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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass

Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Evolutionary Analyses of Gene Expression Divergence in Panicum hallii : Exploring Constitutive and Plastic Responses Using Reciprocal Transplants

Abstract The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST–QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis–environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.

3′ TagSeq↗
DOE OSTI2021

Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis

Dark-induced senescence provokes profound metabolic shifts to recycle nutrients and to guarantee plant survival. To date, research on these processes has largely focused on characterizing mutants deficient in individual pathways. Here, we adopted a time-resolved genome-wide association-based approach to characterize dark-induced senescence by evaluating the photochemical efficiency and content of primary and lipid metabolites at the beginning, or after 3 or 6 days in darkness. We discovered six patterns of metabolic shifts and identified 215 associations with 81 candidate genes being involved in this process. Among these associations, we validated the roles of four genes associated with glycine, galactinol, threonine, and ornithine levels. We also demonstrated the function of threonine and galactinol catabolism during dark-induced senescence. Intriguingly, we determined that the association between tyrosine contents and TYROSINE AMINOTRANSFERASE 1 influences enzyme activity of the encoded protein and transcriptional activity of the gene under normal and dark conditions, respectively. Moreover, the single-nucleotide polymorphisms affecting the expression of THREONINE ALDOLASE 1 and the amino acid transporter gene AVT 1 B, respectively, only underlie the variation in threonine and glycine levels in the dark. Taken together, these results allow us to present a very detailed model of the metabolic aspects of dark-induced senescence, as well as the process itself.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.

Biochemistry & Molecular Biology↗
DOE OSTI2022

The Melampsora americana Population on Salix purpurea in the Great Lakes Region Is Highly Diverse with a Contributory Influence of Clonality

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons via genotyping-by-sequencing to identify single-nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high-density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas, with few sites showing moderate genetic differentiation. These data support the hypothesis of sexual recombination between growing seasons because no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs; however, there is also evidence of high genetic diversity of rust isolates in all settings. This work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.

Plant Sciences↗
DOE OSTI2024

Remarkably High Internal Transcribed Spacer Haplotype Diversity of the Fungal Select Agent Coniothyrium glycines Discovered Throughout Its Range in Sub-Saharan Africa

Red leaf blotch of soybean, caused by the fungus Coniothyrium glycines, is a foliar disease characterized by blotching, necrosis, and defoliation that has only been reported from Africa. The species is listed as a Select Agent by the Federal Select Agent Program due to its potentially devastating impacts to soybean production should it spread to the United States. Despite its potential import, very few isolates are available for study. Herein, we obtained 96 new C. glycines isolates from six soybean-producing countries throughout sub-Saharan Africa. Along with 12 previously collected ones, we sequenced each at the internal transcribed spacer (ITS) region. Between all isolates, we identified a total of 28 single-nucleotide polymorphisms and 23 haplotypes. One hypothesis to explain the tremendous diversity uncovered at the ITS—which is generally conserved within a species—is that our current species concept of C. glycines is too broad and that there may be multiple species that cause red leaf blotch. Zambia contained the highest haplotype diversity, a significant fraction of which remains unsampled. Most haplotypes were specific to a single country, except for two, which were found in Zambia and either neighboring Mozambique or Zimbabwe. This geographic specificity indicates that the ITS region may be useful for identifying source populations or routes of transmission should this pathogen spread beyond Africa. The observed geographic partitioning of this pathogen is likely the result of millions of years of replication on little-studied native hosts, given that soybean has only been cultivated in Africa since the early 1900s.

Plant Sciences↗
DOE OSTI2023

Stable and metastable structures of tin (IV) oxide at high pressure

We have analyzed SnO 2 with a combination of synchrotron X-ray diffraction and X-ray absorption spectroscopy across a pressure range of 0 → 82.9 GPa with thermal annealing by a CO 2 laser allowing access to all of the known high-density polymorphs of SnO 2 , and here report their crystallographic information. The metastability of the post-rutile α -PbO 2 and PdF 2 structures in SnO 2 are investigated by experiment and PW-DFT simulations, revealing a complex energetic landscape and suggesting a significant dependence of the observed phases on the pressure–temperature pathway taken in experiment.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Persistent trade-offs balance competition and colonization across centuries

When a microbe colonizes a host, it must both establish infection and outcompete other organisms. Short-term experiments show that gains in competitive ability can reduce colonization, creating trade-offs, but whether microbes resolve these conflicts over long evolutionary timescales is unknown. We show that a trade-off between competitive killing and host colonization has been stably maintained for centuries in natural Pseudomonas populations infecting Arabidopsis thaliana. Tailocins—phage-derived weapons—provide strong competitive advantages, yet their production reduces colonization success, explaining why the most broadly lethal variants remain rare. Genomic surveys and historical genomes spanning two centuries reveal that the polymorphisms underlying this trade-off have persisted across 10⁵-10⁶ generations. Understanding such long-lived constraints can inform antimicrobial strategies that exploit evolutionary trade-offs.

Backman, Talia↗
DOE OSTI2022

The western redcedar genome reveals low genetic diversity in a self-compatible conifer

We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete genome assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low for a continuous tree species, with many loci showing zero diversity, and the ratio of π at zero- to fourfold degenerate sites is relatively high (approximately 0.33), suggestive of weak purifying selection. Using an array of genetic lines derived from up to five generations of selfing, we explored the relationship between genetic diversity and mating system. Although overall heterozygosity was found to decline faster than expected during selfing, heterozygosity persisted at many loci, and nearly 100 loci were found to deviate from expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains responsive to natural and artificial selection, despite low genetic diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Equation of state of boron carbide B 4 ⁢C

We present the results of recent experiments conducted on the Sandia Z machine and a new tabular equation of state for B 4 ⁢C. The equation of state was calibrated to a combination of density functional calculations reported here and fits to preexisting data. It was constructed partly to recover the effects of a shock-driven, polymorphic phase transition of unknown character beginning at particle velocities of just under 3 km/s (shock pressures of 95 GPa). Some of the Z experiments included sound speeds determined by the overtaking rarefaction method, from which we calculate the Grüneisen parameter and compare with previous experiments conducted at the OMEGA laser [Fratanduono et al ., Phys. Rev. B 94 , 184107 (2016)], our own first principles calculations, and another recent tabular equation of state [Zhang et al ., Phys. Rev. E 102 , 053203 (2020)]. We also compare our results with previous static compression, thermophysical, and melt studies, finding mixed consistency. We predict the onset and completion of shock melting at 225 and 265 GPa, respectively, and predict a melt curve that is largely flat to pressures of several hundred GPa.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Interplay between electron localization, magnetic order, and Jahn-Teller distortion dictates LiMnO2 phase stability

The development of manganese (Mn)-rich cathodes for Li-ion batteries promises to alleviate potential supply chain bottlenecks in battery manufacturing. Fundamental challenges in Mn-rich cathodes arise from phenomena such as structural changes due to cooperative Jahn-Teller (JT) distortions of in octahedral environments, Mn migration, and phase transformations to spinel-like order, all of which affect the electrochemical performance. These physically complex phenomena motivate an re-examination of the Li-Mn-O rock-salt space, with a focus on the thermodynamics of the prototypical, polymorphs. It is found that the generalized gradient approximation (GGA-PBEsol) and meta-GGA ( ) density functionals with empirically fitted on-site Hubbard corrections yield spurious stable phases for , such as predicting a phase with -like order ( ) to be the ground state instead of the orthorhombic (Pmmn) phase, which is the experimentally known ground state. Accounting for antiferromagnetic order in each structure is shown to have a substantial effect on the total energies and resulting phase stability. By using hybrid-GGA (HSE06) and GGA with self-consistent Hubbard parameters (on-site and inter-site ) calculated from linear response theory, the experimentally observed phase stability trends are recovered. The calculated on-site between Mn- states in the experimentally observed orthorhombic, layered, and spinel phases are significantly smaller than in and disordered layered structures, by within GGA. The smaller values of are shown to be correlated with a collinear ordering of JT distortions, in which all orbitals are oriented in the same direction. This cooperative JT effect can lead to greater electron delocalization from Mn along the states due to increased Mn-O covalency, which contributes to the greater electronic stability compared to the phases with noncollinear JT arrangements. The structures with collinear ordering of JT distortions also generate greater vibrational entropy, which helps stabilize these phases at high temperature. These phases are shown to be strongly insulating with large calculated band gaps , which are computed using HSE06 and .

Kam, Ronald L↗
DOE OSTI2025

Ultrafast x-ray diffraction of high-pressure phases in dynamically compressed TiO 2

Here, we investigate the high-pressure polymorphism of Ti⁢O 2 under laser-shock compression from 54(5) to 137(7) GPa using in situ femtosecond x-ray diffraction. Our results provide experimental evidence of the 𝑃⁢𝑐⁢𝑎⁢2 1 -type distorted fluorite structure formed from polycrystalline Ti⁢O 2 dynamically compressed to 54(5) GPa. Upon higher compression, we observe the direct formation of the ninefold coordinated F⁡e 2 ⁢P-type phase at 68(4) and 78(3) GPa in polycrystalline and [001]-oriented Ti⁢O 2 , respectively. This represents an unprecedented 100 GPa reduction in the shock synthesis pressure of the F⁡e 2⁢ P-type structure relative to quasihydrostatic loading conditions. On pressure release, the F⁡e 2⁢ P-type phase transforms to the α-Pb⁢O 2 structure and, at later times, reverts to rutile. Thus, the rutile →F⁡e 2⁢ P and α-Pb⁢O 2 →rutile transformations are both observed to occur on nanosecond timescales. Our results highlight the unique ability of high-strain-rate uniaxial compression to synthesize novel high-pressure phases and also indicate the importance of in situ atomic-level probes in developing pressure-temperature phase diagrams.

Crystal structures↗
DOE OSTI2026

From diamond to BC8 to simple cubic and back: Kinetic pathways to post-diamond carbon phases from metadynamics

Understanding the kinetic pathways connecting carbon polymorphs at multimegabar pressures remains a major unsolved problem in high-pressure physics. Here, we provide insights into the long-standing question of BC8 formation and stability by combining a state-of-the-art SNAP machine-learning interatomic potential with enhanced sampling via metadynamics, enabling direct access to transition mechanisms far beyond the reach of standard molecular dynamics. Our simulations show that carbon phase transformations are intrinsically complex, proceeding through multiple intermediate disordered and crystalline states governed by nontrivial kinetic ordering. We determine the upper pressure limit for BC8 formation and reveal that hexagonal diamond transforms to BC8 faster than cubic diamond—an unexpected and experimentally testable prediction. We also identify a 𝑃⁢222 carbon phase that becomes competitive with diamond and simple cubic above 1.8 TPa, and we demonstrate that BC8 may be quenched to ambient conditions at moderate temperatures. Altogether, these results establish a general and transferable framework for resolving kinetic pathways in solid-solid phase transitions and provide physical insights into carbon's complex high-pressure landscape.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Relationship between atomic and electronic structure in Ln-bearing oxides

Metastable states of matter are of great interest as they offer the promise of novel functionality. They are often a natural consequence of exposure to nonequilibrium environments. In oxides, metastability can take the form of new polymorphs, chemical disorder, and even amorphization. While significant attention has been given to the impact those changes have on the atomic properties of the material, the corresponding changes in the electronic structure have received less attention. Here, using density functional theory, we consider how the electronic structure varies with potential metastable structures in two classes of lanthanide-bearing oxides—pyrochlores and interlanthanide sesquioxides. We find that the changes depend strongly on both the crystal structure and crystal chemistry of the compound with, for example, disordering and amorphization either increasing or decreasing the bandgap depending on the chemistry. For the 𝐴 2 ⁢𝐵 2 ⁢O 7 pyrochlores, we find different dependencies of the bandgap on the 𝐴 = 𝐿⁢𝑛 cations as the 𝐵 cation is changed, which we relate to the nature of the density of states at the conduction band minimum for different 𝐵 chemistries. Our calculations are validated by electron energy loss spectroscopy measurements for two pyrochlore compounds in which amorphization does reduce the bandgap, consistent with our calculations on these two compounds. In conclusion, our results highlight the relationship between atomic and electronic structure and how radiation can be used to modify and potentially control the electronic properties of oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Structure-property relations of oP32-Ge under pressure

The unit-cell parameters, systematic absences, and atomic parameters of the germanium allotrope oP32-Ge show continuous changes up to 6 GPa as shown by single-crystal diffraction analysis. Peak shape and diffuse scattering features remain about unchanged throughout the experiment. Hence, neither the average nor the defect structure behavior offers a structure-property explanation for pressure-induced superconductivity observed at about 2 GPa [1]. Angle dispersive x-ray diffraction reveals a sluggish transformation of oP32-Ge to the Ge-II polymorph, the transition begins around 8 GPa and is complete at 12 GPa, a behavior similar to that of Ge-I. The reconstructive transition was associated with the breakdown of crystals into a powder that was compressed to 32 GPa. Synchrotron infrared absorption measurements up to 8.5 GPa indicate an increase of the band gap of the oP32-Ge prior to its collapse at 8.5 GPa. We suggest that the onset of superconductivity is not associated with a major structural change or that such a change occurs in specific stress and temperature conditions.

Lavina, Barbara↗
DOE OSTI2025

Carbon-carbon interactions in warm dense titanium carbide

Encouraged by experimental reports of diamond precipitation in carbon-containing materials under warm dense matter conditions and in shock compression experiments, we examine the behavior of carbon in TiC using density functional theory-molecular dynamics simulations. Two polymorphs of TiC are considered, the ambient-pressure B1 ($Fm$$\overline{3}$$m$) structure in which C-C interactions are prevented by geometric constraints, and a high-pressure Cmcm structure in which C atoms condense into zigzag chains. Chemistry-inspired bonding analyses confirm the covalently bound nature of these chains and further illuminate important interatomic interactions in both structures. Upon melting of B1 TiC, new short-range C-C interactions develop in the liquid, while the pre-existing C-C interactions in Cmcm TiC persist in the liquid. Here, the resulting carbon networks in the melt provide a promising environment for eventual diamond nucleation.

Ab initio molecular dynamics↗
DOE OSTI2020

Superconducting properties of MoTe 2 from ab initio anisotropic Migdal-Eliashberg theory

Molybdenum ditelluride (MoTe 2 ) is attracting considerable interest since it is the archetypal type-II Weyl semimetal and a candidate for topological superconductivity. In this work, we investigate the superconducting phase diagram of two MoTe 2 polymorphs using the ab initio anisotropic Migdal-Eliashberg theory, and we show that the superconducting dome originates from the synergistic contribution of the density of states at the Fermi level and the transverse acoustic Te modes in the 1$\textit{T}’$ phase. We find that the electron and hole pockets carry trivial $\textit{s}$-wave order parameters of slightly different magnitude, reminiscent of a two-gap structure as suggested by recent experiments. We suggest that a possible route for enhancing the superconducting critical temperature, and realizing $s_{+ –}$ pairing, in the $T_d$ phase is to exploit its nontrivial band topology via electron doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Deep learning of accurate force field of ferroelectric HfO 2

The discovery of ferroelectricity in HfO 2 -based thin films opens up new opportunities for using this silicon-compatible ferroelectric to realize low-power logic circuits and high-density nonvolatile memories. The functional performances of ferroelectrics are intimately related to their dynamic responses to external stimuli such as electric fields at finite temperatures. Molecular dynamics is an ideal technique for investigating dynamical processes on large length and time scales, though its applications to new materials are often hindered by the limited availability and accuracy of classical force fields. Here we present a deep neural network–based interatomic force field of HfO 2 learned from ab initio data using a concurrent learning procedure. The model potential is able to predict structural properties such as elastic constants, equation of states, phonon dispersion relationships, and phase transition barriers of various hafnia polymorphs with accuracy comparable with density functional theory calculations. Here, the validity of this model potential is further confirmed by the reproduction of experimental sequences of temperature-driven ferroelectric-paraelectric phase transitions of HfO 2 with isobaric-isothermal ensemble molecular dynamics simulations. We suggest a general approach to extend the model potential of HfO 2 to related material systems including dopants and defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗