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Research Project: Systematics, Nomenclature, and Genetic Diversity of Priority Genera of Woody Landscape Plants

Location: Floral and Nursery Plants Research

2020 Annual Report

Objective 1: Conduct systematic and genetic analyses of priority woody landscape plant genera (chiefly Ulmus, Quercus, and Fraxinus) to elucidate their systematic relationships, revise their taxonomic classifications, and assess the amount, apportionment, and nature of the genetic diversity they contain. Record and disseminate characterization data via GRIN-Global and other data sources. Subobjective 1A – Elucidate the taxonomy and cytology of Fraxinus (ash) in eastern North America. Subobjective 1B – Determine the distribution of alleles of expressed loci in oaks (Quercus). Subobjective 1C – Clarify the taxonomy and diversity of Ulmus (elms), emphasizing potentially disease-resistant germplasm in subg. Oreoptelea. Subobjective 1D – Clarify the taxonomy and reproductive biology of Celtis. Sub-objective 1E – Carry out taxonomic research that meets the needs of stakeholders, such as the production of regional floras and botanical manuals, in collaboration with other scientists and horticulturists. Objective 2: Efficiently and effectively maintain and expand the U.S. National Arboretum Herbarium, Seed Herbarium, and associated documentation as foundational biological resources for agricultural, botanical, and plant genetic resource research. Objective 3: Determine the identity and basic biological characteristics of selected invasive woody plants in the United States.

Work will involve study of plant material, both in wild habitats and cultivated in our botanical garden. We will carry out classical studies using the morphology of the plants, flow cytometry to estimate genome size and thus ploidy level, and study of various DNA markers, including SSR markers for simple parentage studies and NextGen sequencing studies to gather detailed information on evolutionary relationships and history of plant groups. Research will also involve a wide variety of analyses, including phenetic analyses for investigating overall patterns of variation, and searching for clusters and discontinuities in the distribution of plants through multivariate character space; phylogenetic analysis for investigating ancestral relations among groups of plants; and admixture analysis for detecting hybridization.

Progress Report
Significant progress was made on all three objectives, which fall under NP301. Preliminary analysis of RAD-seq data from eastern North American Fraxinus (ash) suggests that at least some of the polyploids are of hybrid origin, though the ancestry of the different species is not yet proven. Some unexpected relationships are emerging, but more work is needed to obtain robust resolution. Closures due to Covid-19 are delaying further work, which will concentrate on additional collecting of species that are poorly sampled, and will add ash species from the western part of the country. Shotgun sequencing has been less informative for our purposes, and future work will concentrate on securing more complete RAD-seq data. Genetic work in collaboration with Queen Mary University of London and the US Forest Service has identified alleles conferring tolerance to EAB (see Accomplishments). For our studies of Quercus (oaks), we are using two next-gen sequencing approaches for different questions. A collaborator is analyzing HybSeq DNA sequences of selected oaks made using a set of baits that include loci functioning in drought resistance and spring budbreak. This will allow us to directly characterize oaks for variation in genes that affect physiological characteristics that are important for nursery use. We also submitted a manuscript describing a study of variation in morphological characters in bur oak, to test different methods for quantifying and coding so they can be used as genetic markers. Future research is being planned to study how genetic variation in oaks affects associated communities of fungi and insects. In collaboration with scientists at the Morton Arboretum, Univ. of Minnesota, Duke Univ., Univ. of Oklahoma, and the U.S. Geological Survey, a proposal is being submitted to the Chinese government by a collaborator at the Chinese Academy of Sciences. In Ulmus (elms), we have submitted a manuscript presenting a well-supported phylogeny for the genus using RAD-seq DNA sequencing. This will allow us to identify species with maximum potential for introducing compatible genes for disease resistance and other desirable traits. A study of the genetics of offspring of a triploid American elm has been published (see Accomplishments). Further investigation of the relationship between diploid and tetraploid American elms, and investigation into apomixis in Celtis (hackberry), have been delayed due to Covid-19 closures. We continued to survey genome size and morphology in escaped populations of Hedera (ivy), a genus important in horticulture that has become invasive in the United States, from across North America, in order to determine the distribution and degree of invasiveness for different species. Sequencing work has been delayed due to Covid-19 closures; this work will test relationships among ivies and test for hybridization that we postulate based on morphology. Progress in the herbarium continues to advance, despite being impacted by the maximized telework requirement. More than 2000 specimen records were added to the database and much of the old loan, exchange, and gift transaction paperwork has been digitized. Over 100 new collections, including many documenting ARS research and germplasm projects, were made and added to the collection along with 833 specimens via incoming gift transactions. A total of 132 new type specimens were discovered, curated, and incorporated into the type collection. In addition, a project to digitize and upload the herbarium’s type specimens to an online repository was started and we currently have over 400 records online (see Accomplishments).

1. Genes to save ash trees from Emerald Ash Borer. Over the last twenty years, Emerald Ash Borer (EAB) has killed hundreds of millions of ash trees in the U.S. and caused billions of dollars in damage. While individual ash trees can be protected by injecting expensive chemicals into tree trunks, the only long-term solution for saving American ash populations is to breed trees with resistance to EAB. An ARS scientist in Washington, D.C., collaborated with researchers at the Queen Mary University of London and the U. S. Forest Service to determine genetic changes and the level of resistance to EAB in different species of ash trees. The scientists identified 53 candidate genes in ash that can enhance ash trees' resistance to EAB. The genes identified will be valuable targets for the selection and breeding increasing of ash populations that are resistant to EAB.

2. Digitization and online access of Herbarium type specimens. The USNA herbarium houses approximately 2000 priceless type specimens, with physical access to the collection normally being the only means of consulting them. The types are currently being verified, curated, databased, and imaged for inclusion in the JSTOR Global Plants database, an online repository of herbarium material. Over 400 of the USNA herbarium’s type records (high-resolution images and associated data) have been uploaded to Global Plants to date, joining nearly 3 million other specimens contributed from collections all around the world. Making digital versions of these specimens available to the scientific community, and to the public at large, advances botanical research and contributes to greater utilization of our specimens and provides an opportunity for increased publicity for the unique collections at the National Arboretum.

Review Publications
Whittemore, A.T., Xia, Z. 2020. Ploidy of seeds from odd-polyploid American elms (Ulmus americana). Journal of the American Society for Horticultural Science. 145:186-192.
Kelley, L.J., Plumb, W.J., Carey, D.W., Mason, M.E., Cooper, E.D., Crowther, W., Whittemore, A.T., Rossiter, S.J., Koch, J.L., Buggs, R.J. 2020. Convergent molecular evolution among ash species resistant to the Emerald Ash Borer. Nature Ecology and Evolution. 4:1116-1128.