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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
DOE OSTI2021

Understanding Multilevel Selection May Facilitate Management of Arbuscular Mycorrhizae in Sustainable Agroecosystems

Studies in natural ecosystems show that adaptation of arbuscular mycorrhizal (AM) fungi and other microbial plant symbionts to local environmental conditions can help ameliorate stress and optimize plant fitness. This local adaptation arises from the process of multilevel selection, which is the simultaneous selection of a hierarchy of groups. Studies of multilevel selection in natural ecosystems may inform the creation of sustainable agroecosystems through developing strategies to effectively manage crop microbiomes including AM symbioses. Field experiments show that the species composition of AM fungal communities varies across environmental gradients, and that the biomass of AM fungi and their benefits for plants generally diminish when fertilization and irrigation eliminate nutrient and water limitations. Furthermore, pathogen protection by mycorrhizas is only important in environments prone to plant damage due to pathogens. Consequently, certain agricultural practices may inadvertently select for less beneficial root symbioses because the conventional agricultural practices of fertilization, irrigation, and use of pesticides can make these symbioses superfluous for optimizing crop performance. The purpose of this paper is to examine how multilevel selection influences the flow of matter, energy, and genetic information through mycorrhizal microbiomes in natural and agricultural ecosystems, and propose testable hypotheses about how mycorrhizae may be actively managed to increase agricultural sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A sorghum pangenome reference improves global crop trait discovery

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops, like that of the grain and bioenergy crop sorghum, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

agricultural genetics↗
DOE OSTI2020

Biologically Diverse Genetic Engineering Platform

This project focused on methods to genetically edit arbitrary prokaryotes to convert non-agricultural biomass to industrially relevant chemicals at scale and at a price point that would be competitive with petroleum. Our target chemical for this demonstration was succinic acid, a polymer precursor that could theoretically be produced at scale from biomass. We demonstrated genetic control over a selected bacterial type strain: we can make permanent and directed changes to its genome. After thoroughly characterizing its behavior, and the circumstances under which it produced the most succinic acid, the researchers found a wild-type isolate that produces at least eight times more succinic acid than the type strain.

09 BIOMASS FUELS↗
DOE OSTI2024

Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

ABSTRACT The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography–mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas . Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress. IMPORTANCE The development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

SNPeffect: identifying functional roles of SNPs using metabolic networks

Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Microalgae as a future food source

One of the key challenges that we face in the 21st century is the need to feed an ever-increasing human population with increasingly limited natural resources. Even today it is estimated that roughly 1 out of 9 people in the world are undernourished, of which the most important factor is protein-energy malnutrition. By establishing microalgae as a new food and feed platform, we have the opportunity to increase the supply of these essential products to address global demands in a more efficient and environmentally sustainable way. Many types of algae are nutritionally complete foods, their yields outperform most plant crops, and there is a growing set of tools to develop improved strains of algae. Similar improvements were achieved in traditional crops through thousands of years of breeding and strain selection, whereas with the newest genetic engineering tools and advanced strain selection techniques, similar changes can be implemented in microalgae in just a few years. Here we describe different strategies that could be used to enhance the nutritional content, productivity, and organoleptic traits of algae to help drive development of this new crop. Clearly developing more efficient, sustainable, and nutritious foods and feed would be an enormous benefit for the planet, and algae represents an opportunity to develop a new crop that would complement traditional agriculture, and one that could potential result in a more efficient means to meet the world's food and feed supply.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves

Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.

3D reconstruction↗
DOE OSTI2024

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae’s ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.

09 BIOMASS FUELS↗
DOE OSTI2022

Genetic time traveling: sequencing old herbarium specimens, including the oldest herbarium specimen sequenced from kingdom Fungi, reveals the population structure of an agriculturally significant rust

Summary Sequencing herbarium specimens can be instrumental in answering ecological, evolutionary, and taxonomic inquiries. We developed a protocol for sequencing herbarium specimens of rust fungi (Pucciniales) and proceeded to sequence specimens ranging from 4 to 211 yr old from five different genera. We then obtained sequences from an economically important biological control agent, Puccinia suaveolens , to highlight the potential of sequencing herbarium specimens in an ecological sense and to evaluate the following hypotheses: (1) The population structure of a plant pathogen changes over time, and (2) introduced pathogens are more diverse in their native range. Our efforts resulted in sequences from 87 herbarium specimens that revealed a high level of diversity with a population structure that exhibited spatial–temporal patterns. The specimens sequenced from Europe showed more diversity than the ones from North America, uncovering an invasion pattern likely related to its European native host in North America. Additionally, to the best of our knowledge, the specimen from France collected in c. 1811 is the oldest herbarium specimen sequenced from kingdom Fungi. In conclusion, sequencing old herbarium specimens is an important tool that can be extrapolated to better understand plant–microbe evolution and to evaluate old type specimens to solidify the taxonomy of plant pathogenic fungi.

Plant Sciences↗
DOE OSTI2024

Development of modular expression across phylogenetically distinct diazotrophs

Diazotrophic bacteria can reduce atmospheric nitrogen into ammonia enabling bioavailability of the essential element. Many diazotrophs closely associate with plant roots increasing nitrogen availability, acting as plant growth promoters. These associations have the potential to reduce the need for costly synthetic fertilizers if they could be engineered for agricultural applications. However, despite the importance of diazotrophic bacteria, genetic tools are poorly developed in a limited number of species, in turn narrowing the crops and root microbiomes that can be targeted. Here, we report optimized protocols and plasmids to manipulate phylogenetically diverse diazotrophs with the goal of enabling synthetic biology and genetic engineering. Three broad-host-range plasmids can be used across multiple diazotrophs, with the identification of one specific plasmid (containing origin of replication RK2 and a kanamycin resistance marker) showing the highest degree of compatibility across bacteria tested. We then demonstrated modular expression by testing seven promoters and eleven ribosomal binding sites using proxy fluorescent proteins. Finally, we tested four small molecule inducible systems to report expression in three diazotrophs and demonstrated genome editing in Klebsiella michiganensis M5al.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen

Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Impacts of directed evolution and soil management legacy on the maize rhizobiome

Domestication and agricultural intensification dramatically altered maize and its cultivation environment. Changes in maize genetics (G) and environmental (E) conditions increased productivity under high-synthetic-input conditions. However, novel selective pressures on the rhizobiome may have incurred undesirable tradeoffs in organic agroecosystems, where plants obtain nutrients via microbially mediated processes including mineralization of organic matter. Using twelve maize genotypes representing an evolutionary transect (teosintes, landraces, inbred parents of modern elite germplasm, and modern hybrids) and two agricultural soils with contrasting long-term management, here we integrated analyses of rhizobiome community structure, potential microbe-microbe interactions, and N-cycling functional genes to better understand the impacts of maize evolution and soil management legacy on rhizobiome recruitment. We show complex shifts in rhizobiome communities during directed evolution of maize (defined as the transition from teosinte to modern hybrids), with a larger effect of domestication (teosinte to landraces) than modern breeding (inbreds to hybrids) on rhizobiome structure and greater impacts of modern breeding on potential microbe-microbe interactions. Rhizobiome structure was significantly correlated with plant nutrient composition. Furthermore, plant biomass and nutrient content were affected by G x E interactions in which teosinte and landrace genotypes had better relative performance in the organic legacy soil than inbred and modern genotypes. The abundance of six N-cycling genes of relevance for plant nutrition and N loss pathways did not significantly differ between teosinte and modern rhizospheres in either soil management legacy. These results provide insight into the potential for improving maize adaptation to organic systems and contribute to interdisciplinary efforts toward developing resource-efficient, biologically based agroecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Data for Adapting C4 Photosynthesis to Atmospheric Change and Increasing Productivity by Elevating Rubisco Content in Sorghum and Sugarcane

This repository includes data sets and R scripts that were used to perform analysis and produce figures for the following publication: Salesse-Smith, C. E. et al. “Adapting C4 photosynthesis to atmospheric change and increasing productivity by elevating Rubisco content in sorghum and sugarcane.” Proceedings of the National Academy of Sciences 122, e2419943122 (2025) doi:10.1073/pnas.2419943122.

Biomass Analytics↗
DOE OSTI2020

Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor

Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a species-specific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Sorghum bicolor. Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Utilizing digitized occurrence records of Midwestern feral Cannabis sativa to develop ecological niche models

Hemp (Cannabis sativa L.) has historically played a vital role in agriculture across the globe. Feral and wild populations have served as genetic resources for breeding, conservation, and adaptation to changing environmental conditions. However, feral populations of Cannabis, specifically in the Midwestern United States, remain poorly understood. This study aims to characterize the abiotic tolerances of these populations, estimate suitable areas, identify regions at risk of abiotic suitability change, and highlight the utility of ecological niche models (ENMs) in germplasm conservation. The Maxent algorithm was used to construct a series of ENMs. Validation metrics and MOP (Mobility-oriented Parity) analysis were used to assess extrapolation risk and model performance. We also projected the final projected under current and future climate scenarios (2021–2040 and 2061–2080) to assess how abiotic suitability changes with time. Climate change scenarios indicated an expansion of suitable habitat, with priority areas for germplasm collection in Indiana, Illinois, Kansas, Missouri, and Nebraska. This study demonstrates the application of ENMs for characterizing feral Cannabis populations and highlights their value in germplasm conservation and breeding efforts. Populations of feral C. sativa in the Midwest are of high interest, and future research should focus on utilizing tools to aid the collection of materials for the characterization of genetic diversity and adaptation to a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence–absence variation on a local scale. This diversity is invisible to classical reference-based strategies and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.

Thlaspi arvense↗
DOE OSTI2026

Data for Comparison of Genotyping Assays for Detection of Targeted CRISPR/Cas Mutagenesis in Highly Polyploid Sugarcane

Sugarcane ( Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100–130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

Genomics↗
DOE OSTI2024

The complex polyploid genome architecture of sugarcane

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗