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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Methods of improving drought and salt resistance in a plant and genetically engineered plants with improved drought and salt resistance

The present disclosure provides methods for increasing drought resistance, salt resistance, and biomass production of a plant. The methods encompass expression of DiGeorge-Syndrome Critical Region 14 (DGCR14) gene in the plant. In comparison to a plant not manipulated in this manner, the disclosed, genetically-modified, plants display improved drought resistance and salt resistance. Also provided are plants that can be obtained by the method according to the invention, and nucleic acid vectors to be used in the described methods.

Xie, Meng↗
DOE OSTI2023

Episomal DNA vectors for plant genetic engineering

This disclosure pertains to a novel platform for genetic engineering of chloroplasts. The disclosure provides episomal DNA vectors containing a chloroplast origin of replication. These vectors remain extra-plastomic and sustainably and autonomously replicate in chloroplasts of the plant cells transformed with the vectors and in the plants regenerated from the transformed plant cells. The episomal DNA vectors do not contain any sequence that shares sequence homology with the plastome DNA and, thus, do not get integrated into the plastome DNA. The vectors can also comprise one or more genes of interest that confer desirable characteristics to the transformed plant cells. The disclosure also provides methods of transforming plant cells with the episomal DNA vectors and regenerating from the transformed plant cells plants having desirable characteristics. The vectors and methods disclosed herein provide a significant advancement in speed, flexibility, and prospects of introducing genes into plant cells for effective metabolic engineering.

Lenaghan, Scott C.↗
DOE OSTI2026

Development of male-sterile lines of Setaria viridis to accelerate C 4 model plant genetics

Setaria viridis is a diploid C 4 grass in the Poaceae family, notable for its rapid life cycle of 6–8 weeks from sowing to seed—much shorter than the 4–5 months required by crops such as Zea mays and Sorghum bicolor . This fast growth makes S. viridis a valuable model for C 4 crop research. Genetic crosses are essential for studying gene function, but manual crossing is labor-intensive and time-consuming. Here, to address this, we developed a male-sterile line by targeting the S. viridis ortholog of Setaria italica NO POLLEN 1 ( SiNP1 ), which encodes a glucose–methanol–choline oxidoreductase required for pollen exine formation. Using Cas9 and TREX2 -mediated genome editing, we generated SiNP1 knockouts in both the S. viridis ME034V and A10.1 backgrounds that were fully male-sterile. Backcrossing T 0 male-sterile plants to ME034V wild-type followed by selfing yielded a stable BC 1 F 2 line homozygous for a 59 bp deletion in the S. viridis NO POLLEN 1 gene, easily genotyped by PCR and maintained by heterozygous siblings. Using this line, we developed a simple and efficient crossing protocol that eliminates the need for emasculation. This method enables a single person to perform up to 100 crosses per day—compared to 15 using traditional methods—and yields 20–32 F 1 hybrid seeds per panicle with 100% genetic purity. We also quantified pollen flow and outcrossing frequencies under greenhouse conditions to develop optimal bagging strategies and prevent unintended pollination. This resource accelerates genetic research in S. viridis , enhancing its utility as a premier C 4 model for mapping and functional genomics.

C4 research↗
DOE OSTI2026

Learning from nature’s plant engineers: Hijacking metabolism and development beyond genetics

Plant metabolism underpins the food, fiber, and fuel that support our economy, driving strong interest in new strategies to rewire plant metabolism for emerging applications. While most synthetic biology efforts are reliant on genetic engineering, plants can be manipulated in many other ways that remain comparatively underexplored. Across nature, diverse organisms, including bacteria, fungi, and insects, have evolved sophisticated mechanisms to exploit plant metabolic richness, reshaping it for purposes that span from basic nutrition to the construction of complex, novel structures for shelters. These interspecies interactions and non-model systems represent unique manners in which plants can be reprogrammed or hijacked by other organisms, offering inspiration for novel approaches to engineering plant metabolism. By better understanding the basis of how organisms induce these remarkable transformations in plants, we can expand the conceptual boundaries of synthetic biology and reveal alternative routes to manipulating plants for the production of a diverse array of valuable compounds and materials. Deeper insight into these mechanisms will yield novel blueprints for rethinking the scope and breadth in which we can redesign plant metabolism across many applications.

Sarkiss, Anthony E. [University of California, Ber↗
DOE OSTI2022

Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics

In plants, as in other species, genotypic variation in combination with environmental variation leads to differences in the biochemical makeup of cells, measurable as molecular phenotypes. These in turn influence physiological and developmental traits such as organ formation and plant growth, and eventually traits relevant in agriculture, such as yield and stress tolerance. Thus, relating genotypes to phenotypes yields fundamental insights into the regulation of important processes in plant development and physiology, but also provides the ability to predict yield and quality traits in specific environments, which is essential in basic plant science and molecular breeding of resilient plants in changing environments.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Mutagenic effects of heavy ion radiation in plants

Genetic and developmental effects of heavy ions in maize and rice were investigated. Heavy particles with various charges and energies were accelerated at the BEVALAC. The frequency of occurrence of white-yellow stripes on leaves of plants developed from irradiated maize seeds increased linearly with dose, and high Linear Energy Transfer (LET) heavy charged particles, e.g., neon, argon, and iron, were 2-12 times as effective as gamma rays in inducing this type of mutation. The effectiveness of high-LET heavy ion in (1) inhibiting rice seedling growth, (2) reducing plant fertility, (3) inducing chromosome aberration and micronuclei in root tip cells and pollen mother cells of the first generation plants developed from exposed seeds, and (4) inducing mutation in the second generation, were greater than that of low-LET gamma rays. All effects observed were dose-dependent; however, there appeared to be an optimal range of doses for inducing certain types of mutation, for example, for argon ions (400 MeV/u) at 90-100 Gy, several valuable mutant lines with favorable characters, such as semidwarf, early maturity and high yield ability, were obtained. Experimental results suggest that the potential application of heavy ions in crop improvement is promising. Restriction-fragment-length-polymorphism (RFLP) analysis of two semidwarf mutants induced by argon particles revealed that large DNA alterations might be involved in these mutants.

Mei, M.↗
DOE OSTI2023

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes. Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla. We provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1997

W Photoprotection in Tropical Marine Organisms

Increasing levels of ultraviolet (UV) radiation reaching the earth's surface which results from stratospheric ozone depletions could have serious implications for terrestrial plants and for aquatic organisms within the euphotic zone. A documented 9% decline in ozone at mid-latitudes is considered to produce a 12% increase in harmful UV radiation. The biologically damaging effects of higher UV levels, particularly W-B (280-320 rim), could manifest earlier in the tropics because of the relative thinness of the earth's equatorial ozone layer. Tropical marine organisms are also living close to their upper tolerance levels of water temperature, However, despite the large potential effects on plants and animals, little is known about UV effects on tropical ecosystems. Long-term ecological studies are needed to quantify the effects of increased UV radiation on terrestrial and marine ecosystems and to produce reliable data for prediction. Plants have developed several mechanisms to protect themselves from harmful UV radiation, one of which is the production of secondary leaf pigments that absorb W-B radiation (screening pigments). A higher concentration of screening pigments (e.g. flavonoids) in leaves may be interpreted as a natural response to increased W radiation. If higher concentrations of flavonoids filter out the excessive W radiation, no damage will occur, as suggested by Caldwell et al. (1989) and Tevini (1993). Failure to screen all W-B may result in deleterious effects on photosynthesis, plant genetic material, and plant and leaf morphology and growth. Eventually this will have an impact on ecosystem processes, structure, species composition, and productivity. This paper describes an ongoing project that is assessing the responses of mangroves, seagrasses and corals to W radiation by studying pigment concentrations, biophysical parameters, and variations in spectral reflectance in the field and in W-reduction experiments. Preliminary results on the distribution of W-absorbing flavonoid compounds in red mangroves (Rhizophora mangle) and the seagrass Thalassia testudinum, are presented. This research also provides, for the first time, a permanent record of daily W irradiance measurements at a tropical -location.

Armstrong, Roy A.↗
DOE OSTI2021

Engineered Sorghum Bagasse Enables a Sustainable Biorefinery with p-Hydroxybenzoic Acid-Based Deep Eutectic Solvent

Integrating multidisciplinary research in plant genetic engineering and renewable deep eutectic solvents (DESs) can facilitate a sustainable and economic biorefinery. In this work, we leveraged a plant genetic engineering approach to specifically incorporate C6C1 monomers into the lignin structure. By expressing the bacterial ubiC gene in sorghum, p-hydroxybenzoic acid (PB)-rich lignin was incorporated into the plant cell wall while this monomer was completely absent in the lignin of the wild-type (WT) biomass. A DES was synthesized with choline chloride (ChCl) and PB and applied to the pretreatment of the PB-rich mutant biomass for a sustainable biorefinery. The release of fermentable sugars was significantly enhanced (~190 % increase) compared to untreated biomass by the DES pretreatment. In particular, the glucose released from the pretreated mutant biomass was up to 12 % higher than that from the pretreated WT biomass. Lignin was effectively removed from the biomass with the preservation of more than half of the β-Ο-4 linkages without condensed aromatic structures. Hydrogenolysis of the fractionated lignin was conducted to demonstrate the potential of phenolic compound production. In addition, a simple hydrothermal treatment could selectively extract PB from the same engineered lignin, showing a possible circular biorefinery. These results suggest that the combination of PB-based DES and engineered PB-rich biomass is a promising strategy to achieve a sustainable closed-loop biorefinery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Methods for controlling cell wall biosynthesis and genetically modified plants

The present disclosure provides methods of producing plants with preferred levels of cell wall biosynthesis; and uses of such plants. The inventors have identified that the GFR9, CCoAOMT and MYB41 genes are major regulators of the cell wall biosynthesis pathway. Plants with modulated cell wall biosynthesis, based on modulation of the expression or activity of the GFR9, CCoAOMT and MYB41 genes, have divergent uses including pulp and paper production, and bioproduct production.

Tschaplinski, Timothy J.↗
NASA NTRS1999

Engineering plants for spaceflight environments

The conversion efficiency of radiation into biomass and yield has steadily increased for centuries because of continued improvement in both plant genetics and environmental control. Considerable effort has gone into improving the environment for plant growth in space, but work has only begun to engineer plants for spaceflight. Genetic manipulation offers tremendous potential to improve our ability to study gravitational effects. Genetic manipulation will also be necessary to build an efficient regenerative life support system. We cannot fully characterize plant response to the spaceflight environment without understanding and manipulating their genetic composition. Identification and selection of the existing germplasm is the first step. There are thousands of cultivars of each of our major crop plants, each specifically adapted to a unique environment on our planet. Thousands of additional lines are held in national germplasm collections to maintain genetic diversity. Spaceflight imposes the need to tap this diversity. Existing lines need to be evaluated in the environment that is characteristic of closed-system spaceflight conditions. Many of the plant growth challenges we confront in space can be better solved through genetic change than by hardware engineering. Ten thousand years of plant breeding has demonstrated the value of matching genetics with the environment. For example, providing continuous light can increase plant growth in space, but this often induces calcium deficiencies because Ca is not supplied by guttation during a dark period. This deficiency cannot be eliminated through increased root-zone and foliar Ca applications. It can be solved, in wheat, through genetic selection of lines that do not have the deficiency. Subsequent comparison of lines with and without the Ca deficiency has also helped us understand the nature of the problem.

Non-NASA Center↗
DOE OSTI2023

Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa , a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme–substrate relationships. We focus on uridine diphosphate–glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in P. trichocarpa , presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in P. trichocarpa. We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for in silico analyses and evidence-based guidance for in vivo functional characterization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Understanding Plant Signaling Via Innovations in Probe Delivery and Imaging

The goal of this project was to develop tools for studying plant processes in living tissues. We wanted a method for introducing probes for studying plant processes such that plants could remain intact and imaged iteratively. Towards this end, we successfully optimized carbon nanofibers that we showed could deliver non-permeable signaling probes/biomolecules to plant cells. These were created on a rigid backing and also successfully transferred to a flexible backing to use with curved plant structures. We also built fiber optic microscopes that permit iterative non-destructive fluorescence or light micrographs and created protocols and devices to stabilize plant organs during imaging. These tools were developed in conjunction with research aimed understanding receptor-mediated peptide trafficking and responses relevant to plant cell growth and defense tradeoff. During this project, we designed and built two fiberoptic fluorescence microscopes; (b) designed, fabricated and validated different nanospike designs for delivering probes to plants, including the feasibility of delivering DNA constructs for expression studies; (c) developed fluorescent peptide probes (active and inactive versions of a secreted receptor ligand called phytosulfokine or PSK) and performed mobility tests after application to plants using microscopy; (d) used appropriate genetic plant backgrounds to facilitate PSK trafficking and response mechanisms; (e) determined the transcriptional changes due to PSK-induced signaling related to growth/defense tradeoff; (f) performed experiments showing the growth/defense tradeoff involves repression of specific defense components in response to PSK. This project also involved the training of two PhD students and five Masters students.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

A Novel Gene Stacking Method in Plant Transformation Utilizing Split Selectable Markers

Gene stacking, the process of introducing multiple genes into a single plant to enhance desired traits, is essential for plant genetic improvement through both conventional breeding and genetic transformation. In general, transformation-based gene stacking can be achieved through either co-transformation to simultaneously introduce multiple genes or sequential multi-round transformation. While co-transformation is generally faster and more efficient than sequential multi-round transformation, it often requires two selectable marker genes, which confer resistance to antibiotics, for selecting transgenic events. However, in most cases, there is only one best selectable marker gene for a specific plant species or genotype. Also, it is harder to optimize the concentrations of two antibiotics for co-transformation than using one antibiotic for selecting transgenic events. To overcome this challenge, we recently developed an innovative split selectable marker system for plant co-transformation, allowing the use of one selectable marker gene to select transgenic events. This method involves constructing two binary vectors, each carrying a subset of genes of interest and a partial fragment of the selectable marker gene, which is connected to a partial intein fragment. Following Agrobacterium -mediated co-transformation, plants harboring both binary vectors are selected using a single antibiotic, such as kanamycin. This split-marker system can be used to co-transform multiple genes into both herbaceous and woody plants, accelerating genetic improvement of polygenic traits or integrative improvement of multiple traits to simultaneously increase crop yield and quality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines ( Triticum aestivum , CDC Stanley x CDC Landmark), wheat-barley ( T . aestivum x Hordeum vulgare ) and wheat-wheatgrass ( Triticum durum x Thinopyrum intermedium ) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Association mapping across a multitude of traits collected in diverse environments in maize

Abstract Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data—18M markers—from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 distinct trait data sets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be 3 genes based on a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g., above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher-density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype-by-environment interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1

The VCF dataset includes genetic variations found in 1,323 Populus trichocarpa genotypes, providing valuable information for scientists studying plant genetics. Researchers have generated this dataset using whole-genome DNA short-read sequencing on the Illumina Genome Analyzer, HiSeq 2000, and HiSeq 2500 platforms. This sequencing effort ensured a minimum expected sequencing depth of 15×. The dataset comprises more than 9.7 million single nucleotide polymorphisms (SNPs) and indel variants. The combined annotation files are derived from P. trichocarpa v3.0 and v3.1. We merged these files to create a comprehensive annotation file used for GWAS analysis. In total, 38,830 genes overlapped between the two versions. For overlapping genes, we defined the start as the smaller and the end as the larger among the two versions to increase the likelihood of locating candidate genetic loci. Additionally, we included 2,505 unique genes from v3.0 and 4,120 unique genes from v3.1, resulting in a total of 45,455 genes in the updated annotation file.

09 BIOMASS FUELS↗