Research Project: Efficient and Effective Preservation and Management of Plant and Microbial Genetic Resource Collections

Location: Agricultural Genetic Resources Preservation Research

2019 Annual Report

Objectives
Objective 1: Efficiently and effectively preserve and back-up plant genetic resource collections under conventional (freezer) conditions. Objective 2: Efficiently and effectively cryopreserve and back-up plant and microbial genetic resource collections using liquid nitrogen as the cryogen. Objective 3: Design and test methods and strategies for exploiting genomic data to enhance the efficiency and effectiveness of the NPGS’s plant genetic resource management projects. Objective 4: Formulate and validate methods and strategies for efficiently and effectively sampling, preserving, and using the genetic diversity of selected crop wild relatives.

Approach
The continued development of productive crop varieties for U.S. agriculture depends on plant scientists’ access to a wide range of well characterized crop genetic diversity. The U.S. National Plant Germplasm System (NPGS) is one of the largest and most diverse genebank systems in the world, and the Plant and Animal Genetic Resources Preservation Unit at the National Laboratory for Genetic Resources Preservation is a critical component of the NPGS. Our mission is to provide secure long-term preservation of the NPGS base collection, designated non-NPGS seed, and microbial collections, so that these invaluable genetic resources are available to present and future crop scientists (Objective 1). As information about genetic resources highly determines the degree of use of these materials, an integral part of the mission also involves managing and disseminating the data associated with germplasm. We also work to improve our procedures to be both more effective with regard to results and also more efficient with regard to costs (Objective 2). Finally, we play a prominent role in securing and making available our national heritage of U.S. crop wild relatives (Objective 3). We accomplish these tasks via close collaboration with crop curators throughout the NPGS, as well as with other national and international genebanks. Our central focus on U.S. germplasm preservation will ensure that one of the world’s most diverse crop genetic resource collection is safeguarded for the long-term and thus able to continue to underpin the productivity of U.S. agriculture.

Progress Report
The USDA National Plant Germplasm System (NPGS) is among the largest agricultural gene banks in the world and distributes over 250,000 orders annually to users around the globe who require diverse plant genetic resources to support plant breeding, research and educational goals. However, gene banks are vulnerable to natural and manmade disasters. As a security measure, living biological collections need to be backed up at multiple locations to protect against loss. The Plant Genetic Resource Preservation Program (PGRPP), a part of the Plant and Animal Genetic Resources Preservation Unit (PAGRP) in Fort Collins, Colorado plays a central role in the NPGS by providing secure back up storage of our Nation’s plant genetic resources. Our vaults hold one of the largest collections of crop genetic resources in the world. In 2019, we housed 450,300 NPGS security backup samples and 9,500 voucher samples for the Plant Variety Protection (PVP) Office and Journal of Plant Registration (JPR). We provided security backup seed storage for 77 organizations including non-governmental organizations such as botanical gardens, tribal agencies, universities, and national and international seed collections; over 450,000 unique accessions are secured. In addition, we provided secure back up of 19 microbe collections, totaling 112,000 isolates. Objective 1. Our primary objective is to process and store incoming samples, and monitor the viability of base samples in the NPGS collection. In 2019, the PGRPP received 6,886 new samples. Eighty-nine percent were back-up samples from other NPGS sites, including 494 clonal samples. Seven percent were voucher samples from the Plant Variety Protection Office and four percent were voucher samples for the Journal of Plant Registration. NPGS sites also sent us 5,298 samples that we repackaged for storage at the Global Seed Vault in Norway. We also received a safety duplicate of an important wine microbe collection from the University of California, Davis. In the course of a year, we tested viability, packaged, and stored 3567 NPGS safety duplicate samples. We conducted 6213 monitor tests, double the number of monitor tests done in 2018. In 2019, intellectual property right protection expired on 34 PVP varieties and 178 JPR-certified varieties. These newly expired varieties were processed and are now widely available to plant breeders and scientists. We also continued our partnership with the Bureau of Land Management (BLM) Seeds of Success (SOS) program. In 2019, almost half of our incoming samples were seed of wild, native U.S. species collected by the BLM SOS program. Objective 2. In this objective, we work with NPGS cooperators to develop, update, document, and implement more effective long-term maintenance and preservation methods for the plant and microbial genetic resources preserved at the NLGRP. Accomplishments this year included completing an analysis of liquid nitrogen exposure tests conducted since the late 1980’s on 30,000 samples. These results will help us determine what species are best suited for seed storage in liquid nitrogen vapors. We also examined the use of colorimetric tests for assessing viability of cryopreserved dormant buds. We found that phenolic secretions specific to species and time of testing precluded the use of this method. We developed a workable procedure for cryopreservation of hazelnut and quince shoot tips, and are now confirming this new protocol. Objective 3. In this objective we conducted a “gap analyses” of the ecogeographical distribution of 250 high priority U.S. native crop wild relatives to guide their strategic acquisition and conservation in situ and in the NPGS. In 2019, we finalized the determination of which species to include in the high priority list, updated occurrence data, optimized the modelling protocols, and are now systematically modelling species distribution. Once completed we will be prepared to conduct the gap analysis. We also identified and engaged with key research and conservation stakeholders of U.S. crop wild relatives. This resulted in a published road map on conservation, use, and public engagement of useful wild plants that unites conservationists, scientists, and educators around North America’s crop wild relatives and wild utilized plants.

Accomplishments
1. Published comprehensive reference on North American crop wild relatives. The plant species that humans rely upon have an extended family of wild counterparts that are an important source of genetic diversity used to breed productive crops. Many wild plant species are also directly used, especially for revegetation, and as medicinal and ornamental plants. ARS researchers in Fort Collins, Colorado, led efforts to publish a two-volume book that provides a valuable reference describing important crop wild relatives and wild utilized species found in Canada, the United States, and Mexico. The volumes highlight efforts taken by these countries to conserve and use wild resources and provides essential information on best practices for collecting and conserving them. Numerous maps using up-to-date information and methods illustrate the distribution of important species. Maps are supplemented with a detailed description of important species in regard to their potential value as agricultural resources and their conservation status. This comprehensive reference is a valuable resource for students and scientists interested in economic botany, and for practitioners at all levels tasked with conserving plant biodiversity.

Review Publications
Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F. 2018. Preface. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 1: Conservation Strategies. New York, NY: Springer, Cham. p. xiii-xiv.
Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F. 2019. Preface. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 2: Important Species. New York, NY: Springer, Cham. p. xiii-xv.
Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F. 2019. North American Crop Wild Relatives. Volume 2: Important Species. New York, NY: Springer, Cham. 740 p.
McCoy, J., Young, J.H., Nifong, J.M., Hummer, K.E., De Noma, J.S., Avendano-Arrazate, C.H., Greene, S.L., Kantar, M.B. 2019. Species for medicinal and social use with an emphasis on theobroma cacao l. (cacao), nicotiana tabacum l. (tobacco), actaea racemosa l. (black cohosh), and humulus lupulus l. (hops). North American Crop Wild Relatives. Springer. 2:645-692. https://doi.org/10.1007/978-3-319-97121-6_19.
Khoury, C.K., Sosa, C.C. 2018. Appendix 1: Map Methods and Occurrence Data Sources. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 1: Conservation Strategies. New York, NY: Springer, Cham. p. 325-334.
Khoury, C.K., Amariles, D., Soto, J.S., Diaz, M.V., Sotelo, S., Sosa, C.C., Ramirez-Villegas, J., Achicanoy, H.A., Castaneda-Alvarez, N.P., Leon, B., Wiersema, J.H. 2018. Comprehensiveness of conservation of useful wild plants: an operational indicator for biodiversity and sustainable development targets. Ecological Indicators. 98:420-429. https://doi.org/10.1016/j.ecolind.2018.11.016.
Khoury, C.K., Amariles, D., Soto, J.S., Diaz, M.V., Sotelo, S., Sosa, S.C., Ramirez-Villegas, J., Archicanoy, H.A., Velasquez-Tibata, J., Guarino, L., Leon, B., Navarro-Racines, C., Castaneda-Alvarez, N.P., Dempewolf, H., Wiersema, J.H., Jarvis, A. 2018. Data for the calculation of an indicator of the comprehensiveness of conservation of useful wild plants. Data in Brief. 22:90-97. https://doi.org/10.1016/j.dib.2018.11.125.
Jenderek, M.M., Cruz, V., Salywon, A., Jasso De Rodriguez, D., Garcia, R., Dierig, D. 2019. Wild genetic resources of minor oil and rubber crops. North American Crop Wild Relatives. 2:485-542. https://doi.org/10.1007/978-3-319-97121-6_15.
Jenderek, M.M., Frelichowski, J.E. 2019. Fiber crops: cotton and hesperaloe. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 2: Important Species. New York, NY: Springer, Cham. p. 543-578.
Volk, G.M., Jenderek, M.M., Walters, C.T., Bonnart, R.M., Shepherd, A.N., Skogerboe, D.M., Hall, B.D., Moreland, B.L., Krueger, R., Polek, M. 2019. Implementation of citrus shoot tip cryopreservation in the USDA-ARS national plant germplasm system. Acta Horticulturae. 1234:329-334. https://doi.org/10.17660/ActaHortic.2019.1234.43.
Volk, G.M., Jenderek, M.M., Staats, E.R., Shepherd, A.N., Bonnart, R.M., Leado, A., Ayala Silva, T. 2019. Challenges in the development of a widely applicable method for sugarcane (Saccharum spp.) shoot tip cryopreservation. Acta Horticulturae. 1234:335-342. https://doi.org/10.17660/ActaHortic.2019.1234.44.
Krishnan, S., Moreau, T., Kuehny, J., Novy, A., Greene, S.L., Khoury, C.K. 2019. Resetting the table for people and plants: Botanic gardens and research organizations collaborate to address food and agricultural plant blindness. Plants, People, Planet. 1(3):157-163. https://doi.org/10.1002/ppp3.34.
Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F. 2018. North American Crop Wild Relatives. Volume 1: Conservation Strategies. New York, NY: Springer, Cham. 346 p.
Greene, S.L., Khoury, C.K., Williams, K.A. 2018. Wild plant genetic resources in North America: an overview. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 1: Conservation Strategies. New York, NY: Springer, Cham. p. 3-32.
Khoury, C.K., Greene, S.L., Williams, K.A., Kanter, M.B., Marek, L.F. 2019. Conservation and use of the North American Cornucopia: the way forward. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 2: Important Species. New York, NY: Springer, Cham. p. 695-710.
Williams, K. A., Greene, S. L. 2018. Conservation of Crop Wild Relatives in the USA. In: Greene, S., Williams, K.A., Khoury, C., Kantar, M., Marek, L., editors. North American Crop Wild Relatives, Volume 1. Cham, Switzerland: Springer. p. 97-154.
Kesoju, S., Greene, S.L., Martin, R.C., Kramer, M.H., Walsh, D., Boydston, R.A. 2019. Isolation distances for transgenic alfalfa seed production in the Pacific Northwest. Crop Science. 59(4):1701-1708. https://doi.org/10.2135/cropsci2018.07.0414.