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1. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir

   https://doi.org/10.3390/genes12010110  

   De La Torre, Amanda R.; Wilhite, Benjamin; Puiu, Daniela; St. Clair, John Bradley; Crepeau, Marc W.; Salzberg, Steven L.; Langley, Charles H.; Allen, Brian; Neale, David B. (January 2021, Genes)

   Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species’ predictions under climate change. 

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2. A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir)

   https://doi.org/10.1093/g3journal/jkac304  

   Velasco, Vera Marjorie; Ferreira, Alyssa; Zaman, Sumaira; Noordermeer, Devin; Ensminger, Ingo; Wegrzyn, Jill L (December 2022, G3 Genes|Genomes|Genetics)

   Holland, J. (Ed.)

   Abstract Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more “complete” genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation. 

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3. Douglas Fir Multiproxy Tree-Ring Data Glimpse MIS 5 Environment in the U.S. Pacific Northwest

   https://doi.org/10.3390/f13122161  

   Panyushkina, Irina P.; Leavitt, Steven W.; Meko, David M.; Black, Bryan A.; Jull, A. J.; Van de Water, Peter; Squire, Joe; Testa, Nicholas R. (December 2022, Forests)

   Proxy records from the late Quaternary help in understanding climate variability on extended time scales. An ancient landslide deposit in Oregon U.S.A. preserved large logs from Douglas fir trees (Pseudotsuga menziesii (Mirb.) Franco) and afforded an opportunity to explore the response of tree growth to climate on annual and decadal scales. High-precision radiocarbon dating indicates an age exceeding 63 ka, i.e., the trees grew within the generally cool Marine Isotope Stage 5 (MIS 5), likely during a warmer interval optimal for Douglas fir establishment. This would include the prolonged warm MIS 5e (ca. 110–130 ka), corresponding approximately to the Eemian interglacial, which was warm like the current Holocene interglacial. A 297-year tree-ring width chronology from 12 Douglas fir logs and 227-year tree-ring δ13C and δ18O records are analyzed with spectral and wavelet analysis. Variance of the ancient rings is consistent with modern Douglas fir growth sensitive to moisture and ecological disturbances. Spectra of ancient and modern chronologies are dominated by low frequencies with significant spectral peaks appearing at high frequencies (2.1–4 years) and cyclic behavior transient over centuries. It is conceivable that the O-isotopes track moisture and that C-isotopes track temperature or sunlight. The findings illustrate the challenges in assessing the response of ancient tree-ring properties to late Quaternary climate variability. 

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4. Utility of in situ ion‐exchange membranes to assess nutrient availability, productivity, and fertilizer response of coastal Douglas‐fir of the Pacific Northwest

   https://doi.org/10.1002/saj2.20654  

   Littke, K M; Holub, S M; Bremer, E; Turnblom, E (May 2024, Soil Science Society of America Journal)

   Abstract Douglas‐fir [Pseudotsuga menziesii(Mirb.) Franco] is the predominant forest plantation species in the Pacific Northwest (PNW), with site productivity and fertilizer response influenced by climate and soil variations. This study investigates the utility of in situ 12‐week supply measurements of nitrogen (N), calcium (Ca), and phosphorus (P) to ion‐exchange resins (specifically Plant Root Simulator [PRS] probes) to estimate carbon (C):N ratios, soil nutrient contents (0–1 m), foliar nutrient concentrations, Douglas‐fir productivity (site index and basal area mean annual increment), and fertilizer volume response. PRS nutrient supply rates were correlated with N, Ca, and P soil nutrient contents (0–1 m), C:N ratios, and foliar nutrient concentrations. Low PRS NO₃supply rates (<25 mg N·m⁻²·burial period⁻¹) were correlated with lower Douglas‐fir productivity and greater fertilizer volume response. PRS NO₃supply rates performed as well as total soil N contents and foliar N concentrations at estimating volume growth response to fertilizer. Twelve weeks after fertilization, PRS NO₃, NH₄, and Ca supply rates were significantly elevated compared to the unfertilized treatment. This research found that PRS probes were an effective in situ tool and are recommended for understanding N, Ca, and P nutrient availabilities, site productivity, and fertilizer response in Douglas‐fir plantations and for developing fertilizer prescriptions. 

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5. Continental‐scale tree‐ring‐based projection of Douglas‐fir growth: Testing the limits of space‐for‐time substitution

   https://doi.org/10.1111/gcb.15170  

   Klesse, Stefan; DeRose, Robert_Justin; Babst, Flurin; Black, Bryan_A; Anderegg, Leander_D_L; Axelson, Jodi; Ettinger, Ailene; Griesbauer, Hardy; Guiterman, Christopher_H; Harley, Grant; et al (June 2020, Global Change Biology)

   Abstract A central challenge in global change research is the projection of the future behavior of a system based upon past observations. Tree‐ring data have been used increasingly over the last decade to project tree growth and forest ecosystem vulnerability under future climate conditions. But how can the response of tree growth to past climate variation predict the future, when the future does not look like the past? Space‐for‐time substitution (SFTS) is one way to overcome the problem of extrapolation: the response at a given location in a warmer future is assumed to follow the response at a warmer location today. Here we evaluated an SFTS approach to projecting future growth of Douglas‐fir (Pseudotsuga menziesii), a species that occupies an exceptionally large environmental space in North America. We fit a hierarchical mixed‐effects model to capture ring‐width variability in response to spatial and temporal variation in climate. We found opposing gradients for productivity and climate sensitivity with highest growth rates and weakest response to interannual climate variation in the mesic coastal part of Douglas‐fir's range; narrower rings and stronger climate sensitivity occurred across the semi‐arid interior. Ring‐width response to spatial versus temporal temperature variation was opposite in sign, suggesting that spatial variation in productivity, caused by local adaptation and other slow processes, cannot be used to anticipate changes in productivity caused by rapid climate change. We thus substituted only climate sensitivities when projecting future tree growth. Growth declines were projected across much of Douglas‐fir's distribution, with largest relative decreases in the semiarid U.S. Interior West and smallest in the mesic Pacific Northwest. We further highlight the strengths of mixed‐effects modeling for reviving a conceptual cornerstone of dendroecology, Cook's 1987 aggregate growth model, and the great potential to use tree‐ring networks and results as a calibration target for next‐generation vegetation models. 

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