by a regularization multivariate model (spearman rho>0.5, p < 1x10 −16 ), reinforcing the value of hyperspectral measurements for predicting traits linked to tree productivity. These findings highlight the potential of high-throughput, rapid, hyperspectral genome wide association studies GWAS to uncover physiologically meaningful genetic variation and offer promising insights for future acceleration for plant breeding.

09 BIOMASS FUELS↗
DOE OSTI2026

A Multiplexed Quantitative Analysis of Germline Single Amino Acid Variants by Targeted Proteomics in Nondepleted Human Plasma

Single amino acid variants (SAAVs) in protein sequences are often a direct result of single-nucleotide polymorphisms (SNPs). Certain germline SAAVs have shown biological relevance in different disease conditions but lack precise quantification in circulation, which could hinder functional investigations and progress in biomarker development. Here, we have developed a multiplexed liquid chromatography-selected reaction monitoring (LC-SRM) assay that monitors 5 wild-type and variant peptide pairs (Complement Factor B: CFB-R32Q/R32W, Clusterin: CLU-N317H, Fetuin B: FETUB-K360R, and Kininogen: KNG1-L212P) in nondepleted human plasma. The assay was optimized for imprecision, linearity, stability, and calibration assessments with CVs of under 20%. The wild-type and variant peptide pairs were characterized in a set of healthy individual plasma samples. These target identifications were also validated by SNP genotyping with more than 99% accuracy. For all protein targets, we observed significantly lower concentrations of WT species in the presence variant peptides. In CFB, the concentration of R32Q was significantly lower than its counterpart R32W variant and WT species. Furthermore, our results distinguished phenotypes of homozygosity and heterozygosity of the SAAV presence through direct concentration level characterization. These findings provide some insights into how SAAVs affect quantitative assessments of target peptides. The assay demonstrates a platform for proteogenomic analyses with potential applications in both research and clinical settings.

genetics↗
DOE OSTI2021

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Here, using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A genomic data archive from the Network for Pancreatic Organ donors with Diabetes

The Network for Pancreatic Organ donors with Diabetes (nPOD) is the largest biorepository of human pancreata and associated immune organs from donors with type 1 diabetes (T1D), maturity-onset diabetes of the young (MODY), cystic fibrosis-related diabetes (CFRD), type 2 diabetes (T2D), gestational diabetes, islet autoantibody positivity (AAb+), and without diabetes. nPOD recovers, processes, analyzes, and distributes high-quality biospecimens, collected using optimized standard operating procedures, and associated de-identified data/metadata to researchers around the world. Herein describes the release of high-parameter genotyping data from this collection. 372 donors were genotyped using a custom precision medicine single nucleotide polymorphism (SNP) microarray. Data were technically validated using published algorithms to evaluate donor relatedness, ancestry, imputed HLA, and T1D genetic risk score. Additionally, 207 donors were assessed for rare known and novel coding region variants via whole exome sequencing (WES). These data are publicly-available to enable genotype-specific sample requests and the study of novel genotype:phenotype associations, aiding in the mission of nPOD to enhance understanding of diabetes pathogenesis to promote the development of novel therapies.

59 BASIC BIOLOGICAL SCIENCES↗