Engineering topics
Publications and source records attributed to Tuskan, Gerald A..
This dataset contains single-nucleus RNA sequencing data from poplar (Populusspp.) roots under control and methyl jasmonate (MeJA) treatment conditions. It was generated to investigate cell type-specific stress responses and to establish a high-resolution transcriptomic atlas in a perennial woody species.
This dataset contains the stem RNA-seq data of Populus tremula x P. alba genotypes of RGA triple knockout. Populus genotypes in this study includes the empty vector control (EV, Cas9-19) and three independent RGA triple mutants, 267-17 (RGAX4KO_17), 267-2
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
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).
Select leaves from natural variants of Poplar (Populus Trichocarpa) grown in a greenhouse at Oak Ridge National Laboratory were analyzed by Pyrolysis-Molecular Beam Mass Spectrometry (Py-MBMS). Leaves were harvested, cryomilled and kept frozen until analysis. Py-MBMS analysis was conducted using approximately 4 mg of biomass and each sample was analyzed in duplicate. A Frontier PY2020 unit pyrolyzed samples at 500°C for 30 s in 80 µL deactivated stainless steel cups. An Extrel Super-Sonic MBMS Model Max 1000 was used to collect mass spectral data fromm/z30 to 450 at 17 eV and processed using Merlin Automation software (V3). Spectral ion intensities were normalized to the total ion chromatogram signal for each sample for analysis of spectral variance. Lignin content (wt %) was estimated based on relative responses from standards of known Klason lignin content using mean-normalized ion intensities ofm/z120, 124 (G), 137 (G), 138 (G), 150 (G), 152, 154 (S), 164 (G), 167 (S), 168 (S), 178 (G), 180, 181, 182 (S), 194 (S), 208 (S) and 210 (S) where G indicates guaiacyl-derived ions, S indicates syringyl-derived ions, and other ions either derive from other lignin monomers or multiple sources. Ratios of S and G lignin monomer units (S/G) were obtained by dividing the sum of S-based ions by the sum of G-based ions using mean-normalized ion intensities.
Poplar and other woody feedstocks have the potential to provide up to 200 million tons of biomass per year that could be converted to liquid fuels. Most forestry strategies that aim at increasing biomass productivity per hectare rely on short rotation plantations of fast-growing varieties. The improvement of wood density as a key trait itself has largely been overlooked. We evaluated natural variation in wood density across a population of genetically diversePopulus trichocarpatrees grown in a common garden. Wood density varies greatly within this population but is heritable higher wood density was not systematically associated with reduced growth, challenging assumptions of a trade-off between wood density and biomass accumulation. Furthermore, denser wood led to significant improvements throughout the supply chain, including, lowering biomass production and transportation costs. Higher density not correlate to changes in biomass composition. Density did not impact bioconversion in the two feedstock-to-fuel pipelines tested (pretreatment by ionic liquids or soaking in aqueous ammonia, and fermentation to ethanol) on a representative subset of poplars. These findings highlight wood density as a promising breeding target for accelerating the development of high-yielding, conversion-efficient bioenergy crops and as an avenue for increasing land-use efficiency and reducing biomass transportation cost. This data set contain three datasets.
This dataset provides tower-based hyperspectral remote sensing measurements of individualPopulustrees collected with the TSWIFT system to support genetic analyses of canopy photosynthetic traits over time under drought. From 2022-08-18 to 2022-10-18, spectra were repeatedly acquired from the same targeted canopy area of each tree using fixed pointing coordinates. The dataset includes hyperspectral measurements from 400–900 nm and ultraspectral measurements from 730–780 nm. These spectra enable calculation of reflectance-based vegetation indices and other spectral traits, including solar-induced fluorescence (SIF) retrievals from the ultraspectral region. Because measurements were collected exclusively over a drought treatment plot, derived phenotypes are intended for drought-context genetic association and prediction analyses.
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.
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.
In plants, the pre-mRNA alternative splicing has been demonstrated to be a crucial tier that regulates gene expression in response to salt stress. However, the underlying mechanisms remain elusive. Here, in this study, we studied the roles of DIGEORGE-SYNDROME CRITICAL REGION 14-like (AtDGCR14L) in regulating pre-mRNA splicing and salt stress tolerance. We discovered that Arabidopsis AtDGCR14L is required for maintaining plant salt stress tolerance and the constitutively spliced and active isoforms of important stress- and/or abscisic acid (ABA)-responsive genes. We also identified the interaction between AtDGCR14L and splicing factor U1-70k, which needs a highly conserved three amino acid (TWG) motif in DGCR14. Different from wild-type AtDGCR14L, the overexpression of TWG-substituted AtDGCR14L mutant did not change salt stress tolerance or pre-mRNA splicing of stress/ABA-responsive genes. Additionally, SWITCH3A (SWI3A) is a core subunit of the SWI/SUCROSE NONFERMENTING (SWI/SNF) chromatin-remodeling complexes. We found that SWI3A, whose splicing depends on AtDGCR14L, actively enhances salt stress tolerance. These results revealed that AtDGCR14L may play an essential role in crosstalk between plant salt-stress response and pre-mRNA splicing mechanisms. We also unveiled the potential role of SWI3A in controlling salt stress tolerance. The TWG motif in the intrinsically disordered region of AtDGCR14L is highly conserved and crucial for DGCR14 functions.
Sustainable aviation fuel (SAF) production from biomass and biowaste streams is an attractive option for decarbonizing the aviation sector, one of the most-difficult-to-electrify transportation sectors. Despite ongoing commercialization efforts using ASTM-certified pathways (e.g., lipid conversion, Fischer-Tropsch synthesis), production capacities are still inadequate due to limited feedstock supply and high production costs. New conversion technologies that utilize lignocellulosic feedstocks are needed to meet these challenges and satisfy the rapidly growing market. Combining bio- and chemo-catalytic approaches can leverage advantages from both methods, i.e., high product selectivity via biological conversion, and the capability to build C-C chains more efficiently via chemical catalysis. Herein, conversion routes, catalysis, and processes for such pathways are discussed, while key challenges and meaningful R&D opportunities are identified to guide future research activities in the space. Bio and chemo-catalytic conversion primarily utilize the carbohydrate fraction of lignocellulose, leaving lignin as a waste product. This makes lignin conversion to SAF critical in order to utilize whole biomass, thereby lowering overall production costs while maximizing carbon efficiencies. Thus, lignin valorization strategies are also reviewed herein with vital research areas identified, such as facile lignin depolymerization approaches, highly integrated conversion systems, novel process configurations, and catalysts for the selective cleavage of aryl C–O bonds. The potential efficiency improvements available via integrated conversion steps, such as combined biological and chemo-catalytic routes, along with the use of different parallel pathways, are identified as key to producing all components of a cost-effective, 100% SAF.
Summary Our study utilized genome‐wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa , a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co‐expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.
A 6-year study in Sumter Co., SC, to determine crown and leaf attributes, supplemental water and fertilization effects on dry weight productivity, and clonal variation accounts in biomass traits. Eight commercially available clones -- ‘ST148’, ‘S2C20’, ‘3167’, ‘ST72’ ‘20WV’, ‘S7C1’, ‘ST70’, and ‘S7C15’, were studied. Drip irrigation rates were used to maintain soil tension of 33 kPa at 15% volumetric soil moisture or 1500 kPa at 10%. Application of macro- and micronutrients occurred via drip irrigation at a high and low rate. The high rate included an initial application of 85 kg elemental nitrogen ha-1, which increased to 182 kg ha-1 at age 3, which then was reduced to 135 kg ha-1 for remainder of the study. The low treatment received 50% (w/v) of the high treatment. Individual tree measurements across time are provided in this dataset.