Comparative Genomics of Environmental Stress Responses in North American Hardwoods

  • Carlson, John Edward (PI)
  • Romero-Severson, Jeanne (CoPI)
  • Schlarbaum, Scott E. (CoPI)
  • Coggeshall, Mark V. (CoPI)
  • Liang, Haiying (CoPI)

Project: Research project

Project Details


PI: John E. Carlson (Pennsylvania State University)

Co-PIs: Jeanne Romero-Severson (University of Notre Dame), Scott E. Schlarbaum (University of Tennessee - Knoxville), Mark V. Coggeshall (University of Missouri - Columbia), Haiying Liang (Clemson University), Oliver Gailing (Michigan Technological University), and Ketia L. Shumaker (University of West Alabama).

Senior Personnel: Meg Staton (Clemson University) and Nicholas C. Wheeler (Oregon State University).

Most timberlands in the United States are natural forests, of which eastern hardwood forests comprise more than half. The eastern hardwood forests are complex biological systems, covering over 400 million acres of bottomland and riparian sites, major watersheds, mesic sites and upland xeric sites. These forests provide habitat and food for wildlife, stabilization of riparian zones, long-term carbon sequestration and other essential ecosystem services as well as wood and biomass products for human use. The increasing incidence of introduced exotic pests, diseases and invasive plants, combined with climate change and forest fragmentation, threaten the sustainability of these forest ecosystems. Unfortunately, few genomic resources are available for use in studying the consortium of hardwood species that compose the eastern forests. An interdisciplinary team will work together to develop new genomic resources for important species that represent the major taxonomic groups of eastern hardwood trees, from the oldest to more recently evolved, including yellow poplar (Liriodendron tulipifera), sweetgum (Liquidambar styraciflua), honey locust (Gleditsia triacanthos), northern red oak (Quercus rubra), black walnut (Juglans nigra), sugar maple (Acer saccharum), blackgum (Nyssa sylvatica), and green ash (Fraxinus pennsylvannica). The project will produce sequence databases for expressed genes, genetic markers, genetic linkage maps, and reference populations This will provide lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for growth, adaptation and responses to environmental stresses such as drought, heat, insect pests and disease. These resources will be available to the scientific community and the public through the project website ( All original sequence data will be deposited in NCBI's Sequence Read Archive ( and the genetic linkage maps and associated marker data will also be available at the Dendrome database (

The broader impacts from this project will include forest health, tree improvement, forest management, molecular evolution, scientific training, and public education. An increasing incidence of exotic pests and diseases, combined with climate change and forest fragmentation, are threats to the sustainability of forest ecosystems and economies. This project will provide powerful new tools to address such forest health issues and the protection and restoration of forest genetic diversity and productivity. The project will also fill gaps in available genomic resources for important groups of flowering plants, including the taxonomic orders Magnoliales (yellow poplar), Proteales (sweetgum), Fabales (honey locust), Fagales (Northern red oak and black walnut), Sapindales (sugar maple), Cornales (blackgum), and Lamiales (green ash). These resources will enrich the scientific community's ability to study the evolution of not only woody plants, but also all angiosperms at a resolution and depth not previously possible. All of the data generated by the project will be deposited in high-visibility public community databases, and all gene clones, libraries, and reference population DNAs will be stored and available to the public at cost. Descriptions of the resources and analyses of the results will also be published as journal articles, at national and international meetings, and through a public web portal hosted by the Clemson University Genomics Institute. This project will also provide for the training of undergraduate, graduate and postdoctoral students in comparative genomics, evolutionary genomics, population genetics, bioinformatics and forest genetics. Educational programs on plant genomics will be developed for Native American public schools in cooperation with the Cherokee Nation, and substantive research experiences will be provided to minority undergraduate students in collaboration with the University of West Alabama.

Effective start/end date2/1/117/31/15


  • National Science Foundation: $3,784,472.00


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