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DOE OSTI2023

Maize Terpene Synthase 8 (ZmTPS8) Contributes to a Complex Blend of Fungal-Elicited Antibiotics

In maize (Zea mays), fungal-elicited immune responses include the accumulation of terpene synthase (TPS) and cytochrome P450 monooxygenases (CYP) enzymes resulting in complex antibiotic arrays of sesquiterpenoids and diterpenoids, including α/β-selinene derivatives, zealexins, kauralexins and dolabralexins. To uncover additional antibiotic families, we conducted metabolic profiling of elicited stem tissues in mapping populations, which included B73 × M162W recombinant inbred lines and the Goodman diversity panel. Five candidate sesquiterpenoids associated with a chromosome 1 locus spanning the location of ZmTPS27 and ZmTPS8. Heterologous enzyme co-expression studies of ZmTPS27 in Nicotiana benthamiana resulted in geraniol production while ZmTPS8 yielded α-copaene, δ-cadinene and sesquiterpene alcohols consistent with epi-cubebol, cubebol, copan-3-ol and copaborneol matching the association mapping efforts. ZmTPS8 is an established multiproduct α-copaene synthase; however, ZmTPS8-derived sesquiterpene alcohols are rarely encountered in maize tissues. A genome wide association study further linked an unknown sesquiterpene acid to ZmTPS8 and combined ZmTPS8-ZmCYP71Z19 heterologous enzyme co-expression studies yielded the same product. To consider defensive roles for ZmTPS8, in vitro bioassays with cubebol demonstrated significant antifungal activity against both Fusarium graminearum and Aspergillus parasiticus. As a genetically variable biochemical trait, ZmTPS8 contributes to the cocktail of terpenoid antibiotics present following complex interactions between wounding and fungal elicitation.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1982

Use of remote sensing for land use policy formulation

Research projects described include: (1) identifying coniferous forest types in Michigan using LANDSAT imagery; (2) investigating synoptic temperature patterns in Michigan as determined via GOES and HCMM thermal imagery; (3) land surface change detection using satellite data and a geographic data base; (4) determining soil map unit composition by electronic scanning densitometry; and (5) delimiting areas of virus infection in vineyards and blueberry fields in southwestern and western Michigan. Contractual activities involve important farmlands inventory, changes in aquatic vegetation in Saginaw Bay, digitized soil association map of Michigan, and aerial photography for hybrid-poplar research. On-going projects are also being conducted in Jamaica, Honduras, the Dominican Republic and Kenya.

Source record↗

DOE OSTI2022

Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity

SUMMARY Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum ( Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high‐density genomic marker set of 43 983 694 variants including single‐nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower‐density marker sets. WGS identified and scored variants in 5‐kb bins where available genotyping‐by‐sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six F st peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1973

ERTS data user no. 119: Effective use of ERTS multisensor data in the Great Plains. ERTS-1 MSS imagery: A tool for identifying soil associations

The author has identified the following significant results. Soil association maps show the spatial relationships of land units developed in unique climatic, geologic, and topographic environments, and having characteristic slopes, soil depths, textures, available water capacities, permeabilities, and the like. ERTS-1 imagery was found to be a useful tool in the identification of soil associations since it provides a synoptic view of an 8 million acre scene, which is large enough so that the effect can be seen on soils of climate, topography, and geology. A regional view also allows soil associations to be observed over most, if not all, of their extent. ERTS-1 MSS imagery also provides four spectral bands taken every 18 days which give data on relief, hydrology, and vegetation, all of which bear on the delineation and interpretation of soil associations. Enlarged prints derived from the individual spectral bands and shown in gray tones were useful for identifying soil associations.

Myers, V. I.↗

DOE OSTI2020

The geometric theory of charge conservation in particle-in-cell simulations

In recent years, several gauge-symmetric particle-in-cell (PIC) methods have been developed whose simulations of particles and electromagnetic fields exactly conserve charge. While it is rightly observed that these methods’ gauge symmetry gives rise to their charge conservation, this causal relationship has generally been asserted via ad hoc derivations of the associated conservation laws. In this work, we develop a comprehensive theoretical grounding for charge conservation in gauge-symmetric Lagrangian and Hamiltonian PIC algorithms. For Lagrangian variational PIC methods, we apply Noether’s second theorem to demonstrate that gauge symmetry gives rise to a local charge conservation law as an off-shell identity. For Hamiltonian splitting methods, we show that the momentum map establishes their charge conservation laws. We define a new class of algorithms – gauge-compatible splitting methods – that exactly preserve the momentum map associated with a Hamiltonian system’s gauge symmetry – even after time discretization. This class of algorithms affords splitting schemes a decided advantage over alternative Hamiltonian integrators. We apply this general technique to design a novel, explicit, symplectic, gauge-compatible splitting PIC method, whose momentum map yields an exact local charge conservation law. Finally, our study clarifies the appropriate initial conditions for such schemes and examines their symplectic reduction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Simultaneous dissection of grain carotenoid levels and kernel color in biparental maize populations with yellow-to-orange grain

Maize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the US maize nested association mapping panel that have yellow to orange grain. Quantitative trait loci were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color quantitative trait loci ranging from 2.4% to 17.5%. These quantitative trait loci were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized ~27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the α- or β-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with β-branch and total carotenoids and negligible correlations with α-branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1977

Reindeer range inventory in western Alaska from computer-aided digital classification of LANDSAT data

An inventory of reindeer-range resources was conducted for the USDA Soil Conservation Service of 1.6 million hectares of wildlands in western Alaska using clustering techniques with digital Landsat data. Computer-aided digital analysis produced a provisional map of rangeland types which was used to design the field collection of vegetation and soil types data. This field data facilitated refinement of the inventory map and was used to describe the map units. The informational classes important to range resources were wet, moist and alpine tundra, tidal marsh, brush and open spruce forest. A significant feature of the study was the extraction of acreage figures by administrative boundaries within the study area. In addition to soil and vegetation association map products (at scales of 1:250,000 and 1:63,360) acreage values were tallied from the digital data for each of the four grazing permit areas established by the Bureau of Land Management.

George, T. H.↗

NASA NTRS1974

Mapping soils, crops, and rangelands by machine analysis of multitemporal ERTS-1 data

ERTS-1 data, obtained during the period 25 August 1972 to 5 September 1973 over a range of test sites in the Central United States, have been used for identifying and mapping differences in soil patterns, species and conditions of cultivated crops, and conditions of rangelands. Multispectral scanner data from multiple ERTS passes over certain test sites have provided the opportunity to study temporal changes in the scene. Multispectral classifications delineating soils boundaries in different test sites compared well with existing soil association maps prepared by conventional means. Spectral analysis of ERTS data was used to identify, maps, and make areal measurements of wheat in western Kansas. Multispectral analysis of ERTS-1 data provided patterns in rangelands which can be related to soils differences, range management practices, and the extent of infestation of grasslands by mesquite (prosopis fuliflora) and juniper (juniperus spp.).

Baumgardner, M. F.↗

DOE OSTI2024

Mapping of flumioxazin tolerance in a snap bean diversity panel leads to the discovery of a master genomic region controlling multiple stress resistance genes

Effective weed management tools are crucial for maintaining the profitable production of snap bean (Phaseolus vulgaris L.). Preemergence herbicides help the crop to gain a size advantage over the weeds, but the few preemergence herbicides registered in snap bean have poor waterhemp (Amaranthus tuberculatus) control, a major pest in snap bean production. Waterhemp and other difficult-to-control weeds can be managed by flumioxazin, an herbicide that inhibits protoporphyrinogen oxidase (PPO). However, there is limited knowledge about crop tolerance to this herbicide. We aimed to quantify the degree of snap bean tolerance to flumioxazin and explore the underlying mechanisms. We investigated the genetic basis of herbicide tolerance using genome-wide association mapping approach utilizing field-collected data from a snap bean diversity panel, combined with gene expression data of cultivars with contrasting response. The response to a preemergence application of flumioxazin was measured by assessing plant population density and shoot biomass variables. Snap bean tolerance to flumioxazin is associated with a single genomic location in chromosome 02. Tolerance is influenced by several factors, including those that are indirectly affected by seed size/weight and those that directly impact the herbicide's metabolism and protect the cell from reactive oxygen species-induced damage. Transcriptional profiling and co-expression network analysis identified biological pathways likely involved in flumioxazin tolerance, including oxidoreductase processes and programmed cell death. Transcriptional regulation of genes involved in those processes is possibly orchestrated by a transcription factor located in the region identified in the GWAS analysis. Several entries belonging to the Romano class, including Bush Romano 350, Roma II, and Romano Purpiat presented high levels of tolerance in this study. The alleles identified in the diversity panel that condition snap bean tolerance to flumioxazin shed light on a novel mechanism of herbicide tolerance and can be used in crop improvement.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1973

ERTS-1 MSS imagery - A tool for identifying soil associations.

Soil association maps show the spatial relationships of land units developed in unique climatic, geologic, and topographic environments, and having characteristic slopes, soil depths, textures, available water capacities, permeabilities, and the like. From these characteristics of the soil, broad interpretations can be made such as how the soil is suited for various agronomic and engineering uses. ERTS-1 imagery was found to be a useful tool in the identification of soil associations since it provides a synoptic view of an 8 million acre scene, which is large enough so that the effect can be seen on soils of climate, topography, and geology. A regional view also allows soil associations to be observed over most, if not all, of their extent. This aids in selecting typical sampling sites and provides a check on the homogeniety of the associations.

Westin, F. C.↗

NASA NTRS1973

Identification of soil associations in South Dakota on ERTS 1 imagery

Westin, F. C.↗

NASA NTRS1973

Identification of soil associations in western South Dakota on ERTS-1 imagery

Soil association maps show the spatial relationships of land units having characteristic soil depths and textures, available water capacities, permeabilities, pH characteristics, plasticity indices, liquid limits, and the like, from which broad interpretations can be made such as how the soil is suited as a source for top soil, and as a source for sand and gravel, and how corrosive the soil is for steel and concrete, and what crop and grass yields can be expected. Film color composites of bands 4, 5 and 7 viewed over a light table with magnification show the soil associations of western South Dakota that are now recognized, and, in addition, several new soil association areas have been brought to light.

Westin, F. C.↗

DOE OSTI2024

Investigating genomic prediction strategies for grain carotenoid traits in a tropical/subtropical maize panel

Abstract Vitamin A deficiency remains prevalent on a global scale, including in regions where maize constitutes a high percentage of human diets. One solution for alleviating this deficiency has been to increase grain concentrations of provitamin A carotenoids in maize (Zea mays ssp. mays L.)—an example of biofortification. The International Maize and Wheat Improvement Center (CIMMYT) developed a Carotenoid Association Mapping panel of 380 inbred lines adapted to tropical and subtropical environments that have varying grain concentrations of provitamin A and other health-beneficial carotenoids. Several major genes have been identified for these traits, 2 of which have particularly been leveraged in marker-assisted selection. This project assesses the predictive ability of several genomic prediction strategies for maize grain carotenoid traits within and between 4 environments in Mexico. Ridge Regression-Best Linear Unbiased Prediction, Elastic Net, and Reproducing Kernel Hilbert Spaces had high predictive abilities for all tested traits (β-carotene, β-cryptoxanthin, provitamin A, lutein, and zeaxanthin) and outperformed Least Absolute Shrinkage and Selection Operator. Furthermore, predictive abilities were higher when using genome-wide markers rather than only the markers proximal to 2 or 13 genes. These findings suggest that genomic prediction models using genome-wide markers (and assuming equal variance of marker effects) are worthwhile for these traits even though key genes have already been identified, especially if breeding for additional grain carotenoid traits alongside β-carotene. Predictive ability was maintained for all traits except lutein in between-environment prediction. The TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) Genomic Selection plugin performed as well as other more computationally intensive methods for within-environment prediction. The findings observed herein indicate the utility of genomic prediction methods for these traits and could inform their resource-efficient implementation in biofortification breeding programs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Characterizing 4-string contact interaction using machine learning

Abstract The geometry of 4-string contact interaction of closed string field theory is characterized using machine learning. We obtain Strebel quadratic differentials on 4-punctured spheres as a neural network by performing unsupervised learning with a custom-built loss function. This allows us to solve for local coordinates and compute their associated mapping radii numerically. We also train a neural network distinguishing vertex from Feynman region. As a check, 4-tachyon contact term in the tachyon potential is computed and a good agreement with the results in the literature is observed. We argue that our algorithm is manifestly independent of number of punctures and scaling it to characterize the geometry ofn-string contact interaction is feasible.

Physics↗

DOE OSTI2021

Carbon–Nutrient Economy of the Rhizosphere: Improving Biogeochemical Prediction and Scaling Feedbacks from Ecosystem to Regional Scales

Our project has advanced the science of plant-soil-microbial dynamics across these areas: i) nutrient cycling and plant uptake; ii) root exudation and priming; and, iii) mycorrhizal dynamics. Our project has accomplished 5 main developments: 1) Incorporation of phosphorus cycling into the Fixation & Uptake of Nutrients (FUN 3.0) model. 2) Coupling of FUN 3.0 into the E3SM Land Model (ELM). 3) Data collection across a large mycorrhizal gradient in the US, as well data in the tropics, to parameterize, test, and validate the model. 4)Scaling up mycorrhizal association measurements across landscapes using airborne hyperspectral remote sensing data. 5) Evaluation of global carbon and nutrient cycle impacts in the Community Land Model (CLM5.0) from a suite of new global mycorrhizal association maps. Over 25 publications resulted from this project, with more continuing past the project funded lifetime. Paper highlights from most of these publications have already been submitted to the DOE paper submission online system. These publications include journals such as Science and PNAS, as well as top disciplinary journals from the Nature journals, Global Change Biology, New Phytologist, and Ecology Letters, for example. Our project also contributed to improving the process representation, capabilities, and accuracy of the DOE ELM. Overall, this project significantly advanced the science of belowground plant-soil-microbial interactions as well as technical capabilities from remote sensing to modeling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Towards durable resistance to Septoria stem canker and leaf spot: A molecular understanding of resistance (Final Technical Report)

To identify, validate, and functionally characterize alleles that confer resistance to Septoria canker and leaf spot in Populus. The proposed research will elucidate a major mechanism of resistance to Sphaerulina musiva, the major limiting factor to plantations in eastern North America. Genome-wide association mapping, CRISPR/Cas9, and protein-protein assays will be used, enabling marker-aided breeding, reducing costs, and accelerating development of resistant varieties.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Code Demonstration: Approximation of nearly-periodic symplectic maps via structure-preserving neural networks

In this notebook, we use the symplectic gyroceptron architecture from [Duruisseaux et al., 2022] to learn a surrogate map for the nearly-periodic symplectic flow map associated to a nearly-periodic Hamiltonian system composed of two nonlinearly coupled oscillators, where one of them oscillates significantly faster than the other: $\Big\lbrace$ $ {\dot{q}_1 = p_1 \hspace{5mm} \dot{p}_1 = -q_1 - \epsilon \partial_{q1}U(q_1 , q_2 )} \atop {\dot{q}_2 = \epsilon p_2 \hspace{4mm} \dot{p}_2 = -\epsilon q_2 - \epsilon \partial_{q2}U(q_1 , q_2 )}$. These equations of motion are the Hamilton's equations associated to the Hamiltonian $H_{\epsilon}(q_1,q_2,p_1,p_2)=\frac{1}{2}(q^2_1+p^2_1)+\frac{1}{2}\epsilon(q^2_2+p^2_2)+\epsilon$$U(q_1,q_2)$.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Physical Correlations and Predictions Emerging from Modern Core-collapse Supernova Theory

Abstract In this paper, we derive correlations between core-collapse supernova observables and progenitor core structures that emerge from our suite of 20 state-of-the-art 3D core-collapse supernova simulations carried to late times. This is the largest such collection of 3D supernova models ever generated and allows one to witness and derive testable patterns that might otherwise be obscured when studying one or a few models in isolation. From this panoramic perspective, we have discovered correlations between explosion energy, neutron star gravitational birth masses, 56 Ni and α -rich freezeout yields, and pulsar kicks and theoretically important correlations with the compactness parameter of progenitor structure. We find a correlation between explosion energy and progenitor mantle binding energy, suggesting that such explosions are self-regulating. We also find a testable correlation between explosion energy and measures of explosion asymmetry, such as the ejecta energy and mass dipoles. While the correlations between two observables are roughly independent of the progenitor zero-age main-sequence (ZAMS) mass, the many correlations we derive with compactness cannot unambiguously be tied to a particular progenitor ZAMS mass. This relationship depends on the compactness/ZAMS mass mapping associated with the massive star progenitor models employed. Therefore, our derived correlations between compactness and observables may be more robust than with ZAMS mass but can nevertheless be used in the future once massive star modeling has converged.

Astronomy & Astrophysics↗