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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Telomere-to-telomere assemblies of chromosome 10 reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by Helitrons

The model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases ( KCS ), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables the development of telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed. Integrating this information can improve genomic prediction for breeding and provide insights into the evolutionary basis of important traits. Our analysis of 78 long-read haplotypes from chromosome 10 identified more than twice as many KCS genes as previously reported, and numerous intragenic non-synonymous substitutions. Random Forest predictive models highlighted the importance of Potri.010G079500 in producing very long chain alkenes; however, its absence did not predict previously reported alkene-deficient phenotypes. Instead, alkene levels are best predicted by the combinations of KCS copies. Additionally, amino acid substitutions clustered around ligand and donor binding pockets, suggesting they contribute to differing wax cuticle composition. Finally, each KCS gene and copy was linked to a Helitron transposon. A phylogenetic analysis suggests Helitrons are the evolutionary mechanism for generating KCS tandem arrays. Long-read generated telomere-to-telomere assemblies of P. trichocarpa chromosome 10 revealed large-effect loci critical to genetic studies that are unattainable from short-reads. This new resource produced novel insights into genome structure and function, and a novel mechanism for generating tandem gene duplication. Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.

09 BIOMASS FUELS↗
DOE OSTI2026

Populus_trichocarpa_Breeding_Population_SNPs

These data are from the manuscript “Application of Genomic Prediction in a Populus trichocarpa Breeding Program”, by Brian J. Stanton, David Macaya-Sanz, Chanaka Roshan Abeyratne, David Kainer, Kathy Haiby, Austin Himes, Carlos Gantz, Gerald A. Tuskan, and Stephen P. DiFazio. The data are based on genome resequencing to approximately 10X depth on two collections of Populus trichocarpa trees from Oregon, Washington, California, and British Columbia. The first collection consists of 293 genets collected by Poplar Innovations LLC for a breeding program. The second collection consists of 961 trees collected for the purpose of genome-wide association studies. These genets were sequenced using short, paired-end Illumina sequence reads (Chhetri et al. 2019). Reads were aligned to the P. trichocarpa ′Stettler-14′ reference (Hofmeister et al. 2020), with minor modifications to correct mis-assemblies (Zhou et al. 2020), and variants were called as per methods described in (Abeyratne et al. 2023). Identified variants were filtered using GATK’s VariantFiltration tool (DePristo et al. 2011), with filter expression flag set to “AF < 0.01 || AF > 0.99 || QD < 10.0 || ExcessHet > 20.0 || FS > 10.0 || MQ < 58.0”. SNPs with severe departures from Hardy−Weinberg expectations (exact-test p< 0.01) were also removed using vcftools --hwe flag (Danecek et al. 2011), resulting in 15,627,211 bi-allelic SNPs. The data included here consist of 141,903 high quality bi-allelic genome-wide SNPs obtained by further filtering the original SNP dataset using vcftools with flags --maf 0.05, --max-maf 0.95, --max-missing 0.95, --min-meanDP 10.75, --max-meanDP 43.00, --thin 2000. Collectively, these filtering parameters removed SNPs with 1) a minor allele frequency ≤ 0.05; 2) proportion of missing data for individual loci exceeding 5%; 3) sequencing depth more than 2X mean-depth or less than 0.5X mean-depth; or 4) a distance of

09 BIOMASS FUELS↗
DOE OSTI2026

Geographic Distribution of Populus trichocarpa Genotypes by ADMIXTURE Ancestry

An interactive map showing Populus trichocarpa GWAS population structure estimated by ADMIXTURE (k=3, selected as optimal from k=2-11). Sampling locations are colored by their predominant ancestry proportion among the three inferred populations and geographic origins are searchable by genotype or river system using the search bar.

Admixture↗
DOE OSTI2025

Climate adaptation in Populus trichocarpa : key adaptive loci identified for stomata and leaf traits

We investigated adaptive genetic variation in Populus trichocarpa, a potential biofuel feedstock crop, to better understand how physiological traits may influence tolerance to water limitation. Our study focused on leaf and stomatal traits, given their roles in plant–water relations and adaptation. Using a diversity panel of over 1300 genotypes, we measured 14 leaf and stomatal traits under control (well-watered) and drought (water-limited) conditions. We conducted genome-wide association studies (GWAS), climate association analyses, and transcriptome (RNA-seq) profiling to identify genetic loci associated with phenotypic variation and adaptation. Stomatal traits, including size and density, were correlated with the climate of origin, with genotypes from more arid regions tending to have smaller but denser stomata. GWAS identified multiple loci associated with trait variation, including a major-effect region on chromosome 10 linked to stomatal size and abaxial contact angle. This locus overlapped with a tandem array of 3-ketoacyl-CoA synthase (KCS) genes and showed strong allele–climate and gene expression associations. Our findings reveal genetic and phenotypic variation consistent with local adaptation and suggest that future climates may favor alleles associated with smaller stomata, particularly under increasing aridity. This work provides insights into climate adaptation and breeding strategies for resilience in perennial crops.

Populus trichocarpa↗
DOE OSTI2024

Lignin content of Populus trichocarpa residues after CELF pretreatment and CBP fermentation

Here we present a dataset of lignin content from a woody energy crop (Populus trichocarpa) residues after a series of co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment and consolidated bioprocessing (CBP) process. The natural poplar variant GW-9947 from the Center for Bioenergy Innovation (CBI) was used. The poplar was knife milled and passed through a 1 mm sieve and CELF pretreatment was performed in a Parr autoclave reactor with 7.5 wt % solids loading, 0.5 wt% H2SO4 as catalyst at 150°C with 5, 15, 25 and 30 minutes, respectively. Tetrahydrofuran was added in a 1:1 mass ratio with water as the pretreatment solvent. The residues from CELF pretreatment were then subjected to CBP using the bacterium C. thermocellum DSM 1313. CBP fermentations were performed at 60 °C in a shaker at 50, 75, and 100 grams/L solids loadings. The Klason lignin was measured using a two-step acid hydrolysis process. In brief, the poplar samples were first hydrolyzed by 72 wt% sulfuric acid at 30 oC for an hour. The hydrolysates were then diluted to 4 wt% sulfuric acid using deionized water and subsequently autoclaved at 121 oC for 1 h. Upon the completion of the two-step hydrolysis, the resulting solution was cooled to room temperature and the precipitate was then filtered through a G8 glass fiber filter through a crucible, dried at oven for overnight, and weighed to get the Klason lignin content. The lignin data provides information about lignin content changes after CELF and C. thermocellum CBP process.

Lignin Populus trichocarpa CELF pretreatment CBP f↗
DOE OSTI2026

Cuticular wax profiling of Populus trichocarpa and P. balsamifera reveals surface similarities with underlying differences

Cuticular waxes are a mixture of hydrophobic components protecting plant tissues from the environment. Populus trichocarpa and P. balsamifera are closely-related tree species with broad North American distribution; however, variation in their cuticular wax composition across their range remained poorly understood. To address this gap, stem and leaf waxes from both species across three developmental stages were profiled by gas chromatography-mass spectrometry. A core set of compounds shared across tissues, accessions, and developmental stages was detected, as well as tissue- or species-specific constituents such as phenolics and alkenes. Phenolic-derived compounds were more prevalent at early stages of development compared to the predominantly aliphatic composition of mature tissues. Moreover, early stage leaves also showed enhanced protection from desiccation and oxidative stress in a subset of accessions. Alkenes, found exclusively in leaves, segregated the poplar accessions into alkene-producing and alkene-lacking phenotypes. GWAS analysis of 174 P. trichocarpa accessions identified a region on chromosome 10 containing a tandem cluster of ketoacyl CoA synthases associated with alkene accumulation in P. trichocarpa , which was not significantly associated in 133 P. balsamifera individuals examined. These findings reveal dynamic, developmentally regulated, and species-specific variation in poplar wax profiles. Understanding these chemical traits offers new opportunities to develop Populus varieties with enhanced environmental resilience and adaptive potential.

GWAS↗
DOE OSTI2026

APPL Hyperspectral_Imaging_Dataset_for_Heritability_Analysis_in_Populus_trichocarpa

This dataset contains hyperspectral imaging data collected at the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory. Natural variants of Populus trichocarpa were imaged using a high-throughput hyperspectral phenotyping pipeline to quantify spectral reflectance traits for downstream quantitative genetics analyses. The dataset includes hyperspectral image files and derived reflectance data products suitable for extracting spectral features across the measured wavelength range (e.g., VNIR and/or SWIR, depending on instrument configuration), along with associated sample metadata (e.g., genotype identifiers, experimental design factors, and imaging run identifiers). These data were generated to support analyses of broad-sense heritability of hyperspectral traits and their relationships with biochemical phenotypes (including lignin traits from Py-MBMS).

APPL↗
DOE OSTI2025

Genetic_and_epigenetic_signatures_of_Populus_Trichocarpa_in_response_to_abiotic_stress

Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. Approximately 5% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.

CBI↗
DOE OSTI2026

Genetic and epigenetic signatures of Populus trichocarpa in response to abiotic stresses

Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. We found that ∼5-6% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.

DNA methylation↗
DOE OSTI2026

Unraveling plant phenotype to genotype associations with daily hyperspectral traits in Populus trichocarpa

Hyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales. In this study, we combined tower-based continuous hyperspectral sensing with genome-wide association studies to analyze 1423 wavebands (400-900 nm) and derivative vegetation indices across 505 genotypes and the genetic architecture of hyperspectral phenotypes over time in Populus trichocarpa Torr. & Gray grown under field conditions. Wavelengths related to chlorophyll and carotenoid absorption spectra exhibited the strongest genetic variation resulting in 98 significant SNP associations. Notably, we found substantial overlap in genetic association between the blue and red spectral regions, indicative of carotenoids and chlorophyll, respectively, and identified more than 10 candidate genes associated with chloroplast function, underpinning photosynthetic activity. Furthermore, fluctuations in associations for vegetative indices, such as the chlorophyll:carotenoid index (CCI), across the growing season reveal a temporally dynamic genetic architecture of physiological traits associated with fall senescence of this temperate tree species. Finally, we also observed correlations (spearman rho = 0.3, p < 1x10 −8 ) between individual wavebands or vegetative indices and growth rate, assessed as the relative change of tree height over the growing season. The growth rate prediction was substantially improved by a regularization multivariate model (spearman rho>0.5, p < 1x10 −16 ), reinforcing the value of hyperspectral measurements for predicting traits linked to tree productivity. These findings highlight the potential of high-throughput, rapid, hyperspectral genome wide association studies GWAS to uncover physiologically meaningful genetic variation and offer promising insights for future acceleration for plant breeding.

09 BIOMASS FUELS↗
DOE OSTI2024

Lignin molecular weights of Populus trichocarpa residues after CELF pretreatment

Here we present a dataset of molecular weights of lignin from a woody energy crop (Populus trichocarpa) residues after a series of co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment. The natural poplar variant GW-9947 from the Center for Bioenergy Innovation (CBI) was used. The poplar was knife milled and passed through a 1 mm sieve and CELF pretreatment was performed in a Parr autoclave reactor with 7.5 wt % solids loading, 0.5 wt% H2SO4 as catalyst at 150°C with various time. Tetrahydrofuran was added in a 1:1 mass ratio with water as the pretreatment solvent. Lignin was isolated from the pretreated samples after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 580 rpm for 2.5 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The solid residue was isolated by centrifugation and hydrolyzed again with freshly added buffer and enzymes for another 48 h. After filtration, the solid residue was extracted twice with 96% (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover lignin. The lignin samples were then derivatized in an acetic anhydride/pyridine (1:1, v/v) mixture and stirred at room temperature for 24 h. Ethanol was added to the reaction mixture, left for 30 min and then removed with a rotary evaporator. The addition and removal of ethanol was repeated at least 3 times until all traces of acetic acid were removed. Acetylated lignin samples were then dissolved in tetrahydrofuran (THF) at a concentration of 1.0 mg/mL. The molecular weight of acetylated lignin was measured by a gel permeation chromatography (GPC) on a PSS-Polymer Standards Service (Warwick, RI, USA) GPC SECurity 1200 system featuring Agilent HPLC 1200 components equipped with four Waters Styragel columns (HR1, HR2, HR4 and HR6) and an UV detector (270 nm). Tetrahydrofuran was used as the mobile phase and flow rate was 0.3 mL/min. The Polymer Standards Service WinGPC Unity software (Build 6807) was used for data processing for all the samples. The data provides information about the effects of CELF pretreatment time at 150 ºC on lignin molecular weights.

09 BIOMASS FUELS↗
DOE OSTI2024

Complete genome sequence of Luteolibacter sp. strain Populi, a member of phylum Verrucomicrobiota isolated from the Populus trichocarpa rhizosphere

Luteolibacter sp. strain Populi is a bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa, from the Cascade mountains in Washington. Its 6.6-Mb chromosome was completely sequenced using Oxford Nanopore long-read sequencing and is predicted to encode 5,301 proteins and 60 RNAs.

59 BASIC BIOLOGICAL 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 OSTI2024

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from Populus trichocarpa residues after CELF pretreatment and CBP fermentation

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a woody energy crop (Populus trichocarpa) residues after co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment and consolidated bioprocessing (CBP) process. The natural poplar variant GW-9947 from the Center for Bioenergy Innovation (CBI) was used. The poplar was knife milled and passed through a 1 mm sieve. The CELF pretreatment was performed in a Parr autoclave reactor with 7.5 wt % solids loading, 0.5 wt% H2SO4 as catalyst at 150°C with 15, 25 and 30 minutes, respectively. Tetrahydrofuran was added in a 1:1 mass ratio with water as the pretreatment solvent. The residues from CELF pretreatment were then subjected to CBP using the bacterium C. thermocellum DSM 1313. CBP fermentations were performed at 60 °C in a shaker at 50 grams/L solids loadings. Lignin was isolated from the pretreated samples after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 580 rpm for 2.5 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The lignin samples were characterized using 13C–1H HSQC experiments which were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus. A standard Bruker pulse sequence was used on a Prodigy platform cryoprobe. The dry lignin samples were dissolved in deuterated dimethylsulfoxide for HSQC experiments. The spectra were acquired under the following acquisition conditions: 210 ppm spectral width in F1 (13C) dimension with 256 data points and 11 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the TopSpin 3.6 software (Bruker BioSpin). The NMR spectra provides structural characteristics information about lignin remaining in solids after CELF (150 °C with 15, 25 and 30 minutes) process and C. thermocellum CBP.

Lignin structure, HSQC, poplar, CELF, CBP, CBI↗
DOE OSTI2026

Endophyte‐induced systemic spatial reprogramming of metabolism in Populus trichocarpa roots under drought

Beneficial, facultative endophytes help plants thrive in challenging environments by altering their host's metabolism, but how these cellular scale metabolic changes propagate to the systems biology scale is unknown. In this work, we employed a high-resolution chemical imaging approach to map metabolic changes at the Populus trichocarpa root-zone and cell-type levels combined with machine learning (ML) models to identify root metabolites and exudates that have predictive power over treatment class. We found that a nine-strain consortium of beneficial endophytes differentially altered the metabolome of droughted root tissues in a manner specific to cell type and root zone, with endophyte abundance showing a clear correlation to individual metabolites. Our study demonstrates that integrating spatial metabolomics with ML can reveal localized metabolic patterns linked to root–microbe interactions and generate novel hypotheses about underlying biological mechanisms.

Drought↗
DOE OSTI2025

Environmental Metrics of Ethanol Production Improve with Increased Biomass Yield and Carbohydrate Content in Populus Trichocarpa

When selecting economically and environmentally advantageous genotypes for domestication in a biofuel supply chain, variability of cell-wall composition within a feedstock population and its impact on biorefinery metrics must be understood. We performed a life cycle assessment (LCA) on a poplar-to-ethanol supply chain to quantify global warming potential and cumulative energy demand as affected by variable carbohydrate content in a large representative natural variant population of Populus trichocarpa. The results showed that both environmental metrics decrease with increasing tree size and with increasing biomass carbohydrate content. These trends parallel prior economic results and provide clear direction to breeders or genetic engineers when improving poplar cultivars.

09 BIOMASS FUELS↗
DOE OSTI2024

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar ( Populus trichocarpa ). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

59 BASIC BIOLOGICAL SCIENCES↗