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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
NASA NTRS1999

Genetic analysis of the roles of phytochromes A and B1 in the reversed gravitropic response of the lz-2 tomato mutant

The lz-2 mutation in tomato (Lycopersicon esculentum) causes conditional reversal of shoot gravitropism by light. This response is mediated by phytochrome. To further elicit the mechanism by which phytochrome regulates the lz-2 phenotype, phytochrome-deficient lz-2 plants were generated. Introduction of au alleles, which severely block chromophore biosynthesis, eliminated the reversal of hypocotyl gravitropism in continuous red and far-red light. The fri1 and tri1 alleles were introduced to specifically deplete phytochromes A and B1, respectively. In dark-grown seedlings, phytochrome A was necessary for response to high-irradiance far-red light, a complete response to low fluence red light, and also mediated the effects of blue light in a far-red reversible manner. Loss of phytochrome B1 alone did not significantly affect the behaviour of lz-2 plants under any light treatment tested. However, dark-grown lz-2 plants lacking both phytochrome A and B1 exhibited reduced responses to continuous red and were less responsive to low fluence red light and high fluence blue light than plants that were deficient for phytochrome A alone. In high light, full spectrum greenhouse conditions, lz-2 plants grew downward regardless of the phytochrome deficiency. These results indicate that phytochromes A and B1 play significant roles in mediating the lz-2 phenotype and that at least one additional phytochrome is involved in reversing shoot gravitropism in this mutant.

NASA Discipline Plant Biology↗
NASA NTRSDate not supplied

Quantitative Phenotypic Analysis of Arabidopsis Thaliana Grown in Microgravity Using Soap, an Applied Artificial Intelligence

Phenotypic analysis is an essential step in studying the gravitropic responses and gravitational stress experienced by plants grown in microgravity. Many of the phenotypic traits analyzed in gravitropism studies, such as root length, leaf area, secondary root count, and number of root hairs, currently rely upon manual measurement methods for quantification. However, new advances in data analysis technology using artificial intelligence offer an opportunity for more efficient phenotypic analysis and a reduction of time spent in the data collection phase. In this project, the ability of a new artificially intelligent data collection software, SOAP (Simple Object Access Protocol), to collect and quantify phenotypic traits of Arabidopsis thaliana will be assessed. This project will test the measurements taken by an initial draft of the software. SOAP will take measurements of shoot length, a key phenotype used to assess A. thaliana stress response when grown in microgravity conditions. Shoot length measurements made by SOAP will be compared against a series of manual shoot length measurements. The comparison between the two methods of data measurement will provide valuable insight into the relative accuracy of SOAP and the margin of human error when conducting lab measurements.

Arabidopsis↗
DOE OSTI2025

An overview of switchgrass phenotypes variability across diverse populations and their implications for conversion to fuels

There have been substantial changes to the human lifestyle over the past two centuries, which are reflected in the amount of fuel we consume to power our day-to-day needs. The way we use these resources has indeed manifested in an overdependence on non-renewable energy sources, such as coal and petroleum, for generating electricity and powering our transportation needs. There is a pressing need to explore alternative ways of fueling our current lifestyle without impacting the environment. Biofuels have long been touted as a sustainable solution for use as drop-in fuels in aviation and maritime applications. Still, they have yet to establish themselves as a competitive commercial alternative, necessitating further research and development. Lignocellulosic biomass is an underutilized resource that is widely accessible for the commercial processing of renewable biofuels. Bioenergy crops, such as switchgrass (Panicum virgatum L.), which can be cultivated on marginal lands with minimal competition for agricultural land, are an ideal and promising candidate for bulk-scale biofuel synthesis. Over the past 30 years, significant progress has been made in breeding and genetically modifying these grasses to enhance their drought resilience and subsequent yields. However, discrepancies in biomass composition can lead to irregular feedstocks for downstream operations, which in turn affect overall production targets for biofuels. Here, this review examines the variability in switchgrass (P. virgatum L.) biomass phenotypes across diverse populations and plant components, and their implications for biofuel conversion. The study highlights significant variations in biomass yield, composition, and cell wall chemistry both between switchgrass genotypes and within individual cultivars. Key findings include differences in cellulose, hemicellulose, and lignin content between leaves and stems, which affect biomass digestibility and ethanol yield. The review also discusses the impact of lignin chemistry, particularly the syringyl/guaicyl (S/G) ratio, on the efficiency of biomass saccharification. Furthermore, it explores how these variations respond differently to various pretreatment techniques, affecting overall biofuel production. We conclude that understanding and quantifying this variability is crucial for optimizing switchgrass as a feedstock for commercial biofuel production, thereby potentially addressing the pressing need for sustainable energy sources in sectors such as aviation.

Kousika, Rohit [Univ. of Tennessee, Knoxville, TN ↗
NASA NTRS1981

Protective mechanisms and acclimation to solar ultraviolet-B radiation in Oenothera stricta

Plant adaptations ameliorating or repairing the damaging effects of ultraviolet-B (UV-B) radiation on plant tissue were investigated. The degree of phenotype plasticity in UV protective mechanisms and acclimation in relation to the natural solar UV-B radiation flux and in an enhanced UV-B irradiance environment was also examined. Mechanisms by which plants avoid radiation, adaptations altering the path of radiation incident on the leaf, and repair processes were considered. Attenuation of UV-B by tissues, UV-B irradiation into the leaf, and the effects of UV-B on photosynthesis were investigated.

Robberecht, R.↗
NASA NTRS1999

Genetic ablation of root cap cells in Arabidopsis

The root cap is increasingly appreciated as a complex and dynamic plant organ. Root caps sense and transmit environmental signals, synthesize and secrete small molecules and macromolecules, and in some species shed metabolically active cells. However, it is not known whether root caps are essential for normal shoot and root development. We report the identification of a root cap-specific promoter and describe its use to genetically ablate root caps by directing root cap-specific expression of a diphtheria toxin A-chain gene. Transgenic toxin-expressing plants are viable and have normal aerial parts but agravitropic roots, implying loss of root cap function. Several cell layers are missing from the transgenic root caps, and the remaining cells are abnormal. Although the radial organization of the roots is normal in toxin-expressing plants, the root tips have fewer cytoplasmically dense cells than do wild-type root tips, suggesting that root meristematic activity is lower in transgenic than in wild-type plants. The roots of transgenic plants have more lateral roots and these are, in turn, more highly branched than those of wild-type plants. Thus, root cap ablation alters root architecture both by inhibiting root meristematic activity and by stimulating lateral root initiation. These observations imply that the root caps contain essential components of the signaling system that determines root architecture.

Non-NASA Center↗
DOE OSTI2025

Root genetics in the field to understand drought adaptation and carbon sequestration (Final Scientific/Technical Report)

For all crop plants, roots play a critical role in growth. Roots anchor the plants, and are the primary site of nutrient and water uptake. Roots are also the main source of C to soil in the form of root tissues and exudates, and thus greatly influence SOM stocks. To perform these functions, primary roots extend into soil, producing a network of branching roots of characteristic form, known as its root system architecture (RSA). RSA varies among species, and among varieties within a species that are adapted to different environments. Root traits are major targets for the second green revolution because of their potential to improve crop productivity, increase drought tolerance and nutrient acquisition, and increase C capture of soil. Improving the quality of roots in maize will be particularly valuable, since this crop is planted on over 92 million acres annually in the US. The future sustainability of agricultural systems relies on their ability to enhance soil organic matter (SOM) storage and reduce GHG emissions, while maintaining or enhancing productivity. This program had two components, Sensors and Models. For the first component, we designed and built a high-throughput phenotyping platform for root pulling of maize plants. This eliminated the physical labor of manually pulling up plants and reduced the number of personnel required down to one. The standardized pulling mechanism allowed recording force curves during the pulling process, providing additional information. We validated that the maximum force for pulling the root system was well-correlated with the root system mass and provided root crowns for further RSA analysis. These root crowns identified significant correlations with 2D root area and root depth, along with 3D root volume, total root length and number of root tips. We then used this system for field-based studies in maize on the genetics of root system architecture and its relation to nitrogen-use efficiency (NUE), including using lines relevant to the Corteva breeding program. Varieties were also evaluated at Corteva sites in the cornbelt and Danforth farm in Missouri, to establish responses across sites. From these studies we have identified genetic loci associated with root traits and created mutant lines for these loci and correlations of root traits with NUE. For the Models component, we worked to incorporate root and soil characteristics into the MEMS 2.0 soil and ecosystem biogeochemical model. Existing soil C models, such as Century, are unable to represent specific root trait interactions with the soil environment and therefore to accurately forecast the potential C sequestration benefits of root breeding under different climatic and soil type conditions. We have developed the MEMS 2.0 ecosystem biogeochemical model to improve quantification of farm-scale soil carbon and greenhouse gas emissions. The new knowledge and large datasets produced by this project will be used to develop and drive an innovative model capable of forecasting the impacts on soil C stocks and nutrient dynamics. An innovation was to use the empirical data from the field studies (in 1, above) to model genetic variation in nitrogen use efficiencies and soil C input. Our work demonstrated that maize root-derived C rapidly replaces existing soil C and after 3 years of continuous maize, up to 20% of soil organic C in the topsoil (0-15cm) and 3% in the subsoil (15-30cm) was contributed by maize. However, this contribution did not entirely represent a net increase. Root C contribution to soil was affected by maize genetics. We have analyzed soils derived from the CSU field trials for C and N stocks, in the different soil physical fractions represented by the MEMS model, using both physical fractionation with elemental analyses, and Fourier transformed infrared spectroscopy. Data will be used to link crop nitrogen use efficiencies with soil C sequestration and provide data to bridge the field trials with the model development, for verification of model predictions. The project had a number of successful outcomes: we have used the new phenotyping platform to identify new genetic loci that can enhance root phenotypes; we have partnered with multiple maize seed companies phenotype varieties in their breeding programs; we have developed the MEMS model that can help inform industry on the potential for carbon sequestration in the agricultural sector, and which is now available at the CSU Soil Carbon Solutions Center for use.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

A strong loss-of-function mutation in RAN1 results in constitutive activation of the ethylene response pathway as well as a rosette-lethal phenotype

A recessive mutation was identified that constitutively activated the ethylene response pathway in Arabidopsis and resulted in a rosette-lethal phenotype. Positional cloning of the gene corresponding to this mutation revealed that it was allelic to responsive to antagonist1 (ran1), a mutation that causes seedlings to respond in a positive manner to what is normally a competitive inhibitor of ethylene binding. In contrast to the previously identified ran1-1 and ran1-2 alleles that are morphologically indistinguishable from wild-type plants, this ran1-3 allele results in a rosette-lethal phenotype. The predicted protein encoded by the RAN1 gene is similar to the Wilson and Menkes disease proteins and yeast Ccc2 protein, which are integral membrane cation-transporting P-type ATPases involved in copper trafficking. Genetic epistasis analysis indicated that RAN1 acts upstream of mutations in the ethylene receptor gene family. However, the rosette-lethal phenotype of ran1-3 was not suppressed by ethylene-insensitive mutants, suggesting that this mutation also affects a non-ethylene-dependent pathway regulating cell expansion. The phenotype of ran1-3 mutants is similar to loss-of-function ethylene receptor mutants, suggesting that RAN1 may be required to form functional ethylene receptors. Furthermore, these results suggest that copper is required not only for ethylene binding but also for the signaling function of the ethylene receptors.

NASA Discipline Plant Biology↗
NASA NTRS2016

Microarray Data Analysis of Space Grown Arabidopsis Leaves for Genes Important in Vascular Patterning

Venation patterning in leaves is a major determinant of photosynthesis efficiency because of its dependency on vascular transport of photoassimilates, water, and minerals. Arabidopsis thaliana grown in microgravity show delayed growth and leaf maturation. Gene expression data from the roots, hypocotyl, and leaves of A. thaliana grown during spaceflight vs. ground control analyzed by Affymetrix microarray are available through NASAs GeneLab (GLDS-7). We analyzed the data for differential expression of genes in leaves resulting from the effects of spaceflight on vascular patterning. Two genes were found by preliminary analysis to be upregulated during spaceflight that may be related to vascular formation. The genes are responsible for coding an ARGOS like protein (potentially affecting cell elongation in the leaves), and an F-boxkelch-repeat protein (possibly contributing to protoxylem specification). Further analysis that will focus on raw data quality assessment and a moderated t-test may further confirm upregulation of the two genes and/or identify other gene candidates. Plants defective in these genes will then be assessed for phenotype by the mapping and quantification of leaf vascular patterning by NASAs VESsel GENeration (VESGEN) software to model specific vascular differences of plants grown in spaceflight.

Weitzeal, A. J.↗
NASA NTRS2016

Microarray Data Analysis of Space Grown Arabidopsis Leaves for Genes Important in Vascular Patterning

Venation patterning in leaves is a major determinant of photosynthesis efficiency because of its dependency on vascular transport of photo-assimilates, water, and minerals. Arabidopsis thaliana grown in microgravity show delayed growth and leaf maturation. Gene expression data from the roots, hypocotyl, and leaves of A. thaliana grown during spaceflight vs. ground control analyzed by Affymetrix microarray are available through NASA's GeneLab (GLDS-7). We analyzed the data for differential expression of genes in leaves resulting from the effects of spaceflight on vascular patterning. Two genes were found by preliminary analysis to be up-regulated during spaceflight that may be related to vascular formation. The genes are responsible for coding an ARGOS (Auxin-Regulated Gene Involved in Organ Size)-like protein (potentially affecting cell elongation in the leaves), and an F-box/kelch-repeat protein (possibly contributing to protoxylem specification). Further analysis that will focus on raw data quality assessment and a moderated t-test may further confirm up-regulation of the two genes and/or identify other gene candidates. Plants defective in these genes will then be assessed for phenotype by the mapping and quantification of leaf vascular patterning by NASA's VESsel GENeration (VESGEN) software to model specific vascular differences of plants grown in spaceflight.

venation↗
NASA NTRS2016

Microarray Data Analysis of Space Grown Arabidopsis Leaves for Genes Important in Vascular Patterning

Venation patterning in leaves is a major determinant of photosynthesis efficiency because of its dependency on vascular transport of photoassimilates, water, and minerals. Arabidopsis thaliana grown in microgravity show delayed growth and leaf maturation. Gene expression data from the roots, hypocotyl, and leaves of A. thaliana grown during spaceflight vs. ground control analyzed by Affymetrix microarray are available through NASA's GeneLab (GLDS-7). We analyzed the data for differential expression of genes in leaves resulting from the effects of spaceflight on vascular patterning. Two genes were found by preliminary analysis to be upregulated during spaceflight that may be related to vascular formation. The genes are responsible for coding an ARGOS like protein (potentially affecting cell elongation in the leaves), and an F-box/kelch-repeat protein (possibly contributing to protoxylem specification). Further analysis that will focus on raw data quality assessment and a moderated t-test may further confirm upregulation of the two genes and/or identify other gene candidates. Plants defective in these genes will then be assessed for phenotype by the mapping and quantification of leaf vascular patterning by NASA's VESsel GENeration (VESGEN) software to model specific vascular differences of plants grown in spaceflight.

Weitzeal, A. J.↗
DOE OSTI2025

Transcription factor binding divergence drives transcriptional and phenotypic variation in maize

Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here, in this study, we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR–Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.

Galli, Mary [Rutgers Univ., Piscataway, NJ (United↗
DOE OSTI2025

Populus PtrbHLH011 Is a Transcriptional Co‐Regulator Involved in the Activation of Cell Wall Biosynthesis by Iron Deprivation

The lack of a mechanistic understanding of the environmental plasticity of secondary cell wall (SCW) biosynthesis restricts large-scale biomass and bioenergy production on marginal lands. Using Populus (poplar), a key bioenergy crop, we discovered that iron deprivation, a prevalent abiotic stress on marginal lands, stimulates SCW biosynthesis in stems. We identified the transcription factor PtrbHLH011 as a critical regulator underlying this response. Through integrated analyses involving phenotypic characterisation of PtrbHLH011 knockout and overexpression plants, functional genomics and molecular investigations, we established that PtrbHLH011 functions as a central regulator of SCW biosynthesis, iron homeostasis and flavonoid biosynthesis by directly repressing essential genes in these pathways. Iron deprivation downregulates PtrbHLH011 expression, subsequently activating these biosynthetic pathways. Notably, cytosine base editing-based knockout of PtrbHLH011 significantly enhanced plant growth, yielding up to a 110% increase in stem diameter and a 300% increase in leaf iron content. These findings present a novel regulatory mechanism linking environmental iron availability to SCW biosynthesis and illustrate a practical strategy to improve biomass yield on iron-deficient marginal lands. Furthermore, our mechanistic insights into PtrbHLH011 target recognition and regulation provide a valuable foundation for precise manipulation of gene regulatory networks, facilitating the development of high-performance bioenergy crops adapted to marginal environments.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

The BioSensor Instrument Beyond LEIA: a Versatile Platform for Lunar Biology

Introduction: The BioSensor is a deep-space-compatible automated microfluidic culturing instrument. While originally designed to measure the effects of deep space radiation on yeast growth for the BioSentinel mission, it has the potential to host a diverse range of life science experiments with single- and/or multi-celled organisms and can be adapted to interface with a diverse range of platforms in both crewed and uncrewed settings. It is therefore a leading candidate for hosting life sciences experimentation associated with a lunar surface habitat. BioSensor design: The function of the BioSensor is to monitor the growth and metabolic activity of samples in batch fluidic culture, without the need for crew involvement. The current configuration houses organisms in 16 wells within 16 microfluidic cards, accommodating a total of 256 samples, replicates, and controls. Each well has an optical system including three LEDs and a photodiode detector to measure absorbance at three wavelengths, enabling measurement of optical density, color change in dyes such as alamarBlue, and bioproduction of pigmented compounds. Organisms are loaded into fluidic wells and air-dried for storage during integration, launch, and transit, then activated by the introduction of culture medium from storage bags via manifolds that fill one card at a time. Temperature is controlled by individual card heaters, and timing of all activities (fluidics fills, optical measurements, temperatures) is directed by an experiment script. The self-contained BioSensor payload is roughly 4U in volume; with electrical/mechanical/thermal interface, e.g. for operation on ISS or a lunar lander, as well as a linear energy-transfer (LET) charged-particle radiation spectrometer, the entire system is closer to 6U. BioSentinel and LEIA: Flown on the ISS and in a deep-space free flyer for BioSentinel, the BioSensor has been modified for use in the LEIA mission, including improvements to reduce the sensitivity to lengthy launch delays. LEIA will monitor yeast growth in the radiation and reduced-gravity environment of the lunar surface no earlier than 2026, on a CLPS lander [4]. Changes include accommodating additional culture media and an additional LED color for a new biological assay (bioproduction of carotenoids-- dietary antioxidants), as well as modifications to the housing to allow late-load biology changeout and improved isolation between fluidics and electronics. Future prospects: Future work with the BioSensor, beyond LEIA, will include expanding the range and diversity of organisms and assays accommodated. Preliminary work has demonstrated the growth of Arabidopsis seedlings in BioSensor fluidic cards, including optical measurements of growth rate over time. Minor modifications could allow measurement of phenotypes related to photosynthetic capacity in both plants and cyanobacteria. The experimental capabilities of the BioSensor could be dramatically increased by introducing the capability for fluorescence measurements, and/or the design of novel biological assays using luminescence. The BioSensor can also be adapted for new platforms and experiment settings; in addition to free-flyer, ISS, and CLPS lander, a preliminary design concept has been developed for crewed deployment directly to the lunar surface. The instrument could be accommodated inside a lunar habitat, where its automated operation would make it an excellent candidate for experiments from fundamental investigations into the response of organisms to lunar surface conditions to applied-science purposes such as screening engineered strains of various organisms for bioproduction capability.

J A Lee↗
NASA NTRSDate not supplied

Mining the Gravity Mutants of Arabidopsis

Gravity mutants are a valuable resource for understanding gravity perception, signaling, and response in plants. A review of 190 publications resulted in a list of 97 loci with mutations that caused a gravitropic phenotype. While all these mutants show some form of gravity phenotype, several are also generally defective in growth. After removing these nonspecific mutants, 76 loci were deemed to have true gravity mutants. The gene list was then used to create a sortable database containing key factors of gravity signaling as well as data on methodologies and the development of mutant lines. Indexing this database has allowed us to pull out trends that were not visible in individual publications. For example, mutants that are unable to rearrange starch statoliths make up a larger proportion of the described inflorescence stems mutants than any other organ. Comparing these statolith mutants across organs shows that root and inflorescence stems consistently display different phenotypes for the same class of defect. The more severe gravity defects are most commonly described in root tissue while other tissues are more likely to show only a delayed or reduced response to gravity. The experience of members of the GeneLab plant Analytics Working Group (AWG) in data visualization and gene mapping have sparked new ideas for utilizing this database. Knowledge of shared traits, mutant development, and growth can provide a new resource for the production of seed lines specialized for their response to gravity.

gravitropism↗
DOE OSTI2025

The promising role of proteomes and metabolomes in defining the single-cell landscapes of plants

The plant community has a strong track-record of RNA sequencing technology deployment, which combined with the recent advent of spatial platforms (e.g., 10x genomics), has resulted in an explosion of outstanding single cell and nuclei datasets that can be put in an in situ context within tissues (e.g., a cell atlas)1. In the genomics era, application of proteomics technologies in the plant sciences has always trailed behind that of RNA sequencing technologies, largely due to accessibility, ease-of-use and access to expertise along with depth of analysis benefits. On the other hand, the use of early analytical tools for characterizing small molecules (metabolites) from plant systems predates nucleic acid sequencing and proteomics analysis2, as the search for plant-based natural products has played a significant role in improving human health throughout history. However, the employment of proteomics and metabolomics assays for characterizing plant cell processes now remains significantly behind transcriptional approaches, even though both provide a direct functional readout of cell states and phenotypes.

Anderton, Christopher R. [BATTELLE (PACIFIC NW LAB↗
DOE OSTI2026

Plant Bioengineering Atlas: A Knowledge Graph of Genes, DNA Constructs, and Plant Traits.

Plant bioengineering has generated tens of thousands of genotype-to-phenotype relationships, but this knowledge remains fragmented across narrative literature and difficult to use computationally. Inconsistent descriptions of DNA constructs, host species, and traits, including variable species names, omitted regulatory elements, and inconsistent gene symbols, impede data reuse, comparative analysis, and design-build-test-learn cycles. Here, we present the Plant Bioengineering Atlas, a literature-mined, ontology-grounded knowledge base assembled using an artificial intelligence (AI)-aided extraction pipeline. A large language model parsed open-access primary research articles to generate structured, provenance-anchored records of engineered genes, modification types, promoter-gene-terminator constructs, host species, target traits, and reported phenotypes, with every record traceable to its source. The current release contains 14,358 curated records encompassing 6,998 distinct genes across 436 plant species from 6,452 papers published between 2000 and 2026. Corpus analysis reveals that experiments are concentrated in a small group of model and crop species, disease and pathogen resistance is the most frequently engineered trait class, and constitutive regulatory parts (particularly the CaMV 35S promoter and NOS terminator) remain pervasive. Two in five records omit one or both flanking regulatory elements (i.e., promoter and terminator), while only 23.4% describe cassettes in which both elements resolve to named part classes, exposing a systematic reproducibility gap. We organize these data into a knowledge graph linking genes, constructs, species, and traits; provide access through an interactive web portal; and propose an AI-compatible documentation standard for AI-ready reporting. The Plant Bioengineering Atlas provides a foundation for data-driven hypothesis generation and AI-aided plant biodesign.

, Genes, DNA Constructs↗
DOE OSTI2025

Comparative transcriptomic and phenotypic analysis of monoclonal and polyclonal Populus deltoides genotypes

Populus species are highly valued for bioenergy and bioproducts due to their rapid growth and productivity. Polyclonal plantings, or mixtures of Populus clones, have shown the potential to enhance resource utilization and productivity, likely due to phenotypic differences arising from niche differentiation. In this study, we investigated gene expression and productivity in monoclonal and polyclonal stands of P. deltoides . Phenotypic results showed that polyclonal plots exhibited higher leaf area index (LAI; p < 0.01, 2.96 ± 0.057 m 2 ) and total biomass (p < 0.01, 2.74 ± 0.06) compared to monoclonal plots, indicating superior productivity. RNA sequencing revealed upregulation of key genes such as exocyst subunit exo70 family protein H7 (EXO70H7), NDH-dependent cyclic electron flow 5 (NDF5) , and expansin-like A3 (EXLA3) . We also observed enrichment in phenylalanine metabolism and other secondary metabolic pathways in clone S7C8. Phenotypic results, upregulated genes and enriched biological pathways identified in this study may explain the enhanced productivity, increased nitrate content, and expanded canopy in polyclonal plantings. Overall, this study provides a foundation for future research to enhance forest productivity by linking molecular mechanisms to practical applications in field plantings.

differential gene expression↗
DOE OSTI2025

The Pseudoenzyme β‐Amylase9 From Arabidopsis Activates α‐Amylase3: A Possible Mechanism to Promote Stress‐Induced Starch Degradation

ABSTRACT Starch accumulation in plants provides carbon for nighttime use, for regrowth after periods of dormancy, and for times of stress. Both ɑ‐ and β‐amylases (AMYs and BAMs, respectively) catalyze starch hydrolysis, but their functional roles are unclear. Moreover, the presence of catalytically inactive amylases that show starch excess phenotypes when deleted presents questions on how starch degradation is regulated. Plants lacking one of these catalytically inactive β‐amylases, BAM9, have enhanced starch accumulation when combined with mutations in BAM1 and BAM3, the primary starch degrading BAMs in response to stress and at night, respectively. BAM9 has been reported to be transcriptionally induced by stress although the mechanism for BAM9 function is unclear. From yeast two‐hybrid experiments, we identified the plastid‐localized AMY3 as a potential interaction partner for BAM9. We found that BAM9 interacted with AMY3 in vitro and that BAM9 enhances AMY3 activity about three‐fold. Modeling of the AMY3‐BAM9 complex predicted a previously undescribed alpha–alpha hairpin in AMY3 that could serve as a potential interaction site. Additionally, AMY3 lacking the alpha–alpha hairpin is unaffected by BAM9. Structural analysis of AMY3 showed that it can form a homodimer in solution and that BAM9 appears to replace one of the AMY3 monomers to form a heterodimer. The presence of both BAM9 and AMY3 in many vascular plant lineages, along with model‐based evidence that they heterodimerize, suggests that the interaction is conserved. Collectively these data suggest that BAM9 is a pseudoamylase that activates AMY3 in response to cellular stress, possibly facilitating stress recovery.

Biochemistry & Molecular Biology↗