Search NASA⌕ Search

SEARCH · Search NASA

Results for “agricultural genetics”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

229 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Elimination of human rabies in Goa, India through an integrated One Health approach

Dog-mediated rabies kills tens of thousands of people each year in India, representing one third of the estimated global rabies burden. Whilst the World Health Organization (WHO), World Organization for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO) have set a target for global dog-mediated human rabies elimination by 2030, examples of large-scale dog vaccination programs demonstrating elimination remain limited in Africa and Asia. We describe the development of a data-driven rabies elimination program from 2013 to 2019 in Goa State, India, culminating in human rabies elimination and a 92% reduction in monthly canine rabies cases. Smartphone technology enabled systematic spatial direction of remote teams to vaccinate over 95,000 dogs at 70% vaccination coverage, and rabies education teams to reach 150,000 children annually. An estimated 2249 disability-adjusted life years (DALYs) were averted over the program period at 526 USD per DALY, making the intervention ‘very cost-effective’ by WHO definitions. This One Health program demonstrates that human rabies elimination is achievable at the state level in India.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Tree drought physiology: critical research questions and strategies for mitigating climate change effects on forests

Droughts of increasing severity and frequency are a primary cause of forest mortality associated with climate change. Yet, fundamental knowledge gaps regarding the complex physiology of trees limit the development of more effective management strategies to mitigate drought effects on forests. Here, in this work, we highlight some of the basic research needed to better understand tree drought physiology and how new technologies and interdisciplinary approaches can be used to address them. Our discussion focuses on how trees change wood development to mitigate water stress, hormonal responses to drought, genetic variation underlying adaptive drought phenotypes, how trees ‘remember’ prior stress exposure, and how symbiotic soil microbes affect drought response. Next, we identify opportunities for using research findings to enhance or develop new strategies for managing drought effects on forests, ranging from matching genotypes to environments, to enhancing seedling resilience through nursery treatments, to landscape-scale monitoring and predictions. We conclude with a discussion of the need for co-producing research with land managers and extending research to forests in critical ecological regions beyond the temperate zone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

The introduction of invasive microbes compromises the structure, biodiversity, and function of naïve ecosystems. Sphaerulina musiva, a hemibiotrophic pathogen that causes leaf spot and stem cankers in Populus species, exemplifies an invasive fungal pathogen spread by human activities. However, the genetic mechanisms of pathogenicity and virulence are poorly understood, impeding mitigation strategies. We utilized RNA sequencing to identify fungal effectors linked to stem canker formation, informing the development of future strategies for effective disease management. Our analysis revealed 70 genes differentially expressed at 2 weeks and 110 genes at 3 weeks between inoculated trees and controls. Notably, the gene with the highest expression at 2 weeks and the second highest at 3 weeks was homologous to Extracellular protein 2 (Ecp2). Complementary genome-wide association studies linked sequence polymorphisms in this locus to phenotypic variation in disease severity. Infiltration of S. musiva Ecp2 into Populus trichocarpa leaves induced necrosis in susceptible genotypes. Gene disruption using a CRISPR-Cas9 RNP system resulted in a genotype-dependent reduction of stem canker and disease severity. Tracing the evolutionary history of this effector across the fungal kingdom, we uncovered clade-specific gene-family expansions and orthologs in new species. These findings raise questions about the function and adaptive significance of these gene families in fungal lifestyles. Our study provides the first tractable target for breeding resistant poplar genotypes, addressing the challenges of managing S. musiva and uncovering mechanisms that drive its virulence, and provides deeper insights into the evolutionary dynamics of a conserved small-secreted protein with a diversity of functions.

Sondreli, Kelsey L [Oregon State University]↗
DOE OSTI2025

Effects of feruloyl-CoA 6'-hydroxylase 1 overexpression on lignin and cell wall characteristics in transgenic hybrid aspen

In plant cell walls, lignin, cellulose, and the hemicelluloses form intricate three-dimensional structures. Owing to its complexity, lignin often acts as a bottleneck for the efficient utilization of polysaccharide components as biochemicals and functional materials. A promising approach to mitigate and/or overcome lignin recalcitrance is the qualitative and quantitative modification of lignin by genetic engineering. Feruloyl-CoA 6'-hydroxylase (F6'H1) is a 2-oxoglutarate-dependent dioxygenase that catalyzes the conversion of feruloyl-CoA, one of the intermediates of the lignin biosynthetic pathway, into 6'-hydroxyferuloyl-CoA, the precursor of scopoletin (7-hydroxy-6-methoxycoumarin). In a previous study with Arabidopsis thaliana, we demonstrated that overexpression of F6'H1 under a xylem-preferential promoter led to scopoletin incorporation into the cell wall. This altered the chemical structure of lignin without affecting lignin content or saccharification efficiency. In the present study, the same F6'H1 construct was introduced into hybrid aspen (Populus tremula × tremuloides T89), a model woody plant, and its effects on plant morphology, lignin chemical structure, global gene expression, and phenolic metabolism were examined. The transgenic plants successfully overproduced scopoletin while exhibiting severe growth retardation, a phenotype not previously observed in Arabidopsis. Scopoletin accumulation was most pronounced in the secondary walls of tracheary elements and the compound middle lamella, with low levels in the fiber cell walls. Overexpression of F6'H1 also affected the metabolism of aromatics, including lignin precursors. Heteronuclear single-quantum coherence (HSQC) NMR spectroscopy revealed that scopoletin in cell walls was bound to lignin, leading to a reduction in lignin content and changes in its monomeric composition and molar mass distribution. Furthermore, the enzymatic saccharification efficiency of the transgenic cell walls was more than three times higher than that of the wild-type plants, even without pretreatment. Although addressing growth inhibition remains a priority, incorporating scopoletin into lignin demonstrates significant potential for improving woody biomass utilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for "Genetics of flooding tolerance in an F2 Miscanthus sacchariflorus ssp. lutarioriparius × M. sinensis population"

This dataset contains all data and supplementary materials from "Genetics of flooding tolerance in an F2 Miscanthus sacchariflorus ssp. lutarioriparius × M. sinensis population". 1. The dataset S1 table contains the raw phenotypic data collected during the experiment. 2. The dataset S2 table contains the LSmean values for the 24 traits studied. 3. The dataset S3 table contains the TASSEL GBSv2 map, marker information, and genotype data used for mapping. 4. The dataset S4 table contains information on candidate genes found in each of the QTL intervals. 5. The dataset S5 table contains the GO annotations and KEGG enrichment analyses for those candidate genes. 6. The dataset S6 table contains information on the sequences used to classify AP2 ERF transcription factors. 7. The dataset S7 table contains information on AP2 ERF orthologs between Miscanthus and rice based on synteny. 8. Supplementary file 1 contains the ANOVA results using the raw phenotypic data collected from protocol "A". 9. Supplementary file 2 contains the ANOVA results using the raw phenotypic data collected from protocol "B". 10. Supplementary file 3 contains notes on the comparison of SNP calling methods. 11. Supplementary file 4 is a script for analyzing candidate genes found in QTL intervals.

Miscanthus, flood, partial submergence, complete s↗
DOE OSTI2025

Low Mutation Rate and Atypical Mutation Spectrum in Prasinoderma coloniale : Insights From an Early Diverging Green Lineage

Mutations are the ultimate source of genetic diversity on which natural selection and genetic drift act, playing a crucial role in evolution and long-term adaptation. At the molecular level, the spontaneous mutation rate (µ), defined as the number of mutations per base per generation, thus determines the adaptive potential of a species. Through a mutation accumulation experiment, we estimate the mutation rate and spectrum in Prasinoderma coloniale, a phytoplankton species from an early-branching lineage within the Archaeplastida, characterized by an unusually high genomic guanine-cytosine (GC) content (69.8%). We find that P. coloniale has a very low total mutation rate of µ = 2.00 × 10 -10 . The insertion–deletion mutation rate is almost 5 times lesser than the single nucleotide mutation rate with µ ID = 3.40 × 10 -11 and µ SNM = 1.62 × 10 -10 . Prasinoderma coloniale also exhibits an atypical mutational spectrum: While essentially all other eukaryotes show a bias toward GC to AT mutations, no evidence of this AT-bias is observed in P. coloniale. Since cytosine methylation is known to be mutagenic, we hypothesized that this may result from an absence of C-methylation. Surprisingly, we found high levels of C-methylation (14% in 5mC, 25% in 5mCG contexts). Methylated cytosines did not show increased mutation rates compared with unmethylated ones, not supporting the prevailing notion that C-methylation universally leads to higher mutation rates. Overall, P. coloniale combines a GC-rich genome with a low mutation rate and original mutation spectrum, suggesting the almost universal AT-bias may not have been present in the ancestor of the green lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for Promoter Deletion in the Soybean Compact Mutant Leads to Overexpression of a Gene with Homology to the C20-Gibberellin 2-Oxidase Family

Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. These results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.

Biomass Analytics↗
DOE OSTI2025

Plant genotype and rhizobia strain combinations strongly influence the transcriptome under heavy metal stress conditions in Medicago truncatula

Heavy metals such as cadmium (Cd) and mercury (Hg) pose significant threats to plant health and food safety as they are absorbed from the environment. Legumes are generally considered sensitive to heavy metals but possess standing genetic variation for accumulation and tolerance to toxic ions. We conducted a transcriptomic analysis on hydroponically and soil grown Medicago truncatula plants to investigate gene expression responses to Cd and Hg exposure in roots, leaves, and nodules. By using plant genotypes with varying metal tolerance or accumulation levels, we observed distinct clustering of gene ontologies, indicating tissue-specific, genotype-specific, and metal-specific gene expression patterns. Considering the symbiotic relationship between legumes and nitrogen-fixing bacteria, we further examined plant phenotypes and transcriptomes of plant genotypes with contrasting Hg accumulation levels and inoculated them with high or low Hg-tolerant Sinorhizobium medicae strains that have presence-absence variation for a mercury reductase (Mer) operon. Host plants inoculated with the Hg-tolerant rhizobia strain possessing a Mer operon exhibited less reduction in nodule number and plant biomass. A smaller reduction in iron (Fe) distribution in nodules after Hg stress was measured using X-ray Fluorescence (XRF) imaging. Dual transcriptome (host plant and bacteria) analysis of nodules revealed a remarkable decrease in the number of differentially expressed genes (DEGs) and clustering of gene ontologies in plants inoculated with the Hg-tolerant rhizobia strain, including symbiosis related genes. This finding suggests that the Hg-tolerant rhizobia strain has the potential to mitigate Hg stress in host plants. Furthermore, we observed genotype by-genotype interactions between the high Hg accumulating plant genotype and the Hg-tolerant rhizobia strain. These findings provide insights into enhancing plant resilience in contaminated environments through optimizing legume-rhizobia interactions for heavy metal tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Changes in leaf economic trait relationships across a precipitation gradient are related to differential gene expression in a C 4 perennial grass

Summary The leaf economics spectrum (LES) describes a suite of functional traits that consistently covary at large spatial and taxonomic scales. Despite its importance at these larger scales, few studies have examined the major drivers of intraspecific variation in the LES – phenotypic plasticity and standing genetic variation. Using experimental precipitation manipulations, we examined whether covariation among leaf economics traits and selection on leaf economics traits and trait combinations change as diverse genotypes of the widespread perennial grass Panicum virgatum are exposed to differences in precipitation. We also used RNA‐Seq to examine whether groups of co‐expressed genes that align with leaf economics traits function in processes hypothesized to underlie the LES. Water availability impacted leaf economics trait covariation in important ways – covariation between leaf economics traits and selection on covariation between traits (i.e. correlational selection) tended to be strongest when water availability was high. Additionally, many genes associated with leaf economics traits functioned in processes that may explain how the LES originates, such as chloroplasts, cell walls, and nitrogen metabolism. Water availability is likely an important modulator of selection and evolution of the LES in P. virgatum that can be better understood by examining gene expression.

Heckman, Robert W. [Department of Integrative Biol↗
DOE OSTI2023

Local adaptation of switchgrass drives trait relations to yield and differential responses to climate and soil environments

Abstract Switchgrass, a potential biofuel crop, is a genetically diverse species with phenotypic plasticity enabling it to grow in a range of environments. Two primary divergent ecotypes, uplands and lowlands, exhibit trait combinations representative of acquisitive and conservative growth allocation strategies, respectively. Whether these ecotypes respond differently to various types of environmental drivers remains unclear but is crucial to understanding how switchgrass varieties will respond to climate change. We grew two upland, two lowland, and two intermediate/hybrid cultivars of switchgrass at three sites along a latitudinal gradient in the central United States. Over a 4‐year period, we measured plant functional traits and biomass yields and evaluated genotype‐by‐environment (G × E) interaction effects by analyzing switchgrass responses to soil and climate variables. We found substantial evidence of G × E interactions on biomass yield, primarily due to deviations in the response of the southern lowland cultivar Alamo, which produced more biomass in hotter and drier environments relative to other cultivars. While lowland cultivars had the highest potential for yield, their yields were more variable year‐to‐year compared to other cultivars, suggesting greater sensitivity to environmental perturbations. Models comparing soil and climate principal components as explanatory variables revealed soil properties, especially nutrients, to be most effective at predicting switchgrass biomass yield. Also, positive correlations between biomass yield and conservative plant traits, such as high stem mass and tiller height, became stronger at lower latitudes where the climate is hotter and drier, regardless of ecotype. Lowland cultivars, however, showed a greater predisposition to exhibit these conservative traits. These results suggest switchgrass trait allocation trade‐offs that prioritize aboveground biomass production are more tightly associated in hot, dry environments and that lowland cultivars may exhibit a more specialized strategy relative to other cultivars. Altogether, this research provides essential knowledge for improving the viability of switchgrass as a biofuel crop.

09 BIOMASS FUELS↗
DOE OSTI2026

Genomic approaches to accelerate American chestnut restoration

More than a century after two introduced pathogens killed billions of American chestnut trees, introgression of resistance alleles from Chinese chestnuts has contributed to the recovery of self-sustaining populations. However, progress has been slow because of the complex genetic architecture of resistance. To better understand blight resistance, we compared reference genomes, gene expression responses, and stem metabolite profiles of the resistant Chinese and susceptible American chestnut species. To accelerate resistance breeding, we conducted large-scale phenotyping and genotyping in hybrids of these species. Simulation and inoculation experiments suggest that significant resistance gains are possible through selectively breeding trees with an average of 70 to 85% American chestnut ancestry. In conclusion, the resources developed in this work are foundational for breeding to create diverse restoration populations with sufficient disease resistance and competitive growth.

Westbrook, Jared W. [The American Chestnut Foundat↗
DOE OSTI2026

Data for Engineering and Evolution of Yarrowia lipolytica for Producing Lipids from Lignocellulosic Hydrolysates

Yarrowia lipolytica , an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Hydrolysate↗