Source: PACIFIC SOUTHWEST RESEARCH STATION submitted to NRP
DETERMINE THE GENETIC ORIGINS OF TRAITS THAT CAN ENHANCE TREE ADAPTABILITY AND UTILITY
Sponsoring Institution
Forest Service/USDA
Project Status
EXTENDED
Funding Source
USDA INHOUSE
Reporting Frequency
Annual
Accession No.
0419167
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2011
Project End Date
Sep 30, 2023
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
PACIFIC SOUTHWEST RESEARCH STATION
800 BUCHANAN STREET, WEST BLDG
ALBANY,CA 94710-0011
Performing Department
(N/A)
Non Technical Summary
Forest productivity and resilience, including robust populations of individual tree species, are important to a diversity of users, including Federal, State, and private forest managers, State and Federal policy makers, forest industry, energy industry, conservation organizations, and the public. Forest managers need to understand how individual tree species will respond to changing environmental conditions, particularly climate change and its cascading impacts (e.g., changing disease dynamics), in order to inform short- and long-term management plans. Forest industry has a keen interest in opportunities for improving the quality and quantity of trees and associated forest products. The energy industry is interested in the quantity and characteristics of trees that could fuel various sectors of the energy industry (e.g., poplars [Populus sp.]). Conservation organizations are interested in the conservation and restoration of individual tree species (e.g., koa [Acacia koa], western white pine [Pinus monticola]), as well as native forest ecosystems. In California, PSW is a primary source of expertise in tree genetics, including managing genetic resources and working to understand and conserve mechanisms for the adaptation of plants to environmental changes. PSW has been a leader in conifer genetics research, and is uniquely positioned to make significant new contributions. A thorough understanding of the genes regulating adaptive traits is central to determining how genotypes will affect restoration success. Similarly, individual genes that regulate wood formation and disease resistance are of both economic importance and ecological relevance in conservation and restoration efforts. In Hawai`i and the U.S.-affiliated Pacific Islands there is need for expanded capacity in tropical hardwood tree improvement and regeneration. Climate change and new diseases threaten native species across all Pacific Islands, with potentially large impacts for both dry and wet forest species. By understanding genetic diversity and genes associated with adaptive traits, silvicultural techniques can be employed to enhance disease resistance and restore species distributions to enhance long-term species and community viability. Overall, tropical tree improvement lags behind that of temperate regions, despite the global importance of tropical biodiversity, tropical timber production, and a need for large-scale approaches to restoration.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
13606991070100%
Knowledge Area
136 - Conservation of Biological Diversity;

Subject Of Investigation
0699 - Trees, forests, and forest products, general;

Field Of Science
1070 - Ecology;
Goals / Objectives
Native tree species play important ecological, economic, and cultural roles in ecosystems, yet many species are vulnerable to environmental change as evidenced by reductions of geographic range, genetic diversity, adaptability, forest productivity, resilience, and associated forest products and ecosystem services. Trees play a dominant role in maintaining many aspects of global ecosystems (e.g., carbon, atmospheric conditions, climate). Forest trees are under increasing pressure from loss of habitat, forest fragmentation, invasive species, pollutants, changing climates, fire suppression, and forest management. These stressors result in reductions in geographic range, abundance, and genetic diversity, and these losses are predicted to increase in future. All contribute to reduce population sizes, genetic diversity within populations, and gene flow among populations, and thus adaptability and resilience. Invasive plant diseases, whether of long standing (e.g., white pine blister rust), or newly-arrived (e.g., sudden oak death and pine pitch canker), pose growing threats to our forests. Invasive microorganisms, typically introduced accidentally and cryptically, go undetected until the disease organism is well-established. Managers can address these threats by manipulating the growing environment (silviculture) or the genetic composition of trees (directly or indirectly). This problem area focuses on the development of genetic solutions to these pressing problems.

The term genetics covers a broad range of biological phenomena, from the molecular level (understanding what specific genes control a trait) to the landscape level (understanding the spatial partitioning of traits across landscapes and the implications). Likewise, one must also understand how the genetics of one species interacts with the environment (the inheritance of adaptive traits) and the surrounding biota (host-pathogen interactions). Today, the foremost use of population genetics in trees is to maintain forest health in the face of external threats. Knowledge of how genetic diversity, adaptive traits, and molecular mechanisms buffer species response to adverse conditions is essential to forecasting the fates of species and to providing opportunities for mitigation.

This problem area stresses resistance genetics that addresses modes and inheritance to avoid, tolerate, or counteract the attacks of pathogens and parasites, and conservation genetics that explores genetic contributions to survival, reproduction, and the continuing evolution of species and populations. The goal of both is to prevent extinction and foster forest health by maintaining or manipulating genetic diversity. Development of genomic tools that can be applied to problems in forest biology is strategically advantageous; genomic tools can be applied to problems ranging from the distributions of disease resistance to the frequency of desirable adaptive traits. Ecosystem genomics provides an opportunity to broadly characterize plant populations based upon their innate genetic potentials to survive and thrive despite adverse environmental conditions.

Project Methods
PSW uses both traditional host-pathogen inoculation techniques to identify plant responses to infection to characterize potential resistance mechanisms, and laboratory tools to identify potential resistance genes at the molecular level. Coordination between the observed host/pathogen interaction and locating the host genes that underlie such responses is essential to identifying disease resistant populations and individuals. Other studies will compare the similarities and differences between resistance genes of different species to aid in understanding gene function and their value in conserving biodiversity. PSW has pioneered the use of rapid, high-throughput methods that allow for identifying genes in large numbers of trees and associating specific gene alleles with biological traits. These techniques must be developed for each gene in a species and optimized so that the approach can be applied on a large scale. This will be undertaken in populations of Douglas fir to identify genes involved in the interaction and adaptation of trees with their environment. The techniques and approaches established for Douglas fir can serve to guide similar studies in other populations or species, or to screen for additional traits. Wood formation is the biological basis of the forest products industry. It is a fundamental process underlying perennial incremental growth in trees. It influences carbon cycling, provides habitat for wildlife, and can be a component of disease progression. Trees provide a significant ecological foundation to local and global ecosystems, and as such, to the conservation of biodiversity. Despite the importance of wood formation, we still do not understand the basic genetic regulation of the vascular cambium or the differentiation of cell types within wood. The use of molecular and genomic tools in poplar presents an opportunity to understand genes regulating wood formation. For example, the Department of Energy has recently completed sequencing of the poplar genome, representing the first fully sequenced forest tree genome. This resource is anticipated to promote a paradigm shift in forest genetics research, but genetic tools must be established to make use of the sequence information.

Progress 10/01/19 to 09/30/20

Outputs
OUTPUTS: Research in this problem area employs the use of genetic tools to address abiotic and biotic threats to forests, economically important traits of forest trees, and forest conservation. Conservation goals include preventing species extinctions, fostering forest health by maintaining or manipulating genetic diversity, and enhancing ecosystem services provided by plant and animal species and communities. Economically-oriented goals include understanding the genetic basis of yield and wood property traits that are central to forest industries and bioenergy. Overlapping goals for conservation and economically-oriented goals include understanding the genetic basis of resistance to pests and pathogens, and resilience to drought. Projects pursued by the 2 remaining research geneticists focused on four primary areas of inquiry: 1) woody biomass for bioenergy production; 2) genetic linkages for threats to oak species and communities; 3) genetic linkages to adaptive traits in pine species; and 4) consultation to forest managers on forest genetics and its bearing on forest restoration, focusing on seed transfer in a changing climate. Outputs included 13 peer reviewed publications on a wide variety of subjects and 13 presentations. A major challenge for forest management is to understand how underlying genetic variation influences complex traits central to forest tree productivity and response to environmental stresses, including drought. Ongoing work by PSW scientists in collaboration with UC Davis using the model tree poplar has identified gene copy number to be a major contributor to variation observed for biomass production, wood properties, drought-related responses, and to a lesser degree disease resistance. These findings indicated that gene copy number, which has previously been largely ignored for technical reasons, needs to be measured and incorporated into future attempts at predicting phenotypes based on genotypes for conservation, restoration and tree improvement efforts. As more is learned about the genetic regulation of growth and adaptive traits using the model tree poplar, a basic question is to what degree those findings can be extended to other tree species. In collaboration with UC Davis, Western Washington University and the Chinese Academy of Forestry, a genomic survey of angiosperm (broad leaved) tree species found that key genes and molecular mechanisms underlying wood formation can be identified and are conserved among taxonomically distant species. These results support the approach of using ⿿model⿝ species for the initial investigation of genetic and molecular underpinnings of traits influencing forest tree growth and productivity. Scientists also collected and analyzed additional phenotypic measurements of 6000 Valley Oak trees collected from 90 different sites across the range of the species as part of a long-term project to understand seed transfer, genomics and epigenetics of Valley Oaks to inform its conservation. Funding was received to thin the trees, with emphasis on data collection during the process. Manuscripts are being prepared for publication on morphology, landscape genomics, phenology and cold tolerance. Multiple grant-funded projects are ongoing, examining seed transfer using the California seed zone map in a changing climate including a large meta-analysis of common garden test data from many studies across the western US and Canada. In addition, Genotyping by Sequencing data is being collected at multiple sites in 2 pine species to look at how genotypes are associated with early growth and success in field plantings. The goal of this work is to inform reforestation efforts following harvest and fire. Scientists are also working with National Forests to investigate seed source effects on reforestation efforts in large burned landscapes given the challenges of climate change and the potential need to consider different strategies for seed PARTICIPANTS: Individuals in PSW: Andrew Groover (Research Geneticist), Jessica Wright (Research Geneticist), Courtney Canning (Botanist), Heloise Bastiannse (PSW IP Post-doc), and two ORISE fellows Individuals and institutions outside of PSW: Victoria Sork (UC Los Angeles), David Neale (UC Davis), Vladimir Filkov (UC Davis), Katy Hayden (Royal Botanic Gardens, Edinburgh), Matthew Zinkgraf (Western Washington University), Matteo Garbelotto (UC Berkeley), Richard Dodd (UC Berkeley), Luca Comai (UC Davis), Richard Sniezko (R6), Nikolas Dudley and Tyler Jones (Hawaii Agricultural Research Center), Phil Cannon (NFS R5), George Newcombe (University of Idaho), Randy Rousseau (Mississippi State University), Meng Zhu Lu (Chinese Academy of Forestry), Shawn Mansfield (University of British Columbia), Jim Thorne (UC Davis), Emily Moran (UC Merced), Dana Walsh (Eldorado National Forest) Duke University, National Science Foundation, Pacific Southwest Region, University of California Davis, University of California Los Angeles. TARGET AUDIENCES: National Forests and other land managers that are considering potential effects of climate change and adaptation strategies in their management plans, National Forests faced with reforestation of large burned landscapes, National Forests and other hardwood ecosystem managers concerned about and dealing with Sudden Oak death, State of California, hardwood ecosystem managers and conservationists, botanical conservatories across the country, Chinese Academy of Forestry, Department of Energy, Biofuels industry, and international partners (Canada and China, in particular) that are building industries that depend on biofuels.

Impacts
Forest productivity and resilience, including robust populations of individual tree species, are important to a diversity of users, including Federal, State, and private forest managers, State and Federal policy makers, forest industry, energy industry, conservation organizations, and the public. Forest managers need to understand how individual tree species will respond to changing environmental conditions, particularly climate change and its cascading impacts (e.g., changing disease dynamics), in order to inform short- and long-term management plans. Pine and fir adaptive traits are becoming increasingly important in understanding which seed stocks to use from what growing zones and how to replant forests following harvest or fire using species, seed sources, and spatial configurations that maximize long-term survival and productivity. Forest industry has a keen interest in opportunities for improving the quality and quantity of trees and associated forest products, with particular interest in culturally and economically important species such as poplar, native oak species, and sugar pine. The energy industry is interested in the quantity and characteristics of trees that could fuel various sectors of the energy industry, notably poplars. Conservation organizations are interested in the conservation and restoration of individual tree species (e.g., high elevation white pines, Torrey pines), as well as native forest ecosystems.

Publications

  • Mensing, Scott. 2015. The paleohistory of California oaks. In: Standiford, Richard B.; Purcell, Kathryn L., tech. cords. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 35-47.

  • Eckert, A. J.; Lind, B. M.; Friedline, C. J.; Hobson, E.; Zinck, J. W. R.; Rajora, O. P.; Neale, D. B.; Vogler, D.; Maloney, P. E. 2018. The genetic architecture of local adaptation and the genomic exploration of rugged evolutionary landscapes within species of Pinus subgenus Strobus. In: Schoettle, Anna W.; Sniezko, Richard A.; Kliejunas, John T., eds. Proceedings of the IUFRO joint conference: Genetics of five-needle pines, rusts of forest trees, and Strobusphere; 2014 June 15-20; Fort Collins, CO. Proc. RMRS-P-76. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. p. 76-91.
  • Gerttula, Suzanne; Groover, Andrew. 2017. Immunolocalization in secondary xylem of Populus. In: de Lucas, M.; Etchhells, J., eds. Xylem. Methods in Molecular Biology, vol. 1544. New York, NY: Humana Press: 83-90. Chapter 8.
  • Giusti, Gregory A.; Keiffer, R.J.; Feirer, Shane; Keiffer, R.F. 2015. Oak tree selection by nesting turkey vultures (Cathartes aura). In: Standiford, Richard B.; Purcell, Kathryn L., tech. cords. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 107-110.
  • Groover, Andrew. 2020. Woody plant evolution: exceptional lianas reveal rules of woody growth. Current Biology. 30(2): R76-R78. https://doi.org/10.1016/j.cub.2019.11.051.
  • Groover, Andrew; Mansfield, Shawn D. 2020. An introduction to a Virtual Issue on wood biology. New Phytologist. 225(4): 1401-1403. https://doi.org/10.1111/nph.16384.
  • He, Xinqiang; Groover, Andrew T. 2017. The genomics of wood formation in angiosperm trees. In: Groover, A.; Cronk, Q., eds. Comparative and Evolutionary Genomics of Angiosperm Trees. Plant Genetics and Genomics: Crops and Models, vol 21. Cham, Switzerland: Springer International Publishing. Chapter 17.
  • Kasuga, Takao; Garbelotto, Matteo; Eyre, Catherine A.; Croucher, Peter J.P.; Schechter, Shannon; Hayden, Katherine J.; Wright, Jessica W. 2020. Dual transcriptome analysis reveals insights into innate and phosphite-induced resistance of tanoak to Phytophthora ramorum. In: Frankel, Susan J.; Alexander, Janice M., tech. cords. Proceedings of the seventh sudden oak death science and management symposium: healthy plants in a world with Phytophthora. Gen. Tech. Rep. PSW-GTR-268. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 24.
  • Mead, Alayna; Peñaloza Ramirez, Juan; Bartlett, Megan K.; Wright, Jessica W.; Sack, Lawren; Sork, Victoria L. 2019. Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations. Molecular Ecology. 28(24): 5248-5264. https://doi.org/10.1111/mec.15289.
  • Starrs, Paul F. 2015. People and oaks. In: Standiford, Richard B.; Purcell, Kathryn L., tech. cords. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 3-12.
  • Bartolome, James W.; Huntsinger, Lynn. 2015. Oak policy and management in California: Spanish origins and future considerations. In: Standiford, Richard B.; Purcell, Kathryn L., tech. cords. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 49-58.
  • Bontemps, A.; Wright, J.; Sniezko, R.; Savin, D.; Schmitt, J. 2018. Using historical provenance test data to understand tree responses to a changing climate in sugar pine (Pinus lambertiana). In: Schoettle, Anna W.; Sniezko, Richard A.; Kliejunas, John T., eds. Proceedings of the IUFRO joint conference: Genetics of five-needle pines, rusts of forest trees, and Strobusphere; 2014 June 15-20; Fort Collins, CO. Proc. RMRS-P-76. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. p. 99.
  • Browne, Luke; Wright, Jessica W.; Fitz-Gibbon, Sorel; Gugger, Paul F.; Sork, Victoria L. 2019. Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow . Proceedings of the National Academy of Sciences. 116(50): 25179-25185. https://doi.org/10.1073/pnas.1908771116.
  • Dunlap, J.; Burton, D.; Davis, D.; Vogler, D.; Westfall, B. 2018. Sugar pine (Pinus lambertiana) partial resistance heritability study. In: Schoettle, Anna W.; Sniezko, Richard A.; Kliejunas, John T., eds. Proceedings of the IUFRO joint conference: Genetics of five-needle pines, rusts of forest trees, and Strobusphere; 2014 June 15-20; Fort Collins, CO. Proc. RMRS-P-76. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. p. 162.
  • Tietje, William D.; Hardy, Michael A.; Yim, Christopher C. 2015. Coarse woody debris metrics in a California oak woodland. In: Standiford, Richard B.; Purcell, Kathryn L., tech. cords. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 61-72.
  • Van Nuland, Michael E.; Vincent, John B.; Ware, Ian M.; Mueller, Liam O.; Bayliss, Shannon L. J.; Beals, Kendall K.; Schweitzer, Jennifer A.; Bailey, Joseph K. 2020. Intraspecific trait variation across elevation predicts a widespread tree species' climate niche and range limits. Ecology and Evolution. 10(9): 3856-3867. https://doi.org/10.1002/ece3.5969.
  • Young, Derek J. N.; Blush, Thomas D.; Landram, Michael; Wright, Jessica W.; Latimer, Andrew M.; Safford, Hugh D. 2020. Assisted gene flow in the context of large⿐scale forest management in California, USA . Ecosphere. 11(1): 309. https://doi.org/10.1002/ecs2.3001.
  • Zinkgraf, Matthew; Zhao, Shu⿐Tang; Canning, Courtney; Gerttula, Suzanne; Lu, Meng⿐Zhu; Filkov, Vladimir; Groover, Andrew. 2020. Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees. New Phytologist. 139: 963. https://doi.org/10.1111/nph.16819.


Progress 10/01/16 to 09/30/17

Outputs
OUTPUTS: Research in this problem area stresses the use of genetic tools to address threats (pathogens, parasites, adaptations), opportunities (favorable characteristics for human use), and conservation genetics (survival, reproduction, and the continuing evolution of species and populations). The goal is to prevent extinction, foster forest health by maintaining or manipulating genetic diversity, and enhance ecosystem services provided by plant and animal species and communities. Ecosystem genomics provides an opportunity to broadly characterize plant populations based upon their innate genetic potentials to survive and thrive despite adverse environmental conditions. Projects focused on four primary areas of inquiry: 1) woody biomass for bioenergy production; 2) genetic linkages for threats to oak species and communities; 3) genetic linkages to adaptation in pine species; and 4) consultation to forest managers on forest genetics and its bearing on forest restoration. Outputs included 12 peer reviewed publications on a wide variety of subjects and over 10 presentations, including 6 University lectures and 3 invited papers. Progress was made on a DOE-funded project to establish and characterize ploidy variants in Populus for rapid development of new bioenergy cultivars and for research into the role of genes and chromosomes in hybrid performance. This year scientists continued phenotypic measurements of 600 genetic variants of poplar to determine phenotypic variation and associated genes. Research findings from a USDA-AFRI funded a new project to understand the transcriptional networks regulating the cambium and wood formation in Populus were published, in collaboration with UC Davis. Another USDA-AFRI funded project further progressed toward understanding the genetic and hormonal regulation of tension wood in Populus. Tension wood is composed of low-lignin, high cellulose wood, which is ideal for biofuels conversion. Scientists also analyzed phenotypic measurements of 12,000 Valley Oak trees collected from 90 different sites across the range of the species as part of a long-term project to understand genetic traits and adaptations of Valley Oak to inform its conservation. The transcriptome of tanoak and valley oak were studied to reveal new understanding about the genetic drivers of resistance and resilience. The megagenome of the sugar pine was also analyzed. Continued a grant-funded project to examine common garden test data from two studies to look at how genotypes determine short-term adaptation abilities of multiple species of pines from multiple seed zones. Work on blister rust vulnerability of white pines was furthered, including organizing a workshop for managers to relay the most current science on rust in white pines in California. Scientists are also working with National Forests to investigate seed source effects on reforestation efforts in large burned landscapes given the challenges of climate change and the potential need to consider different strategies for seed sources and species mixes in restoring burned landscapes. A major conference on the future of oak species and communities in California was sponsored and co-organized by PSW scientists, and many of the papers pertained to genetic diversity and drivers of traits relevant to conservation and ecosystem services. PARTICIPANTS: Individuals in PSW: Andrew Groover (Research Geneticist), Jessica Wright (Research Geneticist), Christina Liang (Research Ecologist), Det Vogler (Research Geneticist), Kathie Jermstad (Geneticist), Paul Hodgskiss (Biologist), Annie Mix (Biologist), Courtney Cannon (Pathways indefinite student), Heloise Bastiannse (PSW IP Post-doc). Individuals and institutions outside of PSW: Victoria Sork (UC Los Angeles), David Neale (UC Davis), Vladimir Filkov (UC Davis), Katy Hayden (UC Berkeley), Matthew Zinkgraf (University of Washington), Matteo Garbelotto (UC Berkeley), Richard Dodd (UC Berkeley), Luca Comai (UC Davis), Richard Sniezko (R6), Cindy Roessler (Midpeninsula Regional Office), Nikolas Dudley and Tyler Jones (Hawaii Agricultural Research Center), Tom Blush and Phil Cannon (NFS R5), Duke University, National Science Foundation, Region 5 National Forests, University of California Davis, UC Los Angeles. TARGET AUDIENCES: Hardwood ecosystem managers and conservationists, National Forests and other land managers that are considering potential effects of climate change and adaptation strategies in their management plans, National Forests faced with reforestation of large burned landscapes, National Forests and other hardwood ecosystem managers concerned about and dealing with Sudden Oak death, State of California, Botanical conservatories across the country, Chinese Academy of Forestry, Department of Energy, Biofuels industry, and international partners (Canada and China, in particular) that are building industries that depend on biofuels.

Impacts
Forest productivity and resilience, including robust populations of individual tree species, are important to a diversity of users, including Federal, State, and private forest managers, State and Federal policy makers, forest industry, energy industry, conservation organizations, and the public. Forest managers need to understand how individual tree species will respond to changing environmental conditions, particularly climate change and its cascading impacts (e.g., changing disease dynamics), in order to inform short- and long-term management plans. Pine and fir adaptation traits and abilities are becoming increasingly important in understanding which seed stocks to use from what growing zones and how to replant forests following harvest or fire using species, seed sources, and spatial configurations that maximize long-term survival and productivity. Forest industry has a keen interest in opportunities for improving the quality and quantity of trees and associated forest products, with particular interest in culturally and economically important species such as koa and sugar pine. The energy industry is interested in the quantity and characteristics of trees that could fuel various sectors of the energy industry (e.g., poplars [Populus sp.]). Conservation organizations are interested in the conservation and restoration of individual tree species (e.g., koa [Acacia koa], high elevation white pines), as well as native forest ecosystems. Internal PSW funding was used to support burned landscape reforestation research. Forest productivity and resilience, including robust populations of individual tree species, are important to a diversity of users, including Federal, State, and private forest managers, State and Federal policy makers, forest industry, energy industry, conservation organizations, and the public. Forest managers need to understand how individual tree species will respond to changing environmental conditions, particularly climate change and its cascading impacts (e.g., changing disease dynamics), in order to inform short- and long-term management plans. Pine and fir adaptation traits and abilities and vulnerabilities are becoming increasingly important in understanding which seed stocks to use from what growing zones and how to replant forests following harvest or fire using species, seed sources, and spatial configurations that maximize long-term survival and productivity. Forest industry has a keen interest in opportunities for improving the quality and quantity of trees and associated forest products, with particular interest in culturally and economically important species such as koa and sugar pine. The energy industry is interested in the quantity and characteristics of trees that could fuel various sectors of the energy industry (e.g., poplars [Populus sp.]). Conservation organizations are interested in the conservation and restoration of individual tree species (e.g., koa [Acacia koa], high elevation white pines), as well as native forest ecosystems.

Publications

  • Gugger, Paul F.; Peñaloza-Ramírez, Juan Manuel; Wright, Jessica W.; Sork, Victoria L.; Schnitzler, Jörg-Peter 2016. Whole-transcriptome response to water stress in a California endemic oak, Quercus lobata. Tree Physiology. 37: 632-644. https://doi.org/10.1093/treephys/tpw122.
  • Hamilton, Jill A.; Royauté, Raphaël; Wright, Jessica W.; Hodgskiss, Paul; Ledig, F. Thomas 2017. Genetic conservation and management of the California endemic, Torrey pine (Pinus torreyana Parry): implications of genetic rescue in a genetically depauperate species. Ecology and Evolution. 8(2): 194. https://doi.org/10.1002/ece3.3306.
  • Eyre, Catherine A.; Hayden, Katherine J.; Croucher, Peter; Schechter, Shannon; Wright, Jessica W.; Garbelotto, Matteo 2017. Transcriptome analysis of tanoak reveals divergent mechanisms of innate and phosphite-induced resistance to Phytophthora ramorum. In: Frankel, Susan J.; Harrell, Katharine M., tech. coords. Proceedings of the sudden oak death sixth science symposium. Gen. Tech. Rep. GTR-PSW-255. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 36.
  • Gonzalez-Ibeas, Daniel; Martinez-Garcia, Pedro J.; Famula, Randi A.; Delfino-Mix, Annette; Stevens, Kristian A.; Loopstra, Carol A.; Langley, Charles H.; Neale, David B.; Wegrzyn, Jill L. 2016. Assessing the gene content of the megagenome: sugar pine (Pinus lambertiana). G3: Genes, Genomes, Genetics. 6(12): 3787-3802.
  • Groover, Andrew 2017. Age-related changes in tree growth and physiology. eLS. 1-7
  • Lind, Brandon M.; Friedline, Christopher J.; Wegrzyn, Jill L.; Maloney, Patricia E.; Vogler, Detlev R.; Neale, David B.; Eckert, Andrew J. 2017. Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA. Molecular Ecology. 259. https://doi.org/10.1111/mec.14106.
  • Standiford, Richard B.; Purcell, Kathryn L., tech. cords. 2015. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. 579 p.
  • Vogler, D. R.; Geils, B. W.; Coats, K. 2017. First report of the white pine blister rust fungus, Cronartium ribicola, infecting Ribes inerme in north-central Utah. Plant Disease. 101(2): 386.
  • Vogler, Detlev R.; Maloney, Patricia E.; Burt, Tom; Snelling, Jacob W. 2017. First report of the white pine blister rust fungus, Cronartium ribicola, infecting Pinus flexilis on Pine Mountain, Humboldt National Forest, Elko County, northeastern Nevada, U.S.A. Plant Disease. 101(5): 839.
  • Wright, Jessica W.; Sork, Victoria L. 2017. Early results from a newly-established provenance test in Valley Oak (Quercus lobata) show significant population differentiation. In: Sniezko, Richard A.; Man, Gary; Hipkins, Valerie; Woeste, Keith; Gwaze, David; Kliejunas, John T.; McTeague, Brianna A., tech. cords. 2017. Gene conservation of tree species⿿banking on the future. Proceedings of a workshop. Gen. Tech. Rep. PNW-GTR-963. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. p. 164.
  • Zinkgraf, Matthew; Gerttula, Suzanne; Groover, Andrew 2017. Transcript profiling of a novel plant meristem, the monocot cambium. Journal of Integrative Plant Biology. 59(6): 436-449. https://doi.org/10.1111/jipb.12538.
  • Zinkgraf, Matthew; Liu, Lijun; Groover, Andrew; Filkov, Vladimir 2017. Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions. New Phytologist. 214(4): 1464-1478. https://doi.org/10.1111/nph.14492.


Progress 10/01/15 to 09/30/16

Outputs
OUTPUTS: Research in this problem area stresses the use of genetic tools to address threats (pathogens, parasites, adaptations), opportunities (favorable characteristics for human use), and conservation genetics (survival, reproduction, and the continuing evolution of species and populations). The goal is to prevent extinction, foster forest health by maintaining or manipulating genetic diversity, and enhance ecosystem services provided by plant and animal species and communities. Ecosystem genomics provides an opportunity to broadly characterize plant populations based upon their innate genetic potentials to survive and thrive despite adverse environmental conditions. Projects focused on four primary areas of inquiry: 1) woody biomass for bioenergy production; 2) genetic linkages for threats to oak species and communities; 3) genetic linkages to adaptation in pine species; and 4) consultation to forest managers on forest genetics and its bearing on forest restoration. Outputs included eight peer reviewed publications on a wide variety of subjects and 11 presentations, including three University lectures. Progress was made on a DOE-funded project to establish and characterize ploidy variants in Populus for rapid development of new bioenergy cultivars and for research into the role of genes and chromosomes in hybrid performance. This year scientists completed phenotypic measurements of 600 genetic variants of poplar to determine phenotypic variation for traits ranging from drought resistance to wood formation, and associated this variation with specific regions of the genome for each trait. This is the first genome-wide assessment of genetic variation for these important trait in a tree species. Progress was also made on a USDA-AFRI funded a new project to understand the transcriptional networks regulating the cambium and wood formation in Populus, in collaboration with UC Davis. This research is generating the first ever comprehensive descriptions of how individual transcription factors regulate genes for a forest tree. Another USDA-AFRI funded project yielded a major publication using advanced computational genomic approaches to describe the genetic and hormonal regulation of tension wood in Populus. Tension wood is composed of low-lignin, high cellulose wood, which is ideal for biofuels conversion. Scientists also completed phenotypic measurements of 7,000 Valley Oak trees collected from 95 different sites across the range of the species as part of a long-term project to understand genetic traits and adaptations of Valley Oak to inform its conservation. Genetic adaptation and traits were also studied in Acacia koa trees in Hawaii and identified new spatial patterns of genetic diversity within and among the Hawaiian Islands for this ecologically and culturally important species. Continued a grant-funded project to examine common garden test data from two studies to look at how genotypes determine long-term adaptation abilities of multiple species of pines. Work on blister rust vulnerability of white pines was furthered, including organizing a workshop for managers to relay the most current science on rust in white pines in California. Scientists are also working with National Forests to investigate seed source effects on reforestation efforts in large burned landscapes given the challenges of climate change and the potential need to consider different strategies for seed sources and species mixes in restoring burned landscapes. PARTICIPANTS: Individuals in PSW: Andrew Groover (Research Geneticist), Jessica Wright (Research Geneticist), Christina Liang (Research Ecologist), Det Vogler (Research Geneticist), Kathie Jermstad (Geneticist), Paul Hodgskiss (Biologist), Annie Mix (Biologist), Courtney Canning (Pathways indefinite student), Heloise Bastiannse (PSW IP Post-doc). Individuals and institutions outside of PSW: Victoria Sork (UC Los Angeles), David Neale (UC Davis), Vladimir Filkov (UC Davis), Matthew Zinkgraf (UC Davis), (UC Berkeley), Richard Sniezko (R6), Nikolas Dudley and Tyler Jones (Hawaii Agricultural Research Center), Tom Blush and Phil Cannon (NFS R5), Christopher Ivey (California State University, Chico), Johanna Schmitt (UC Davis), Aurore Bontemps (UC Davis), Alejandra Martinez-Berdeja, CSU Chico,Duke University, National Science Foundation, Region 5 National Forests, University of California Davis, UC Los Angeles. TARGET AUDIENCES: Hardwood ecosystem managers and conservationists, National Forests and other land managers that are considering potential effects of climate change and adaptation strategies in their management plans, National Forests faced with reforestation of large burned landscapes, National Forests and other hardwood ecosystem managers concerned about oak conservation, Department of Energy, Biofuels industry, European countries and China - countries that are building and/or depending on biofuels.

Impacts
Forest productivity and resilience, including robust populations of individual tree species, are important to a diversity of users, including Federal, State, and private forest managers, State and Federal policy makers, forest industry, energy industry, conservation organizations, and the public. Forest managers need to understand how individual tree species will respond to changing environmental conditions, particularly climate change and its cascading impacts (e.g., changing disease dynamics), in order to inform short- and long-term management plans. Pine and fir adaptation traits and abilities are becoming increasingly important in understanding which seed stocks to use from what growing zones and how to replant forests following harvest or fire using species, seed sources, and spatial configurations that maximize long-term survival and productivity. Forest industry has a keen interest in opportunities for improving the quality and quantity of trees and associated forest products, with particular interest in culturally and economically important species such as koa and sugar pine. The energy industry is interested in the quantity and characteristics of trees that could fuel various sectors of the energy industry (e.g., poplars [Populus sp.]). Conservation organizations are interested in the conservation and restoration of individual tree species (e.g., koa [Acacia koa], high elevation white pines), as well as native forest ecosystems. Internal PSW funding was used to support burned landscape reforestation research.

Publications

  • Albarrán-Lara, Ana L.; Wright, Jessica W.; Gugger, Paul F.; Delfino-Mix, Annette; Peñaloza-Ramírez, Juan Manuel; Sork, Victoria L. 2015. Phenotypic variation in California populations of valley oak (Quercus lobata Née) sampled along elevational gradients. In: Standiford, Richard B.; Purcell, Kathryn L., tech. cords. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 433-445.
  • Delfino-Mix, Annette; Wright, Jessica W.; Gugger, Paul F.; Liang, Christina; Sork, Victoria L. 2015. Establishing a range-wide provenance test in valley oak (Quercus lobata Née) at two California sites. In: Standiford, Richard B.; Purcell, Kathryn L., tech. cords. Proceedings of the seventh California oak symposium: managing oak woodlands in a dynamic world. Gen. Tech. Rep. PSW-GTR-251. Berkeley, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 413-424.
  • Gerttula, Suzanne; Zinkgraf, Matthew; Muday, Gloria K.; Lewis, Daniel R.; Ibatullin, Farid M.; Brumer, Harry; Hart, Foster; Mansfield, Shawn D.; Filkov, Vladimir; Groover, Andrew 2015. Transcriptional and Hormonal Regulation of Gravitropism of Woody Stems in Populus. The Plant Cell. 27(10): 2800-2813.
  • Groover, Andrew 2015. Genomic science provides new insights into the biology of forest trees. New Phytologist. 208(2): 302-305.
  • Groover, Andrew 2016. Gravitropisms and reaction woods of forest trees - evolution, functions and mechanisms. New Phytologist. 211(3): 790-802.
  • Henry, Isabelle M.; Zinkgraf, Matthew S.; Groover, Andrew T.; Comai, Luca 2015. A system for dosage-based functional genomics in poplar. The Plant Cell. 27(9): 2370-2383.
  • Zinkgraf, M.; Haiby, K.; Lieberman, M.C.; Comai, L.; Henry, I.M.; Groover, A. 2016. Creation and genomic analysis of irradiation hybrids in Populus. Current Protocols in Plant Biology. 1: 431-450.


Progress 10/01/14 to 09/30/15

Outputs
OUTPUTS: Research in this problem area stresses the use of genetic tools to address threats (pathogens, parasites, adaptations), opportunities (favorable characteristics for human use), and conservation genetics (survival, reproduction, and the continuing evolution of species and populations). The goal is to prevent extinction, foster forest health by maintaining or manipulating genetic diversity, and enhance ecosystem services provided by plant and animal species and communities. Ecosystem genomics provides an opportunity to broadly characterize plant populations based upon their innate genetic potentials to survive and thrive despite adverse environmental conditions. Projects focused on four primary areas of inquiry: 1) woody biomass for bioenergy production; 2) genetic linkages for threats to oak species and communities; 3) genetic linkages to adaptation in pine species; and 4) consultation to forest managers on forest genetics and its bearing on forest restoration. Outputs included four peer reviewed publications on a wide variety of subjects, 10 presentations, 3 University lectures, and 2 new grants totaling over $300,000 were secured. Progress was made on a DOE-funded project to establish and characterize ploidy variants in Populus for rapid development of new bioenergy cultivars and for research into the role of genes and chromosomes in hybrid performance. This year we completed field outplanting of 600 genetic variants of poplar to determine phenotypic variation and associated genes. Progress was also made on a USDA-AFRI funded a new project to understand the transcriptional networks regulating the cambium and wood formation in Populus, in collaboration with UC Davis. This research is generating the first ever descriptions of how individual transcription factors regulate genes for a forest tree. Another USDA-AFRI funded project progressed focused on understanding the genetic and hormonal regulation of tension wood in Populus. Tension wood is composed of low-lignin, high cellulose wood, which is ideal for biofuels conversion. More broadly, progress was made in understanding the evolution of the cambium and wood formation in angiosperms. This project was funded by a competitive grant from Harvards Arnold Arboretum, and it has the potential to uncover regulatory pathways controlling wood formation across angiosperms, using a comparative genomics approach. Scientists planted 12,000 Valley Oak trees collected from 90 different sites across the range of the species as part of a long-term project (at least 50 years) to understand genetic traits and adaptations of Valley Oak to inform its conservation. Genetic adaptation and traits were also studied in Acacia koa trees in Hawaii as a comparative study to the Valley oak, and to further our understanding of this ecologically and culturally important species. A NSF-funded grant was awarded a collaborator on the valley oak project which will greatly further its impact. Continued a grant-funded project to examine common garden test data from two studies to look at how genotypes determine long-term adaptation abilities of multiple species of pines. Work on blister rust vulnerability of white pines, with particular emphasis on high elevation white pines, which could experience increased exposure to the rust as a result of warming climates at higher elevations. This work is concluding in FY16 and 3 papers are currently in review. Scientists are also working with National Forests to investigate seed source effects on reforestation efforts in large burned landscapes given the challenges of climate change and the potential need to consider different strategies for seed sources and species mixes in restoring burned landscapes. PARTICIPANTS: Individuals in PSW: Andrew Groover (Research Geneticist), Jessica Wright (Research Geneticist), Christina Liang (Research Ecologist), Det Vogler (Research Geneticist), Kathie Jermstad (Geneticist), Paul Hodgskiss (Biologist), Annie Mix (Biologist), Courtney Cannon (Pathways indefinite student), Heloise Bastiannse (PSW IP Post-doc). Individuals and institutions outside of PSW: Victoria Sork (UC Los Angeles), David Neale (UC Davis), Vladimir Filkov (UC Davis), Katy Hayden (UC Berkeley), Matthew Zinkgraf (UC Davis), Matteo Garbelotto (UC Berkeley), Richard Dodd (UC Berkeley), Richard Sniezko (R6), Cindy Roessler (Midpeninsula Regional Office), Nikolas Dudley and Tyler Jones (Hawaii Agricultural Research Center), Tom Blush and Phil Cannon (NFS R5), Institutions: Duke University, National Science Foundation, Region 5 National Forests, University of California Davis, UC Los Angeles. TARGET AUDIENCES: Hardwood ecosystem managers and conservationists, National Forests and other land managers that are considering potential effects of climate change and adaptation strategies in their management plans, National Forests faced with reforestation of large burned landscapes, National Forests and other hardwood ecosystem managers concerned about and dealing with Sudden Oak death, Department of Energy, Biofuels industry, European countries and China - countries that are building and/or depending on biofuels.

Impacts
Forest productivity and resilience, including robust populations of individual tree species, are important to a diversity of users, including Federal, State, and private forest managers, State and Federal policy makers, forest industry, energy industry, conservation organizations, and the public. Forest managers need to understand how individual tree species will respond to changing environmental conditions, particularly climate change and its cascading impacts (e.g., changing disease dynamics), in order to inform short- and long-term management plans. Pine and fir adaptation traits and abilities are becoming increasingly important in understanding how to replant forests following harvest or fire using species, seed sources, and spatial configurations that maximize long-term survival and productivity. Forest industry has a keen interest in opportunities for improving the quality and quantity of trees and associated forest products. The energy industry is interested in the quantity and characteristics of trees that could fuel various sectors of the energy industry (e.g., poplars [Populus sp.]). Conservation organizations are interested in the conservation and restoration of individual tree species (e.g., koa [Acacia koa], high elevation white pines), as well as native forest ecosystems. Internal PSW funding was used to support burned landscape reforestation research.

Publications

  • Liu, Lijun; Ramsay, Trevor; Zinkgraf, Matthew; Sundell, David; Street, Nathaniel Robert; Filkov, Vladimir; Groover, Andrew 2015. A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus . The Plant Journal, Vol. 82(5): 12 pages.: 887-898.
  • Liu, Lijun; Zinkgraf, Matthew; Petzold, H. Earl; Beers, Eric P.; Filkov, Vladimir; Groover, Andrew 2014. The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. New Phytologist. 205(2): 682-694.
  • Hussey, Steven G; Mizrachi, Eshchar; Groover, Andrew; Berger, Dave K; Myburg, Alexander A 2015. Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. BMC Plant Biology. 15(117).
  • Kidner, Catherine; Groover, Andrew; Thomas, Daniel C.; Emelianova, Katie; Soliz-Gamboa, Claudia; Lens, Frederic [In press]. First steps in studying the origins of secondary woodiness in Begonia (Begoniaceae): combining anatomy, phylogenetics, and stem transcriptomics. Biological Journal of the Linnean Society.


Progress 10/01/13 to 09/30/14

Outputs
OUTPUTS: Research in this problem area stresses the use of genetic tools to address threats (pathogens, parasites, adaptations), opportunities (favorable characteristics for human use), and conservation genetics (survival, reproduction, and the continuing evolution of species and populations). The goal is to prevent extinction, foster forest health by maintaining or manipulating genetic diversity, and enhance ecosystem services provided by plant and animal species and communities. Ecosystem genomics provides an opportunity to broadly characterize plant populations based upon their innate genetic potentials to survive and thrive despite adverse environmental conditions. Projects focused on four primary areas of inquiry: 1) woody biomass for bioenergy production; 2) genetic linkages for threats to oak species and communities; 3) genetic linkages to adaptation in pine species; and 4) consultation to forest managers on forest genetics and its bearing on forest restoration. Outputs included five peer reviewed publications on a wide variety of subjects, 11 presentations, 3 University lectures, and 3 new grants totaling over $1,000,000 were secured. A DOE-funded project to establish and characterize ploidy variants in Populus for rapid development of new bioenergy cultivars and for research into the role of genes and chromosomes in hybrid performance. This year we completed genome sequencing of several hundred unique genotypes. USDA-AFRI funded a new project to understand the transcriptional networks regulating the cambium and wood formation in Populus, in collaboration with UC Davis. This research is generating the first ever descriptions of how individual transcription factors regulate genes for a forest tree. Another USDA-AFRI funded project began focused on understanding the genetic and hormonal regulation of tension wood in Populus. Tension wood is composed of low-lignin, high cellulose wood, which is ideal for biofuels conversion. More broadly, progress was made in understanding the evolution of the cambium and wood formation in angiosperms. This project was funded by a competitive grant from Harvard⿿s Arnold Arboretum, and it has the potential to uncover regulatory pathways controlling wood formation across angiosperms, using a comparative genomics approach. As part of the Sierra Nevada Science Synthesis published in 2014 in support of land management planning in the Sierra Nevada, scientists developed a chapter on Forest Genetics with emphasis on ecological restoration efforts in light of climate change. Scientists fostered the second year of growth for 12,000 Valley Oak trees collected from 90 different sites across the range of the species for outplanting early in FY15 as part of a long-term project (at least 50 years) to understand genetic traits and adaptations of Valley Oak to inform its conservation. Genetic adaptation and traits were also studied in Acacia koa trees in Hawaii as a comparative study to the Valley oak, and to further our understanding of this ecologically and culturally important species. Continued a grant-funded project to examine common garden test data from two studies to look at how genotypes determine long-term adaptation abilities of multiple species of pines. Researchers reinventoried the 70 year-old Eddy pine arboretum located at the Institute of Forest Genetics to further our understanding of pine resilience and environmental plasticity over long time periods. PARTICIPANTS: Individuals in PSW: Andrew Groover (Research Geneticist), Jessica Wright (Research Geneticist), Christina Liang (Research Ecologist), Matt Zinkgraf (PSW post-doc), Kathie Jermstad (Geneticist), Paul Hodgskiss (Biologist), Carlene Carvelo (Biologist), Annie Mix (Biologist), Shani Sahadi (Student), Courtney Cannon (Student), Jonathan Long (Research Ecologist), Susan Frankel (Biologist). Individuals and institutions outside of PSW: Victoria Sork (UC Los Angeles), David Neale (UC Davis), Vladimir Filkov (UC Davis), Katy Hayden (UC Berkeley), Matteo Garbelotto (UC Berkeley), Richard Dodd (UC Berkeley), Richard Sniezko (R6), Cindy Roessler (Midpeninsula Regional Office), Nikolas Dudley and Tyler Jones (Hawaii Agricultural Research Center), Tom Blush and Phil Cannon (NFS R5), Institutions: Duke University, National Science Foundation, Region 5 National Forests, University of California Davis, UC Los Angeles. TARGET AUDIENCES: Hardwood ecosystem managers and conservationists, National Forests and other land managers that are considering potential effects of climate change and adaptation strategies in their management plans, National Forests and other hardwood ecosystem managers concerned about and dealing with Sudden Oak death, Department of Energy, Biofuels industry, European countries and China - countries that are building and/or depending on biofuels.

Impacts
Forest productivity and resilience, including robust populations of individual tree species, are important to a diversity of users, including Federal, State, and private forest managers, State and Federal policy makers, forest industry, energy industry, conservation organizations, and the public. Forest managers need to understand how individual tree species will respond to changing environmental conditions, particularly climate change and its cascading impacts (e.g., changing disease dynamics), in order to inform short- and long-term management plans. Pine and fir adaptation traits and abilities are becoming increasingly important in understanding how to replant forests following harvest or fire using species, seed sources, and spatial configurations that maximize long-term survival and productivity. Forest industry has a keen interest in opportunities for improving the quality and quantity of trees and associated forest products. The energy industry is interested in the quantity and characteristics of trees that could fuel various sectors of the energy industry (e.g., poplars [Populus sp.]). Conservation organizations are interested in the conservation and restoration of individual tree species (e.g., koa [Acacia koa], western white pine [Pinus monticola]), as well as native forest ecosystems.

Publications

  • Hayden, Katherine J.; Garbelotto, Matteo; Knaus, Brian J.; Cronn, Richard C.; Rai, Hardeep; Wright, Jessica W. 2014. Dual RNA-seq of the plant pathogen phytophthora ramorum and its tanoak host. Tree Genetics & Genomes. 10: 489-502.
  • Liang, Christina T.; Wright, Jessica W.; Gugger, Paul F.; Dudley, Nicklos; Jones, Tyler; Yeh, Aileen; Hodgskiss, Paul; Rai, Hardeep; Sork, Victoria L. 2014. Associations between environment and genetics in Hawaiian koa, Acacia koa. IUFRO Acacia 2014 Conference, Hue, Vietnam.
  • Liu, L.; Missirian, V.; Zinkgraf, M.; Groover, A.; Filkov, V. (2014). Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. BMC Genomics 15(Suppl 5):S3
  • Wright, J. 2014. Genetics of forest trees. In: Long, J.W.; Quinn-Davidson, L.; Skinner, C.N., eds. Science synthesis to support socioecological resilience in the Sierra Nevada and southern Cascade Range. Gen. Tech. Rep. PSW-GTR-247. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 129-139. Chap. 3.1.
  • Wright, Jessica W.; Dodd, Richard S. 2013. Could tanoak mortality affect insect biodiversity? Evidence for insect pollination in tanoaks. Madroño 60(2):87-94.


Progress 10/01/12 to 09/30/13

Outputs
OUTPUTS: Projects focused on three primary areas of inquiry: 1) woody biomass for bioenergy production; 2) genetic linkages for threats to oak species and communities; 3) genetic linkages to adaptation in pine species; and 4) consultation to forest managers on forest genetics and its bearing on forest restoration. Outputs included peer reviewed publications on a wide variety of subjects and over $1,000,000 in grant funds secured, primarily for the biomass research. As part of the Sierra Nevada Science Synthesis in support of land management planning in the Sierra Nevada, we developed a chapter on Forest Genetics with emphasis on ecological restoration efforts in light of climate change. Continued growing 12,000 Valley Oak trees collected from 10 sites across the range of the species for outplanting in FY14 as part of a long-term project (at least 50 years) to understand genetic drivers of Valley Oak traits. Formed a collaborative relationship with Dave Neale at UC Davis and USFS scientists that holds promise for future research on using provenance tests to understand forest responses to climate change. This collaboration is focused on collected genomic data from a historical PSW test to compare tree performance in the field test site with genotypic data. Worked a grant-based project to examine provenance test data from 2 studies to look at how genotypes from the Tahoe Basin might respond to being planted in novel climates. Resampled trees along a 50 year-old elevational gradient provinance test to determine long-term adaptation abilities of multiple species of pines. Inventoried the 70 year-old arboreta associated with the Institute of Forest Genetics, and continued to update the organanization of the PSW-IFG seed bank. PARTICIPANTS: Individuals: Andrew Groover (PSW), Jessica Wright (PSW), Christina Liang (PSW), Matt Zinkgraf (PSW post-doc), Kathie Jermstad (PSW), Paul Hodgskiss (PSW), Carlene Carvelo (PSW), Annie Mix (PSW), Shani Sahadi (PSW), Courtney Cannon (PSW),, Quentin Cronk (U. British Columbia), Victoria Sork (UC Los Angeles), David Neale (UC Davis), Katy Hayden , Matteo Garbelotto, and Richard Dodd (UC Berkeley), Richard Cronn (PNW), Richard Sniezko (R6), Susan Frankel (PSW), Cindy Roessler (Midpeninsula Regional Office), Nikolas Dudley and Tyler Jones (Hawaii Agricultural Research Center), Tom Blush and Phil Cannon (NFS R5), Carl Skinner (PSW), Jonathan Long (PSW). Institutions: Duke University, National Science Foundation, Region 5 National Forests, University of California Davis, UC Los Angeles. TARGET AUDIENCES: Other researchers, tree breeders, and biofuels from trees industry. PSW scientists and professional staff interested in learning about genetics. Scientists, land managers- particularly those managing land infested with Sudden Oak Death, members of the public who are concerned about loss of trees due to SOD. Genetics researchers who will be able to access the seeds from IFG in a way that they have not been able to do so before.

Impacts
PSW is recognized as a national and international leader in tree genetics and conservation. Progress on genetic-basis for biomass formation has become of great interest in Europe and other countries around the world. The Valley Oak research will yield short-term results on genetic drivers of seedling survival and growth, followed by longer-term survival and growth rates. Pine adaptation traits and abilities arebecoming increasingly important in understanding how to replant forests following harvest or fire using species, seed sources, and spatial configurations that maximize long-term survival and productivity. Seed project goal is to have a working, research collection of properly stored seeds at IFG, as well as a conservation collection of seeds at UC Davis. The updated conifer seedbank is searchable by the public and readily accessible for national and international research applications.

Publications

  • Dodd, Richard S; Nettel, Alejandro; Wright, Jessica W.; Afzal-Rafii, Zara. 2013. Genetic structure of Notholithocarpus densiflorus(Fagaceae) from the species to the local scale: A review of our knowledge for conservation and replanting. Madroño. 60(2):130-138.
  • Hayden, Katherine J.; Garbelotto, Matteo; Fai, Hardeep; Knaus, Brian; Cronn, Richard; Wright, Jessica W. 2012. Gene expression in the tanoak-Phytophthora ramorum interaction. In: Sniezko, Richard A.; Yanchuk, Alvin D.; Kliejunas, John T.; Palmieri, Katharine M.; Alexander, Janice M.; Frankel, Susan J., tech. coords. Proceedings of the fourth international workshop on the genetics of host-parasite interactions in forestry: Disease and insect resistance in forest trees. Gen. Tech. Rep. PSW-GTR-240. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture. p. 310.
  • Hayden, Katherine J.; Wright, Jessica W.; Dodd, Richard S.; Garbelotto, Matteo. 2012. Developing a disease resistance research program for tanoaks. In: Sniezko, Richard A.; Yanchuk, Alvin D.; Kliejunas, John T.; Palmieri, Katharine M.; Alexander, Janice M.; Frankel, Susan J., tech. coords. Proceedings of the fourth international workshop on the genetics of host-parasite interactions in forestry: Disease and insect resistance in forest trees. Gen. Tech. Rep. PSW-GTR-240. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture. p. 252.
  • Liang, Christina T.; Wright, Jessica W.; Rai, Hardeep; Dudley, Nick; Jones, Tyler; Yeh, Aileen; Gugger, Paul F.; Sork, Victoria L. 2013. Associating genetic variation with climate variables in Hawaiian koa (Acacia koa). In: 21st Annual Hawaii Conservation Conference; 2013 July 16-18; Honolulu, Hawaii. Poster. Available at http://hawaiiconservation.org/files/content/activities/hawaii_conservation_confe rence/conferences/2013/final_2013_hcc_abstract_book.pdf.
  • Liu, Lijun; Filkov, Vladimir; Groover, Andrew. 2013. Modeling transcriptional networks regulating secondary growth and wood formation in forest trees. Physiologia Plantarum. DOI: 10.1111/ppl.12113
  • Lucas, William J.; Groover, Andrew; Lichtenberger, Raffael; Furuta, Kaori; Yadav, Shri-Ram; Helariutta, Yka; He, Xin-Qiang; Fukuda, Hiroo; Kang, Julie; Brady, Siobhan M.; Patrick, John W.; Sperry, John; Yoshida, Akiko; Lopez-Millan, Ana-Flor; Grusak, Michael A.; Kachroo, Pradeep. 2013. The plant vascular system: Evolution and functions. J. Int. Plant Biol. 55(4):294-388.
  • McDonald, Philip M.; Zhang, Jianwei; Senock, Randy S.; Wright, Jessica W. 2013.Morphology, physiology, genetics, enigmas, and status of an extremely rare tree: Mutant tanoak. Madroño 60(2):107-117.
  • Eckert, Andrew J.; Bower, Andrew D.; Jermstad, Kathleen D.; Wegrzyn, Jill L.; Knaus, Brian J.; Syring, John V.; Neale, David B. 2013. Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus). Mol. Ecol. (22) 5635-5650.
  • Groover, Andrew; Cronk, Quentin. 2013. From Nehemiah Grew to Genomics: the emerging field of evo-devo research for woody plants. International Journal of Plant Science 174(7), 959-963.
  • Hayden, Katherine J.; Dodd, Richard S.; Eyre, Catherine; Garbelotto, Matteo; Wright, Jessica W. 2013. Scaling up from greenhouse to field resistance in tanoaks. In: Frankel, S.J.; Kliejunas, J.T.; Palmieri, K.M.; Alexander, J.M. tech. coords. Proceedings of the sudden oak death fifth science symposium. Gen. Tech. Rep. PSW-GTR-243. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: p. 146.
  • Hayden, Katherine J.; Garbelotto, Matteo; Dodd, Richard; Wright, Jessica W. 2013. Scaling up from greenhouse resistance to fitness in the field for a host of an emerging forest disease. Evolutionary Applications 6(6):970⿿982.


Progress 10/01/11 to 09/30/12

Outputs
OUTPUTS: Conference: Evolution and Development of Woody Plants. Dr Groover co-organized this NSF-funded conference at the National Evolutionary Synthesis Center at Duke University. J. Wright and K. Jermstad organized 3 lunchtime VTC seminars on the topic of Genetics. J. Wright gave an invited seminar for the UC Davis Department of Plant Pathology- this was an overview of the whole project. J. Wright gave an invited talk at the Sudden Oak Death Science Symposium (SOD5) special session on Tanoaks- this talk focused on the idea that tanoaks may be insect pollinated. J. Wright hosted a graduate student from Scotland who is focusing on Sudden Oak Death. Formed mentor-mentee relationship with student, and provided student with opportunities to visit professors and other graduate students at UC Davis and UC Berkeley. Student had the opportunity to take part in a flight with a USFS aerial survey crew. Four papers are currently in review for this project. Conducted a trial experiment, growing 3000 Valley Oak trees collected from 10 sites across the range of the species. This trial experiment was in preparation for planting 10,000 Valley Oak seedlings taking place right now (FY13), with the larger goal to establish a provenance test in Valley Oaks growing in two field sites in California. This is a long-term project (at least 50 years). Formed a collaborative relationship with Dave Neale at UC Davis and USFS scientists that holds promise for future research on using provenance tests to understand forest responses to climate change. This collaboration is focused on collected genomic data from a historical PSW test to compare tree performance in the field test site with genotypic data. J. Wright Received the ⿿Excellence in Pollinator Management⿝ award for the work on the pollination ecology of tanoaks. Received funding from SNPMLA to hire a postdoc for approximately one year to examine provenance test data from 2 studies to look at how genotypes from the Tahoe Basin might respond to being planted in novel climates. The funding has not yet become available to me, so I anticipate future results from this effort in FY13. Joined the Sierra Nevada Science Synthesis team to write a chapter on Forest Genetics. The emphasis of my chapter is on data land managers need for informed ecological restoration efforts in light of climate change. Currently managers use the California Seed Zone map- which has worked well in the past, but given predictions of climate change, it is not clear how well it will work into the future. My chapter discusses this issue, and the types of data that would inform those decisions. Overseeing the reorganization of the PSW-IFG seed bank. Neale⿿s collection is searchable online, and seeds can be made available to the research public. PARTICIPANTS: ⿢ Individuals: Quentin Cronk at U. British Columbia; Andrew Groover; Jessica Wright; Kathie Jermstad; ⿢ Partner Organizations: Duke, NSF ⿢ Collaborators and contacts: Katy Hayden , Matteo Garbelotto, and Richard Dodd at UC Berkeley. Richard Cronn at PNW made the gene expression work possible. Richard Sniezko, R6, started the whole collaboration. Susan Frankel, PSW- Sudden Oak Death Program and Cindy Roessler, Midpeninsula Regional Open Space District provided funding and support. Paul Hodgskiss provided technical support. Victoria Sork, UCLA; Nikolas Dudley and Tyler Jones, Hawaii Agricultural Research Center; Christina Liang, PSW. David Neale, UC Davis Tom Blush and Phil Cannon- R5, Carl Skinner and Jonathan Long, PSW. Annie Mix and 2 Student employees at PSW-IFG. TARGET AUDIENCES: Other researchers, tree breeders, and biofuels from trees industry. PSW scientists and professional staff interested in learning about genetics. Scientists, land managers- particularly those managing land infested with Sudden Oak Death, members of the public who are concerned about loss of trees due to SOD. Genetics researchers who will be able to access the seeds from IFG in a way that they have not been able to do so before. PROJECT MODIFICATIONS: We changed Hawaiian study species from what was listed in the PSW proposal to Koa. This has greatly expanded the interest and potential impact in our work.

Impacts
The Evolution and Development of Woody Plants conference was the first to specifically address the evolution and developmental biology of trees. The conference brought together researchers from formerly disparate research areas to identify future opportunities for genomics-based forest biology research. Two publications emerged from that meeting on which Dr Groover is an author. The first details the use of living collections for genomics-based evolution and development research with woody plants. The second paper details the establishment of a new controlled vocabulary for genomics-based research in woody plants. Our outcomes/impacts were to help more PSW scientists and staff members learn about genetics. One specific outcome was that Christina Liang attended the talks, and was very interested by the landscape genetics section, and as a result she and J. Wright applied for funding through the PSW internal RFP in FY12. Liang and Wright were funded, and are currently collaborating on a project together. This project has 3 facets to it right now- pollination ecology, gene expression and a common garden study. Work on flower visitation in tanoaks showed that tanoak flowers are visited by a large number of insects. This is significant because prior to the work, it was generally assumed that tanoak flowers are exclusively wind pollinated. The gene expression work showed that there are approximately 800 genes that get turned on in tanoak leaves in the presence of the pathogen that causes Sudden Oak Death. The common garden work showed that tests performed in the lab to determine how resistant a tree is to SOD also predict the survival of trees growing in a common garden in an infested field site. Seed project goal is to have a working, research collection of properly stored seeds at IFG, as well as a conservation collection of seeds at UC Davis.

Publications

  • Adams, Robert P.; Wright, Jessica W. 2012. Alkanes and terpenes in wood and leaves of Pinus jeffreyi and P. sabiniana. Journal of Essential Oil Research. 6 p. DOI:10.1080/10412905.2012.703512
  • Dosmann, Michael; Groover, Andrew. 2012. The important of living botanical collections for plant biology and the ⿿next generation⿝ of evo-devo research. Frontiers in Plant Evolution and Development. 3: 1-5.
  • Du, Juan; Miura, Eriko; Robischon, Marcel; Martinez, Ciera; Groover, Andrew. 2011. The Populus Class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems. PLoS ONE 6(2): e17458. doi:10.1371/journal.pone.0017458
  • Moyer, Leonie C.; Levine, Mia; Stanton, Maureen L.; Wright, Jessica W.2012. Hybrid sterility over tens of meters between ecotypes adapted to serpentine and non-serpentine soils. Evolutionary Biology. 39:207-218. DOI: 10.1007/s11692-012-9180-9.
  • Robischon, Marcel; Du, Juan; Miura, Eriko; Groover, Andrew. 2011. The Populus Class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems. Plant Physiology 155(3): 1214-1225
  • Lens, Federic; Cooper, Laurel; Gandolfo, Maria Alejandra; Groover, Andrew; Jaiswal, Pankaj; Lachenbruch, Barbara; Spicer, Rachel; Staton, Margaret E.; Stevenson, Dennis W.; Walls, Ramona L.; Wegrzyn, Jill. 2012. An extension of the plant ontology project supporting wood anatomy and development research. IAWA Jounrnal. 33(2): 113-117.