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Research Project: Plant and Microbial Genetic Resource Preservation and Quality Assessment

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2017 Annual Report


Objectives
Over the next five years, the Plant Genetic Resources Preservation Program (PGRPP) at the National Center for Genetic Resources Preservation (NCGRP) will focus on the following four objectives that are both hypothesis and non-hypothesis driven. Objective 1: Ensure secure, long-term preservation of the NPGS base collections and associated information and of safety back-up storage for designated non-NPGS plant genetic resources. Objective 2: Facilitate and promote the secure, long-term preservation of plant-associated and other key collections of microbial genetic resources by backing-up collections from ARS and other public-sector institutions. Sub-objective 2a: Provide secure back-up storage of public microbial collections and aid in the development of a U.S. Culture Collections Network. Sub-objective 2b: Develop improved long-term storage systems for selected microbes. Objective 3: Devise, adapt, and/or apply optimal methods for secure long-term preservation of plant genetic resources, and promote research, training, and domestic and international technology transfer of the preceding approaches. Sub-objective 3a: Set priorities to monitor viability of seed collections. Sub-objective 3b: Evaluate effects of LN2 storage on plant germplasm. Sub-objective 3c: Establish optimal harvest time for dormant winter buds used for cryopreservation of selected tree species. Sub-objective 3d.1: Develop protocols for cryopreservation of selected crops. Sub-objective 3d.2: Determine genebanking protocols for crop wild relatives, medicinal plants, and alternative crops. Objective 4: Devise and apply new methods for high throughput phenotyping and genetic analyses of root system architectural diversity in selected crops and their wild relatives.


Approach
The changing needs in U.S. agriculture place new demands on farmers and plant breeders for new improved varieties which require access to a wide range of well characterized plant diversity. An increasing global population will require more efficient food production, and a changing climate requires crop varieties adapted to stresses. Limited, and sometimes compromised, water resources are having greater impacts on crop yields. The National Center for Genetic Resources Preservation is one of the largest and most diverse genebanks in the world and the flagship of the U.S. National Plant Germplasm System. Our project’s overarching mission is two-fold: to provide secure long-term preservation, and documentation of diverse genetic resources. We accomplish this by close collaboration with individual crop curators from the National Plant Germplasm System to back-up and monitor their unique collections. We work to back-up world plant collections, collaborating with other national and international genebanks. Along with preserving crops for U.S. agriculture, we safeguard storage of threatened and endangered plants, crop wild relatives, plants for medicinal uses, and new crops being considered for future biofuel or bioproduct use. Linked to our mission, we propose to develop improved storage protocols of seed, clonally preserved crops, and microbes to become more efficient in our standard operating procedures. Our focus on germplasm preservation and will ensure that farmers have access to the most productive cropvarieties and help the U.S. remain as a world leader in genetic resources preservation.


Progress Report
The crop diversity housed by this project is foundational for plentiful food supplies. Breeders mine our collection for traits that convey resistance to adverse climate, devastating insects and disease or provide superior nutrition. Our collections also support basic and applied biological research. The collection is among the largest in the world and largest distributor of plant germplasm, distributing over 250,000 orders annually to users around the globe. But gene banks are vulnerable to natural and manmade disasters and germplasm collections need to be backed up at multiple locations to protect against loss. The Plant Genetic Resource Preservation Program (PGRPP), a part of the Animal Genetic Resources Preservation Unit (PAGRP) in Fort Collins, Colorado plays a central role in the National Germplasm Resources System (NPGS) by storing of our Nation’s crop genetic resources. Our first objective is to ensure secure, long-term preservation of the U.S. base collections of plants and associated information and to provide safety back-up storage for non-NPGS plant genetic resources. Our vaults hold one of the largest collections of crop genetic resources in the world. We have close to 2 million seed packets representing 420,000 NPGS accessions, and store an additional 363,000 accessions for non NPGS organizations such as the USDA Forest Service, U.S. Tribes, botanical gardens, seed saving organizations, and national and international seed collections. We have almost 10,000 clonal accessions in cryogenic storage. In 2017, the PGRPP received 12,291 new samples. Sixty-one percent were back-up samples from NPGS sites. Thirty-four percent of the samples we received in 2017 came from non NPGS agencies (i.e. Canada gene bank). Four percent were seed voucher samples from the Plant Variety Protection Office and Journal of Plant Registration. The remaining samples came from NPGS sites and will be placed in storage at the Svalbard Global Seed Bank in Norway. In the course of a year, we tested seed viability, packaged and stored 3961 packets in conventional storage and 480 seed packets in cryogenic storage. We also conducted 2158 monitor tests. In addition to seed samples, we processed 145 NPGS clonal samples (exceeding the FY17 clonal cryo objective (Obj. 1: Cryopreserve 125 clonally propagated accessions), important citrus, potato, pear, currant- and gooseberry germplasm were added to the collection. We continued our partnership with the Bureau of Land Management (BLM) Seeds of Success (SOS) program. In 2017 we received 679 new samples of native species, bringing our total SOS samples to 10,762. A significant vulnerability was addressed by scanning over 800,000 germination cards. Before completing this activity much of the historical information about the various accessions was at risk of being lost as no electronic version existed. After scanning, technical staff determined the scanned documents could be used instead of the hard copies thereby increasing their efficiency. Our second objective is to facilitate and promote the secure, long-term preservation of plant-associated microbial genetic resources by backing-up collections from ARS and other public-sector, and our first sub-objective focuses on this. In 2017 we reviewed and strengthened our standard operating procedures, and set up a new laboratory that will allow us to work with microbes. The microbial technician also attended two training sessions and the curator attended a meeting hosted by the U.S. Culture Collection Network on the Nagoya Protocol. A second sub-objective is developing improved long term storage systems for microbe storages. In 2017 we completed a research project in collaboration with other ARS and university scientists to evaluate the viability of Fusarium species stored in LN2 to provide insight into the effectiveness of LN2 storage to preserve Fusarium species. Our third objective is to devise, adapt, and/or apply optimal methods for securing long-term preservation of plant genetic resources, and promote research, training, and domestic and international technology transfer of the preceding approaches. An important sub objective is to set priorities to monitor viability of our seed collection. In 2017 we continued to focus on monitor testing short lived species that have not been tested in 10-20 years and met our monitoring goals through a specific cooperative agreement with the Colorado State University (CSU) Seed lab. Research completed found that overall LN2 storage is comparable to conventional storage on rye. Comparison of pre-harvest twig temperature on post cryopreservation viability was conducted on blueberry in FY 15/16. This led to defining pre-harvest temperature that supports high dormant bud survival and suggested a strategy for optimizing timing of dormant bud harvest. In FY 2017, optimal pre-harvest temperature ranges established for effective blueberry dormant bud cryopreservation were applied to dormant bud of other species (apricot, peach and plum) with a promising effect. The dormant bud cryopreservation method with various cryoprotenctants and antioxidants was tested on pecan germplasm; post cryopreservation viability is currently being evaluated promising results using colorimetric techniques to test post cryo viability of dormant buds was obtained. Such an approach will simplify viability testing. Sub-objective 3d2 focuses on determining gene banking protocols for crop wild relatives (CWR) including the use of Geographical Information Systems (GIS) and gap analysis to identify and prioritize U.S. CWR. ARS scientists collaborated with The International Center for Tropical Agriculture, to perform gap analysis of U.S. CWR using GIS. We have also been active in information dissemination of our results on CWR. We presented two papers at the National Native Seed Conference, developed a white paper that outlines a national strategy for securing CWR. This was widely distributed to potential partners. ARS scientists published a special issue on CWR use in Crop Science. The special issue contained 17 invited articles that outlined how CWR have been utilized to breed a broad range of crops. We also have been leading efforts to produce the book, Valuable Plants of North America: Crop Wild Relatives and Wild Utilized Species which will be submitted to Springer Publishing by October 1, 2017. This book consists of 30 chapters written by leading experts. The book has three sections: 1) current conservation activities and perspectives of Canada, Mexico, the U.S. and Native American tribes of the U.S. 2) a primer on plant genetic resource conservation, 3) individual chapters on economically important plant classes, and the associated CWR and wild utilized species found in North America.


Accomplishments
1. Wading into the gene pool: progress using wild species to improve crops. A variable and changing climate, coupled with burgeoning population growth threatens to undermine global food security. Crop wild relative species have adaptive characteristics that can be used to develop more resilient crops. But are plant breeders utilizing these resources, and are emerging genomic tools helping them? ARS researchers in Fort Collins, Colorado led efforts to publish a special issue in the journal Crop Science that highlights the innovative strategies being used to transfer useful traits from wild species into cultivars. The special issue contained seventeen open access articles and covered a broad range of crops; 17 ARS researchers contributed to the project. This Special Issue outlines the progress being made, and constraints being overcome, and serves as an educational resource to help scientists and plant breeders better utilize crop wild relative species to develop more climate resilient and productive crops.


Review Publications
Volk, G.M., Henk, A.D., Jenderek, M.M., Richards, C.M. 2016. Probabilistic viability calculations for cryopreserving vegetatively propagated collections in genebanks. Genetic Resources and Crop Evolution. doi:10.1007/S10722-016-0460-6.