Comparative Genomics of Environmental Stress Responses in North American Hardwoods

PI：John E.卡尔森（宾夕法尼亚州立大学）合作PI：珍妮罗梅罗塞弗森（圣母大学），斯科特E。Schlarbaum（田纳西大学-诺克斯维尔）、Mark V.科格斯霍尔（密苏里州大学-哥伦比亚）、Haiying Liang（克莱姆森大学）、奥利弗盖林（密歇根理工大学）和Ketia L. Shumaker（西亚拉巴马大学）。 高级人员：梅格斯塔顿（克莱姆森大学）和尼古拉斯C。惠勒（俄勒冈州州立大学）。美国大部分林地是天然林，其中东部硬木林占一半以上。东部硬木林是复杂的生物系统，覆盖4亿多英亩的洼地和河岸、主要流域、中温带和高地。这些森林为野生动物提供栖息地和食物，稳定河岸带，长期固碳和其他基本生态系统服务，以及供人类使用的木材和生物质产品。外来害虫、疾病和入侵植物的日益增加，加上气候变化和森林破碎化，威胁到这些森林生态系统的可持续性。 不幸的是，很少有基因组资源可用于研究组成东部森林的硬木物种的财团。 一个跨学科的团队将共同努力，为代表东部硬木树主要分类群的重要物种开发新的基因组资源，从最古老的到最近进化的，包括黄色白杨（鹅掌楸）、枫香（枫香）、皂荚（三棘皂荚）、北方红橡木（红栎）、黑胡桃（黑胡桃）、糖枫（糖槭）、黑胶树（尼萨）和绿色白蜡（白蜡树）。 该项目将建立表达基因、遗传标记、遗传连锁图和参考种群的序列数据库，这将为发现和保护硬木树的生长、适应和对干旱、高温、病虫害等环境胁迫的反应基因提供持久的基因组和生物资源。 这些资源将通过项目网站（www.hardwoodgenomics.org）向科学界和公众提供。 所有原始序列数据将保存在NCBI的Sequence Read Archive（http：//www.ncbi.nlm.nih.gov/sra）中，并且遗传连锁图谱和相关标记数据也可在Dendrome数据库（http：//dendrome.ucdavis.edu/）中获得。该项目的更广泛影响将包括森林健康、树木改良、森林管理、分子进化、科学培训和公共教育。 外来病虫害的发生率不断增加，加上气候变化和森林区块化，威胁着森林生态系统和经济的可持续性。 该项目将提供强有力的新工具，以解决这些森林健康问题，保护和恢复森林遗传多样性和生产力。该项目还将填补重要开花植物群体现有基因组资源的空白，包括分类学上的木兰目（白杨）、Proteales（枫香）、Fabales（皂荚）、Fagales（北方红橡树和黑胡桃）、Sapindales（糖枫）、Cornales（黑胶）和Lamiales（绿色灰）。这些资源将丰富科学界的能力，不仅研究木本植物的进化，而且研究所有被子植物的分辨率和深度是以前不可能的。 该项目产生的所有数据将存放在高知名度的公共社区数据库中，所有基因克隆、文库和参考群体DNA将被存储并以成本价向公众提供。 对资源的描述和对结果的分析也将作为期刊文章、在国家和国际会议上发表，并通过克莱姆森大学基因组学研究所主办的公共门户网站发表。 该项目还将为本科生、研究生和博士后提供比较基因组学、进化基因组学、人口遗传学、生物信息学和森林遗传学方面的培训。 将与切罗基民族合作，为美洲土著公立学校制定植物基因组学教育方案，并将与西亚拉巴马大学合作，为少数民族本科生提供实质性研究经验。

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 (www.hardwoodgenomics.org). All original sequence data will be deposited in NCBI's Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) and the genetic linkage maps and associated marker data will also be available at the Dendrome database (http://dendrome.ucdavis.edu/). 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.