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At least 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Maast: genotyping thousands of microbial strains efficiently

Existing single nucleotide polymorphism (SNP) genotyping algorithms do not scale for species with thousands of sequenced strains, nor do they account for conspecific redundancy. Here we present a bioinformatics tool, Maast, which empowers population genetic meta-analysis of microbes at an unrivaled scale. Maast implements a novel algorithm to heuristically identify a minimal set of diverse conspecific genomes, then constructs a reliable SNP panel for each species, and enables rapid and accurate genotyping using a hybrid of whole-genome alignment and k-mer exact matching. We demonstrate Maast’s utility by genotyping thousands of Helicobacter pylori strains and tracking SARS-CoV-2 diversification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Solid-state NMR of unlabeled plant cell walls: high-resolution structural analysis without isotopic enrichment

Abstract Background Multidimensional solid-state nuclear magnetic resonance (ssNMR) spectroscopy has emerged as an indispensable technique for resolving polymer structure and intermolecular packing in primary and secondary plant cell walls. Isotope ( 13 C) enrichment provides feasible sensitivity for measuring 2D/3D correlation spectra, but this time-consuming procedure and its associated expenses have restricted the application of ssNMR in lignocellulose analysis. Results Here, we present a method that relies on the sensitivity-enhancing technique Dynamic Nuclear Polarization (DNP) to eliminate the need for 13 C-labeling. With a 26-fold sensitivity enhancement, a series of 2D 13 C– 13 C correlation spectra were successfully collected using the unlabeled stems of wild-type Oryza sativa (rice). The atomic resolution allows us to observe a large number of intramolecular cross peaks for fully revealing the polymorphic structure of cellulose and xylan. NMR relaxation and dipolar order parameters further suggest a sophisticated change of molecular motions in a ctl1 ctl2 double mutant: both cellulose and xylan have become more dynamic on the nanosecond and microsecond timescale, but the motional amplitudes are uniformly small for both polysaccharides. Conclusions By skipping isotopic labeling, the DNP strategy demonstrated here is universally extendable to all lignocellulose materials. This time-efficient method has landed the technical foundation for understanding polysaccharide structure and cell wall assembly in a large variety of plant tissues and species.

09 BIOMASS FUELS↗
DOE OSTI2022

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro - and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ( π and θ ), and selective pressures (pN/pS and Tajima’s D ) within and fixation indices ( F ST ) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ( π ) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro - and microdiversity across microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability

Accurate predictions of the pathogenicity of mutations associated with genetic diseases are key to the success of precision medicine. Inherited missense mutations in the myocilin (MYOC) gene, within its olfactomedin (OLF) domain, constitute the strongest genetic link to primary open-angle glaucoma via a toxic gain of function, and thus MYOC is an attractive precision-medicine target. However, not all mutations in MYOC cause glaucoma, and common variants are expected to be neutral polymorphisms. The Genome Aggregation Database (gnomAD) lists ~100 missense variants documented within OLF, all of which are relatively rare (allele frequency <0.001%) and nearly all are of unknown pathogenicity. To distinguish disease-causing OLF variants from benign OLF variants, we first characterized the most prevalent population-based variants using a suite of cellular and biophysical assays, and identified two variants with features of aggregation-prone familial disease variants. Next, we considered all available biochemical and clinical data to demonstrate that pathogenic and benign variants can be differentiated statistically based on a single metric: the thermal stability of OLF. Our results motivate genotyping MYOC in patients for clinical monitoring of this widespread, painless and irreversible ocular disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data for Genome-Wide Association and Genomic Prediction for Yield and Component Traits of Miscanthus sacchariflorus

Accelerating biomass improvement is a major goal of miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of miscanthus breeding. The present study conducted genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single-nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus .

Biomass Analytics↗
DOE OSTI2025

RatXcan: A framework for cross-species integration of genome-wide association and gene expression data

Genome-wide association studies (GWAS) have implicated specific alleles and genes as risk factors for numerous complex traits. However, translating GWAS results into biologically and therapeutically meaningful discoveries remains extremely challenging. Most GWAS results identify noncoding regions of the genome, suggesting that differences in gene regulation are the major driver of trait variability. To better integrate GWAS results with gene regulatory polymorphisms, we previously developed PrediXcan (also known as “transcriptome-wide association studies” orTWAS), which maps SNPs to predicted gene expression using GWAS data. In this study, we developed RatXcan, a framework that extends this methodology to outbred heterogeneous stock (HS) rats. RatXcan accounts for the close familial relationships among HS rats by modeling the relatedness with a random effect that encodes the genetic relatedness. RatXcan also corrects for polygenic-driven inflation because of the equivalence between a relatedness random effect and the infinitesimal polygenic model. To develop RatXcan, we trained transcript predictors for 8,934 genes using reference genotype and expression data from five rat brain regions. We found that the cis genetic architecture of gene expression in both rats and humans was sparse and similar across brain tissues. We tested the association between predicted expression in rats and two example traits (body length and BMI) using phenotype and genotype data from 5,401 densely genotyped HS rats and identified a significant enrichment between the genes associated with rat and human body length and BMI. Thus, RatXcan represents a valuable tool for identifying the relationship between gene expression and phenotypes across species and paves the way to explore shared biological mechanisms of complex traits.

Genetics & Heredity↗
DOE OSTI2022

A large accessory genome and high recombination rates may influence global distribution and broad host range of the fungal plant pathogen Claviceps purpurea

Pangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (~ 38%), high recombination rates (ρ = 0.044), and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion may be controlled by frequent recombination. We additionally identified that within the ergoline biosynthetic cluster the lpsA1 and lpsA2 were the result of a recombination event. However, the high recombination rates observed in C. purpurea may be influencing an overall trend of purifying selection across the genome. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular basis of P[II] major human rotavirus VP8* domain recognition of histo-blood group antigens

Initial cell attachment of rotavirus (RV) to specific cell surface glycan receptors, which is the essential first step in RV infection, is mediated by the VP8* domain of the spike protein VP4. Recently, human histo-blood group antigens (HBGAs) have been identified as receptors or attachment factors for human RV strains. RV strains in the P[4] and P[8] genotypes of the P[II] genogroup share common recognition of the Lewis b (Le b ) and H type 1 antigens, however, the molecular basis of receptor recognition by the major human P[8] RVs remains unknown due to lack of experimental structural information. Here, we used nuclear magnetic resonance (NMR) spectroscopy-based titration experiments and NMR-derived high ambiguity driven docking (HADDOCK) methods to elucidate the molecular basis for P[8] VP8* recognition of the Leb (LNDFH I) and type 1 HBGAs. We also used X-ray crystallography to determine the molecular details underlying P[6] recognition of H type 1 HBGAs. Unlike P[6]/P[19] VP8*s that recognize H type 1 HBGAs in a binding surface composed of an α-helix and a β-sheet, referred as the “βα binding site”, the P[8] and P[4] VP8*s bind Le b HBGAs in a previously undescribed pocket formed by the edges of two β-sheets, referred to as the “ββ binding site”. Importantly, the P[8] and P[4] VP8*s retain binding capability to non-Le b type 1 HBGAs using the βα binding site. The presence of two distinct binding sites for Le b and non-Le b HBGA glycans in the P[8] and P[4] VP8* domains suggests host-pathogen co-evolution under structural and functional adaptation of RV pathogens to host glycan polymorphisms. Assessment and understanding of the precise impact of this co-evolutionary process in determining RV host ranges and cross-species RV transmission should facilitate improved RV vaccine development and prediction of future RV strain emergence and epidemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Synthesis and structural characterization of orthorhombic Cu 3– δ Sb ( δ ≈ 0.1) and hexagonal Cu 3 Sb 1–x In x (x ≈ 0.2) phases

Cu 3 Sb is a known copper-rich phase in the Cu–Sb binary phase diagram. It is reported to be dimorphic, with a low-temperature form adopting the orthorhombic Cu 3 Ti structure type (space group Pmmn , No. 59). The high-temperature form crystallizes in the cubic space group F m 3 - m $Fm&#x203e;{3}m$ (No. 225), and is isostructural with BiF 3 . Neither polymorph has been carefully characterized to date, with both structures being assigned to the respective structure type, but never refined. With this study, we provide structural evidence, based on single-crystal and powder X-ray diffraction data that the low-temperature orthorhombic phase exists with a significant amount of defects on one of the Cu-sites. As a result, its composition is not Cu 3 Sb, but rather Cu 3– δ Sb ( δ = 0.13(1)). The cubic form could not be accessed as a part of this study, but another Cu-rich phase, Cu 3 Sb ≈0.8 In ≈0.2 , was also identified. It adopts the hexagonal Ni 3 Sn structure type (space group P 6 3 / mmc , No. 194) and represents an In-substituted variant of a hitherto unknown structural modification of Cu 3 Sb. Whether the latter can exist as a binary phase, or what is the minimum amount of In inclusions needed to stabilize it remains to be determined. Measurements of the thermopower of Cu 3– δ Sb ( δ = 0.13(1)) were conducted in the range of 300–600 K and demonstrated a maximum value of ca. 50 μV/K at 600 K, indicative of a p -type transport mechanism. Electrical resistivity measurements for the same sample confirmed that it exhibits metallic-like behavior, with a room temperature value of 0.43 mΩ cm. Electronic structure calculations show the absence of a band gap. Thermal analysis was utilized to ascertain the congruent melting of both phases.

Crystallography↗
DOE OSTI2023

Molecular and functional properties of human Plasmodium falciparum CSP C-terminus antibodies

Human monoclonal antibodies (mAbs) against the central repeat and junction domain of Plasmodium falciparum circumsporozoite protein (PfCSP) have been studied extensively to guide malaria vaccine design compared to antibodies against the PfCSP C terminus. Here, we describe the molecular characteristics and protective potential of 73 germline and mutated human mAbs against the highly immunogenic PfCSP C-terminal domain. Two mAbs recognized linear epitopes in the C-terminal linker with sequence similarity to repeat and junction motifs, whereas all others targeted conformational epitopes in the α-thrombospondin repeat (α-TSR) domain. Specificity for the polymorphic Th2R/Th3R but not the conserved RII+/CS.T3 region in the α-TSR was associated with IGHV3-21/IGVL3-21 or IGLV3-1 gene usage. Although the C terminus specific mAbs showed signs of more efficient affinity maturation and class-switching compared to anti-repeat mAbs, live sporozoite binding and inhibitory activity was limited to a single C-linker reactive mAb with cross-reactivity to the central repeat and junction. The data provide novel insights in the human anti-C-linker and anti-α-TSR antibody response that support exclusion of the PfCSP C terminus from malaria vaccine designs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Genomic Dissection of Anthracnose ( Colletotrichum sublineolum ) Resistance Response in Sorghum Differential Line SC112-14

Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum , is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F 2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.

Genetics & Heredity↗
DOE OSTI2020

QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants

Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. Although it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. The average precision was 0.027 for Arabidopsis and 0.029 for rice. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validated Sorghum bicolor and Setaria viridis models. The S. bicolor model was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. Furthermore, we applied the S. viridis model and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The influence of Al2O3 on the structural properties of MgSiO3 akimotoite

Abstract Akimotoite, a MgSiO3 polymorph present in the lower transition zone within ultramafic portions of subducting slabs and potentially also in the ambient mantle, will partition some amount of Al, raising the question of how this will affect its crystal structure and properties. In this study, a series of samples along the MgSiO3-Al2O3 (akimotoite-corundum) solid solution have been investigated by means of single-crystal X-ray diffraction to examine their crystal chemistry. Results show a strong nonlinear behavior of the a- and c-axes as a function of Al content, which arises from fundamentally different accommodation mechanisms in the akimotoite and corundum structures. Furthermore, two Al2O3-bearing akimotoite samples were investigated at high pressure to determine the different compression mechanisms associated with Al substitution. Al2O3-bearing akimotoite becomes more compressible at least up to 20 mol% Al2O3, due likely to an increase in compressibility as the Al cation is incorporated into the SiO6 octahedron. This observation is in strong contrast to the stiffer corundum end-member having a KT = 250 GPa, which is larger than that of the akimotoite end-member [KT = 205(1) GPa]. These findings have implications for mineral physics models of elastic properties, which have in the past assumed linear mixing behavior between the MgSiO3 akimotoite and Al2O3 corundum end-members to calculate sound wave velocities for Al-bearing akimotoite at high pressure and temperature.

Geochemistry & Geophysics↗
DOE OSTI2023

Thermal equation of state of ice-VII revisited by single-crystal X-ray diffraction

Abstract Ice-VII is a high-pressure polymorph of H2O ice and an important mineral widely present in many planetary environments, such as in the interiors of large icy planetary bodies, within some cold subducted slabs, and in diamonds of deep origin as mineral inclusions. However, its stability at high pressures and high temperatures and thermoelastic properties are still under debate. In this study, we synthesized ice-VII single crystals in externally heated diamond-anvil cells and conducted single-crystal X-ray diffraction experiments up to 78 GPa and 1000 K to revisit the high-pressure and high-temperature phase stability and thermoelastic properties of ice-VII. No obvious unit-cell volume discontinuity or strain anomaly of the high-pressure ice was observed up to the highest achieved pressures and temperatures. The volume-pressure-temperature data were fitted to a high-temperature Birch-Murnaghan equation of state formalism, yielding bulk modulus KT0 = 21.0(4) GPa, its first pressure derivative KT0′ = 4.45(6), dK/dT = –0.009(4) GPa/K, and thermal expansion relation αT = 15(5) × 10–5 + 15(8) × 10–8 × (T – 300) K–1. The determined phase stability and thermoelastic properties of ice-VII can be used to model the inner structure of icy cosmic bodies. Combined with the thermoelastic properties of diamonds, we can reconstruct the isomeke P-T paths of ice-VII inclusions in diamond from depth, offering clues on the water-rich regions in Earth’s deep mantle and the formation environments of those diamonds.

Geochemistry & Geophysics↗
DOE OSTI2026

Raman spectroscopic investigation of ianthinite [U$_2^{4+}$(UO$_2$)$_4$O$_6$(OH)$_4$(H$_2$O)$_4$]·$5$H$_2$O, a rare mixed-valence uranium oxide hydrate

Ianthinite ([[U$_2^{4+}$(UO$_2$)$_4$O$_6$(OH)$_4$(H$_2$O)$_4$]·$5$H$_2$O) is an exotic mineral that possesses U in both tetravalent and hexavalent oxidation states and is structurally related to the U 3 O 8 polymorphs, which are commonly encountered technogenic materials in the nuclear fuel cycle. Despite the similarities between U 3 O 8 and ianthinite, and the importance of ianthinite in U paragenesis, no Raman spectra have been reported for this mineral. Here, to gain a more complete understanding of how structural attributes of ianthinite give rise to observable spectroscopic features and how these may relate to important materials in the nuclear fuel cycle, we provide, for the first time, Raman spectra of ianthinite. Ianthinite readily oxidizes at ambient conditions, complicating analysis of phase-pure material. Several analytical methods are employed herein to decouple the Raman features of ianthinite from its alteration product(s). First, a simple difference spectrum is presented, then results of Raman spectroscopic mapping are employed, and finally, we use a novel processing and analysis method. Each analysis method provides different insight into structural features that are unique to ianthinite, in particular, features that are attributable to U(IV) in distorted octahedral coordination in both ianthinite and U 3 O 8 phases.

Spano, Tyler L. [Oak Ridge National Laboratory (OR↗
DOE OSTI2023

Genomic dissection of anthracnose resistance response in sorghum [Sorghum bicolor (L.) Moench]

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important grain crop behind maize, wheat, rice, and barley. Today, it is of interest as a source of fermentable sugars for the production of renewable fuels and chemicals, and as a source of biomass for co-firing. The productivity and profitability of sorghum are limited by several biotic constraints, most notably anthracnose caused by the fungal pathogen Colletotrichum sublineolum. The most cost-effective and environmentally benign strategy to control anthracnose is through the incorporation of resistance genes. Over the last three years, our research efforts have been directed to identify new sources of resistance in temperate adapted and tropical germplasm, and to delimited genomic regions associated with the observe anthracnose resistant response. Three biparental mapping populations derived from the resistant lines SC112-14, QL3 and IS18760 were evaluated for anthracnose resistance response in Texas, Georgia, Florida and Puerto Rico. In parallel, three high density recombination maps were constructed and used to identify resistant loci. Anthracnose resistant response in line SC112-14 is controlled by a major locus on chromosome 5. Segregation analysis of 1,500 progenies delimited the resistance locus on chromosome 5 to a 23-kb region harboring three candidate genes, including Sobic.005G17230 identified by GWAS of the sorghum association panel (SAP). The latter gene belongs to a family of genes encoding F-box proteins indicating that this resistance response involved in signaling cascades and transcriptional reprograming, rather than recognition of pathotype-associated molecular patterns. In contrast, anthracnose resistant response in lines QL3 and IS18760 is controlled by multiple small-effect genes. Greenhouse evaluation of a representative subset of the three mapping populations against nine pathotypes found that lines susceptible in the field could be resistant to a single pathotype in the greenhouse. Thus, the activation of a resistance response system by a single pathotype could not provide a broader resistance response against multiple pathotypes. The screening of 1,801 sweet sorghum accessions from the National Plant Germplasm System identified 654 accessions with Brix value larger than 10, which in turn was used to select a subset of 233 accessions for evaluation of anthracnose resistant response. Even though most of the accessions were not completely infected by anthracnose, 28 accessions were completely resistant against pathotypes from Texas, Georgia, Florida and Puerto Rico. Genotyping-by-sequencing analysis of this subset identified 157,843 single nucleotide polymorphisms. Population structure analysis of the subset based on a subset of 2,345 unlinked SNPs found that the genetic diversity could be divided into four populations. The genetic relatedness among accessions within populations suggests most of the resistant germplasm may contain few different resistance sources. These resistance sources present in sweet sorghum germplasm could expedite the development of new resistant sweet sorghum cultivars and hybrids by avoiding time-consuming introgression breeding approaches with non-sweet sorghums serving as donor of the resistance alleles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thermoelasticity Model for Lithium Fluoride

Lithium fluoride (LiF) is a typical ionic solid, and at the same time a typical polymorphic (multi-phase) material. Its phase diagram contains two solid phases, B1 (rock salt) and B2 (CsCl), which are typical of ionic solids. The phase diagram of LiF was suggested by Smirnov. We have carried out extensive study of the properties of LiF using one of the most recent versions of VASP (Vienna Ab initio Simulation Package) which allows one to carry out calculations on ionic solids; more detail will be presented elsewhere.

36 MATERIALS SCIENCE↗
DOE OSTI2020

MOCVD Growth and Characterization of Wide Bandgap ZnGeN 2 Thin Films

ZnGeN 2 is a wide bandgap material having less than 0.1% lattice mismatch with GaN and bandgap within few percent of that of GaN. Based on the first principle calculations, the valence band of ZnGeN 2 is situated ~1.4 eV above that of GaN at the heterointerface. Such a staggered band alignment between two closely lattice matched materials has already been demonstrated promising for novel optoelectronic device designs, for example, high efficiency blue and green light emitting diodes. However, the research on ZnGeN 2 is yet to pass the inceptive period. We report on the growth of single crystalline ZnGeN 2 films using metalorganic chemical vapor deposition and investigation on the crystalline, optical, electrical properties. Diethylzinc (DEZn), germane (GeH 4 ) and ammonia were used as the precursors for Zn, Ge and N, respectively. Films were grown on GaN and sapphire substrates. The Zn/Ge atomic ratio in the films determined from energy dispersive X-ray spectroscopy was found to decrease with increase in growth temperature but to increase with increase in pressure and DEZn/GeH 4 molar flow rate ratio. The X-ray diffraction (XRD) 2θ-ω spectra of the single crystalline ZnGeN 2 films resembled those of orthorhombic (perfectly ordered cations) or distorted wurtzite (disordered cations) polymorphs. High resolution scanning transmission electron microscopy imaging was used to further investigate the crystalline quality and crystalline structure of the films. The single crystalline films on c-sapphire or GaN substrates were found to have planar surface from scanning electron micrographs while those on r-sapphire substrate had stepped surface. No near band edge peak but a broad peak at ~2.05 eV was observed in the photoluminescence (PL) spectra, which was attributed to the transitions involving deep level defects. The PL excitation spectra peaked around 3.4 eV, which is due to the enhanced absorption of photons having energy close to the band gap. The as grown films were found to be n-type with 10 18 – 10 19 cm -3 carrier densities and mobility up to 17 cm 2 /V·s. In the end, the advancement made in this work regarding the growth of ZnGeN 2 thin films is a footstep towards the understanding of the material itself and in turn, towards the implementation of ZnGeN 2 based novel device designs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗