W6: Management and Utilization of Plant Genetic Resources and Associated Information
(Multistate Research Project)
W6: Management and Utilization of Plant Genetic Resources and Associated Information
Duration: 10/01/2016 to 09/30/2021
Statement of Issues and Justification
The need, as indicated by stakeholders:
This project addresses the Food Production, Food Security and Horticulture issues under the Sustainable Production Systems in the Western Agenda recently released by Western Association of Agricultural Experiment Station Directors. Agricultural production in the Western Region involves more than 400 plant species and contributes almost one-quarter to the total U.S. farm gate value or $87.7 billion. Researchers in both public and private sectors, primarily in land grant universities in the western region, have played, and will continue to play a critically important role in the development of robust agricultural and natural resource economies. Improving the current crop varieties or developing new crop varieties relies on available plant genetic resources acquired throughout the world and managed by the National Plant Germplasm System (NPGS). Plant researchers in the western region have requested a large number of accessions from NPGS to use in both basic and applied research. As a crucial component of the NPGS, this project manages the genetic resources of cool season food and forage legumes, grasses, common beans, oilseeds, vegetables, beets, ornamentals, medicinal crops and related wild species. These introduced plant genetic resources harbor valuable genes or alleles for researchers and breeders to improve crop productivity for food security, to develop new varieties, to breed cultivars with improved resistance to diseases and pests and with resilience to environmental stresses such as drought and temperature extremes associated with climate change. The stakeholders and customers for this project include researchers, plant breeders, educators, and commercial producers in the western states, in the U.S. and throughout the world. In the past seven years (2008-2014), researchers within the western region used a total of 47,069 packets of seed samples from this project in various research, education and extension activities. The extensive use of the available plant genetic resources managed by this project contribute to new knowledge of plant science generated by basic studies and to increased agricultural productivity resulting from improved crop varieties and new crops developed by applied plant breeding.
The importance of the work, and what the consequences are if it is not done:
According to United Nations estimates, the global population is predicated to increase by 2.4 billion by 2050, with the U.S. population increasing 21% to approximately 389 million. This, along with warmer temperatures and disrupted precipitation patterns associated with climate change, presents a food security challenge that will require breeding crop cultivars that are more productive in less favorable environments. In response, scientists and breeders are mining genes that confer resistances to pathogens and pests and tolerance to abiotic stresses from existing plant genetic resources. U.S. scientists and breeders rely on introduced germplasm to provide new genes to improve major crops, minor regional crops, and to develop new crops. Access to germplasm is thus a critical need. This project “Management and Utilization of Plant Genetic Resources and Associated Information” plays a vital role in conserving and providing needed genetic resources for numerous crop species to support such endeavors.
As of September 30, 2015, this project manages a total of 97,219 accessions collected worldwide. Assigned plant species, both cultivated crops and their wild relatives, represent 1,133 genera, 4,996 species and 5,690 taxa. Almost all of the seed samples are available upon request for research, education and extension purposes. The value of these collections continues to grow as international access to germplasm is increasingly limited by political and environmental factors, and scientists continue to develop new tools that enable them to identify valuable traits within the collection.
This collection has had enormous impact on agriculture in the U.S., and especially in the western states, where many of these crop species are economically important. For example, alfalfa is the fourth largest crop grown in the U.S., behind corn, soybeans, and wheat. According to the USDA Crop Statistics, more than 53 million metric tons of alfalfa, worth over $10 billion, was produced on more than 7 million hectares in the U.S. in 2012. More than one-third of that was in the western states. The alfalfa collection has more than 50,000 evaluation data entries and has been extensity utilized. A pedigree analysis of 500 U.S. alfalfa varieties found that 245 or 69% of these varieties had one or more parents that could be traced to a PI accession in the temperate forage legume collection managed by this project. Another example is lettuce, second only to potato in term of per capita consumption in the U.S. with annual production value exceeding $2 billion. Two western states, California and Arizona, account for 96% of U.S. lettuce production. The lettuce collection of both wild and cultivated accessions has been screened extensively for disease resistance and other favorable traits to improve and sustain the production of this crop. Cool season food legumes (chickpea, pea, and lentil) are major crops in Washington and Idaho. The recent booming chickpea industry is supported by cultivars developed from the germplasm collection managed by this project. Our collection of native plant species ensures the availability of native species needed for the revegetation and ecosystem restoration for the inter-mountain west. In addition to the Western States, the W6 project fills germplasm needs nationwide, such as the lentil industry in North Dakota, beans in Michigan and many other states, and forage and turf grasses throughout the Midwest and Atlantic states.
U.S. agriculture is based on plant species many of which are not indigenous to this country. It is hard to picture what the U.S. food production system would be without the introduced plant genetics resources. Almost all the major crops of commercial importance would not exist. Just to improve existing crops, researchers would have to travel afar to the centers of origin or centers of diversity of each specific crop to collect needed germplasm. Nowadays, many areas or countries are not easily accessible for various reasons. The majority of landraces of many crops are no longer available in many agricultural areas as they have been steadily replaced by modern varieties. The natural habitats of many crop wild relatives have disappeared through the destruction and degradation of natural environments or their conversion to other uses. The management and conservation of the worldwide collected crop genetic resources in NPGS must be continued for the use by researchers and educators of the current and future generations.
This project also provides needed germplasm to researchers producing high-impact scientific results with practical application. There is no better example than purple false brome, Brachypodium distachyon (L.) Beauv. This grass has a small stature, a rapid life cycle, and most importantly, a small genome evolutionarily similar to important cereal crops like wheat and barley. In 2001 this little known grass species was proposed as a model plant for studying grass functional genomics. Functional genes discovered in this model plant have had immediate applications to the genetic improvement of food (wheat) and energy (switchgrass) crops. In February 2010, the complete genomic DNA sequence of this grass was published in the journal Nature. The sequenced diploid inbred line was derived from an accession (PI 254867), that was collected from Iraq and maintained in WRPIS since 1959. Since 2001, WRPIS has distributed seed samples of this PI to over 150 requesters in more than 20 countries. A search with Google Scholar shows over 6,500 published research papers using this model plant (http://scholar.google.com/scholar?q=Brachypodium+distachyon+&hl=en&as_sdt=0%2C48&as_ylo=2001&as_yhi). These published results greatly increase our understanding of basic plant molecular biology from gene function, the regulation of gene expression to genome organization and evolution.
The technical feasibility of the research:
The Agricultural Research Center, the College of Agricultural, Human, and Natural Resource Sciences of Washington State University (WSU) provides required farm land for regeneration, seed increase, phenotypic evaluation and genetic enhancement of germplasm on three research farms at Pullman, WA, Central Ferry, WA and Prosser, WA. Each site provides suitable climate conditions to respective plant species. Standard cultivation practices have been developed by dedicated and experienced staff for specific plant species and genera. USDA-Agricultural Research Service completed an expensive retrofit of the existing seed storage facilities on the WSU campus in 2014 that resulted in a much better insulation of the seed storage space so it is adequate for proper conservation of seed samples for short and medium term storage. However, the storage space is almost full, and we are exploring how to expand storage to house our growing collection. The National Center for Genetic Resources Preservation, Fort Collins, Colorado and the Svalbard Global Seed Vault, Svalbard, Norway are available for security back-up and long-term storage of our collections. The Internet-based Genetic Resource Information Network (GRIN) database connects our managed accessions and associated information with our users. We receive excellent technical support from the USDA-ARS Database Management Unit, Beltsville, Maryland to ensure researchers and breeding programs have updated access to GRIN for searching and requesting needed genetic resources for research and education purposes.
The advantages for doing the work as a multistate effort:
Over the past 68 years, this project has been supported through a joint partnership, designated as the Multistate Research Project W-006, between the USDA-Agricultural Research Service (USDA-ARS) and the Western State Agricultural Experiment Stations (WSAES). Although the germplasm collection managed by this project has national and international significance, most of the species are important crops in the western states. The full potential of certain germplasm accessions can only be realized when they are evaluated under particular conditions, many of which could be found in the broad geographic expanse of the Western Region. Our stakeholders and customers include professors, professional researchers and breeders in public universities, private companies, non-profit organizations and government agencies. The multistate effort allows an effective interaction between our germplasm curatorial staff and the user community. The germplasm collection managed by this project is covered by eleven crop specific Crop Germplasm Committees (CGC) whose members consist of state, federal, and private researchers that meet either annually or biennially to provide guidance for plant genetic resource acquisition, conservation, management, and distribution. More importantly, the W6 Regional Technical Advisory Committee (RTAC) has dedicated representatives from each participating state and meets annually to assess the need and the status of the conservation and utilization of the plant genetic resources and associated information managed by this project.
What the likely impacts will be from successfully completing the work:
This project will provide a continuous supply of critically needed high quality germplasm samples to the plant research community in the Western region, in the U.S. as well as in foreign countries, for scientific research and product development. Phenotypic evaluation and genomic characterization provided by this project will enable breeders to more efficiently identify and utilize germplasm with desirable traits and alleles for improvement in both quality and productivity of crop species. Marker-assisted selection has been a powerful tool for expediting the process of genetic improvement for many crop species. This project will generate information on marker-trait associations and identify user-friendly DNA markers for breeders to use. Genetically enhanced breeding lines developed through this project will speed the development of new cultivars with desirable agronomic traits and improved resistance to diseases and abiotic stresses. The germplasm samples distributed from this project will contribute to the genetic improvement of the quality and productivity of crop plants to ensure that U.S. agriculture remains viable and competitive and for feeding the growing world population.
Related, Current and Previous Work
This project was initiated in 1947 and has been supported since through a joint partnership, designated as the Multistate Research Project W-006, also known as the Western Regional Plant Introduction Station (WRPIS) on the Pullman campus of Washington State University, between the USDA-Agricultural Research Service (USDA-ARS) and the Western State Agricultural Experiment Stations (WSAES). For 68 years, WRPIS has served as a major genebank of the National Plant Germplasm System (National Plant Genetic Resources Board, 1984; Janick, 1989; National Research Council, 1991) and made satisfactory progress in each of the mission areas of acquisition, conservation, evaluation, characterization, documentation and distribution of plant genetic resources important to the Western Region and to the country. The WRPIS collection has grown from 72,000 accessions to over 96,000 accessions in the past ten years (Attachment 1. Growth of WRPIS Germplasm Collections) and accounts for approximately 17% of the total accessions and over one-third of the total taxa in the NPGS. The crop genetic resources managed by this project include cool season forage and turf grasses, common beans, cool season food legumes (pea, chickpea, lentil, faba bean, lupine, etc.), lettuce, safflower, onion relatives, and temperate forage legumes (alfalfa, clover and trefoil), to name just a few. Other important taxa are crop wild relatives, ornamental species, medicinal plants, native plant and potential new crops (Attachment 2. Major crop groups maintained at WRPIS). Currently, the WRPIS collections are assigned to five curatorial programs, each of which is responsible for 14,000 to 24,000 accessions. In addition, four research scientists conduct mission-related research in agronomy, plant pathology and genetics to help the curators effectively and efficiently manage the assigned genetic resources.
This project provides a valuable service to the scientific community by supplying needed plant genetic resources and associated information which contribute tremendously to scientific research and crop improvement in the Western Region, in the U.S., and around the world. Our annual distribution, which was in the 20,000s prior to 2008 and climbed to the 30,000s in recent years, indicates an increased demand for plant germplasm by the user community (Attachment 3. WRPIS annual distribution (number of seed packets) in the past ten years). During the past seven years, public and private sector plant researchers in the Western Region requested and received a total of 283,168 packets of seed samples from NPGS genebanks; the number of samples fluctuated greatly from year to year, from a low of 31,318 in 2008 and high of 50,411 in 2010 (Attachment 4A). Among these, 47,298 samples (approximately 17%) were distributed from WRPIS with an average of 6,756 samples per year ranging from 4,739 in 2011 to 8,789 in 2013 (Attachment 4B). These distributed plant germplasm samples are utilized in the region to support crop improvement, help to sustain small farm agriculture, and to develop new crops. They are also used in a variety of scientific research projects. Thus, the use of plant genetic resources by researchers in the Western Region, particularly scientists associated with the SAES Universities, is significant. Among the 3,722 research projects identified by CRIS search at the website http://cris.nifa.usda.gov/cgi-bin/starfinder/5819/crisassist.txt using individual crop names such as alfalfa, lettuce, grass, common bean, pea, chickpea, etc., 1,228 (about one-third) were located in the Western Region. Considering the fact that the WRPIS germplasm is primarily used as raw materials in plant breeding, we made a second round of search using “alfalfa breeding”, “lettuce breeding, “common bean breeding” and “chickpea breeding” etc. as key words. This round returned a total of 154 research projects with 98 (63.6%) in the Western Region. All of these breeding projects used genetic resources from the NPGS and from WRPIS. For example, a published pedigree analysis reported that 69% (245 out of 500) U.S. alfalfa varieties had one or more parents that could be traced to a PI accession in the temperate forage legume collection managed by this project (Bauchan and Greene, 2002).
Not only are our collections important to the Western Region, our project is unique. A CRIS search for active projects using the term “germplasm management” and “germplasm management and not production” identified 75 and 20 CRIS projects, respectively. A search of “Plant Germplasm Acquisition” revealed 16 projects. Almost all of these projects are sister projects in the NPGS, coordinated at the national level. Each NPGS genebank or repository is assigned to manage a different set of crop species and each is complementary to the other in supporting overall NPGS goals. The majority of the proposed research in our project plan is unique and does not overlap with any other projects.
Driven by the demand of our stakeholders and customers, the germplasm holdings at Pullman have been growing at a steady pace. Over the last several years we have continued to strategically expand the genetic diversity in our collections. We conducted three international and three domestic plant collection trips in the last five years to bring new germplasm to fill gaps in our collections and to fill the needs of our customers. The horticultural crops germplasm curator collected 56 wild beet accessions with potential drought and disease tolerance from the Atlantic and Mediterranean coasts of Morocco and the research agronomist collected cool season grass Phalaris arundinacea germplasm from Italy. This species is used as a pasture grass and a potential biofuel crop. In response to the need for resistance sources to Verticillium wilt race 2, a serious soil-borne fungal disease threatening the lettuce industry, we worked with the ARS Plant Exchange Office and arranged to acquire 32 wild lettuce germplasm accessions from Armenia, Georgia and Russia. One of these new accessions showed partial resistance and is being used in a lettuce breeding project in California. We also collected wild relatives of beans and beets from the Southeast and California, respectively. Worth mentioning is our effort in collecting and testing native plant species. The research agronomist partnered with the Bureau of Land Management (BLM)’s Seeds of Success (SOS) program and acquired approximately 10,000 new native plant accessions from the Western Region. Most of these newly collected accessions were added to WRPIS holdings and some were sent to other genebanks for incorporation into permanent National Plant Germplasm System collections. Over the last 8 years we have filled more than 1,400 seed requests and distributed more than 5,000 SOS seed samples for restoration research and germplasm development.
Associated phenotypic evaluation and genotypic characterization data adds value to germplasm collections since it enables users to choose the right accessions for their projects. WRPIS has been independently or collaboratively conducting evaluation and characterization studies and has generated substantial amounts of information associated with the collection. On average, we uploaded approximately 50,000 observation data points annually on diverse plant accessions into the Germplasm Resources Information Network (GRIN) database (being upgraded to GRIN Global), which includes measurement or scores of the established descriptors of specific crop species, digital images of the field grown plants, molecular marker data, and laboratory analytic results on nutritional components. The GRIN database is accessible by researchers worldwide via the internet.
This project also uses scientific publications to disseminate associated information on our germplasm to the scientific community. Over the past five years, scientists in this project have published independent or collaborative research results on genetic diversity of faba bean, (Kwon et al., 2010), pea (Smýka et al., 2011), chickpea (Kumar et al., 2014), and lupine (Iqbal et al., 2012); mapping major genes or quantitative trait loci conferring resistance to pea Fusarium wilt Race 1 (Kwon et al., 2013), pea Fusarium wilt Race 2 (McPhee et al., 2012), partial resistance to Fusarium root rot (Coyne et. al., 2015), partial resistance to Aphanomyces (Hamon et al., 2011; 2013) and pea seed borne mosaic virus resistance (Konečná et al., 2014); genome wide association mapping of between economically important traits (seed quality and disease resistance) and DNA markers in the WRPIS pea core collection (Kwon et al., 2012; Cheng et al., 2015).
In addition to providing raw materials and information for breeding and research, this project is responding to specific research need of the Western Region. Frequent fires, overgrazing, invasive weeds, and climate change combine to threaten the diversity and function of millions of hectares of land resources in the Western Region. This has led to an increasing need for restoration with diverse, adapted genetic resources. Collaborating with BLM and the U.S. Forest Service, the WRPIS research agronomist conducted genecology research for developing seed zones to guide the choice of germplasm for restoration on numerous key restoration species. This includes mountain brome (Johnson et al., 2010), tapertip onion (Johnson et al., 2013), Indian ricegrass (Johnson et al., 2012), bluebunch wheatgrass (St Clair et al., 2013), Sandberg bluegrass (Johnson et al., 2015), basin wildrye (manuscript submitted) and Thurber’s needlegrass (manuscript in preparation). For all species investigated, extensive genetic variation in adaptive plant traits was observed. We have linked that genetic variation to diverse seed source climates through multivariate and linear correlation, suggesting climate driven natural selection and evolution. Regression models integrating genetic variation and source climates were developed and used with GIS software to map seed zones. For all species only 4-8 seed zones represented most of the mapped areas, showing that their implementation is practical. These seed zones will promote the use of adapted and ecologically suitable germplasm for large-scale restoration in the Western Region.
Alfalfa is an important crop in the Western Region. The production of alfalfa is challenged by endemic and emerging diseases and adverse environmental factors. To enhance resistance to disease and drought, in collaboration with scientists from Alforex Seeds, S & W Seed, Forage Genetics and the Noble Foundation, the research geneticist working on alfalfa at Prosser, WA led the effort to identify resistance loci in three alfalfa populations. Using bulk segregant analysis, they identified 11 molecular markers associated with Verticillium wilt resistance in two alfalfa populations (Zhang et al., 2014). Field and greenhouse trials were carried out for phenotyping important traits associated with drought tolerance in 200 alfalfa accessions which had been selected based on drought tolerant potential suggested by their passport data, i.e., being developed in or collected from a dry area. The resultant superior drought tolerant accessions performed better than the known drought tolerant varieties under water limited conditions in both greenhouse and field experiments. Genome-wide association identified twenty and fifteen loci associated with drought resistance index and leaf relative water content, respectively (Zhang et al., 2015). These initial results and plant materials have been shared with collaborators and used in a collaborative alfalfa improvement research project supported by competitive extramural funding.
Regeneration, distribution and utilization of plant species in the custody of WRPIS and the NPGS are impaired by plant diseases, including those long known and those previously not described or not reported for a given host or locale. The research plant pathologist in this project conducts research on such diseases in collaboration with scientists at state universities (including those in the Western Region), USDA-ARS (including other WRPIS staff) and international collaborators. Accomplishments include defining host range and resistance for Penicillium agents of blue mold of bulb crops (Dugan et al., 2011; Dugan et al., 2014b), and documenting resistance and susceptibility for stripe rust in Basin wild rye (Dugan et al., 2014a). Reports of diseases previously unreported in the United States include fungi on pome fruit (Wiseman et al., 2015; Wiseman et al., 2015) and dodder on chickpea (Chen et al., 2014). Multiple other disease notes and first reports are published (Dugan, Lupien et al., 2105, Dugan, 2013, 2012, 2011; Dugan and Nazaire, 2011; Dugan et al., 2012). Biogeography of white rot of onion and garlic was updated for the Pacific Northwest and management recommendations provided (Lupien et al., 2013). Accessions of white lupine seed were systematically surveyed for fungal associates, including pathogens (Alomran et al., 2013). Fungal associates (including a species of Alternaria new to science) of cool-season forage grasses and other western region crops were described phylogenetically and morphologically (Lawrence et al., 2014). NPGS and WRPIS accessions (including the GRIN web address) were discussed in popular literature on medicinal (Dugan, 2015a) or regional (Dugan, 2015b) plant taxa of interest to ethnobotanists or ecologists, respectively.
For pre-breeding for germplasm enhancement, this project has recently developed and released useful materials for our stakeholders and researchers. The winter hardy trait of the previously released safflower germplasm lines (Johnson and Li, 2008) is being incorporated into new varieties with high oil content and high oleic acid by a California-based small oil seed company. Aphanomyces root rot in peas is a major constraint limiting pea production worldwide and can cause yield losses up to 100%. The cool season food legume curator in this project led an international effort for development of pea germplasm lines with partial resistance to aphanomyces root rot and recently released eight such lines (McGee et al., 2012). These released lines were requested by researchers and breeders in Idaho and Washington states as well as in several other countries. The ARS pea breeder at Pullman is using these lines as donor parents in developing aphanomyces root rot resistant varieties (R. McGee, per comm). Faba bean is cultivated worldwide as a pulse, feed, vegetable or cover crop and has good potential in the Western Region. The faba bean germplasm research and enhancement project recently released four winter hardy lines that could survive the harsh winter season in the Palouse (Landry et al., 2015). These lines have been requested by researchers in California, Oregon, Washington, New Mexico and other states. According to a News Release from Washington State Department of Agriculture (http://agr.wa.gov/News/2015/15-29.aspx), the Washington Dry Pea and Lentil Commission is proposing to change its name to Washington Pulse Crops Commission and to add dried faba beans and lupine as commodities covered by a state marketing order for pulse crops.
Conserve and regenerate common bean, pea, chickpea, lentil, alfalfa, lettuce, sugar beet, safflower, turf and forage grasses, native rangeland plants and other specialty and industrial crop genetic resources, and distribute germplasm samples and associated information to support research, education and extension purposes.
Comments: States participating: WA, ID, CA, OR
Refine and establish regeneration protocols for efficiently and effectively regenerating diverse germplasm accessions, monitor pathogenic fungi and viruses, use best management practice and ensure the health and the integrity of the germplasm collection.
Comments: States participating: WA,ID, CA, OR
Evaluate priority crop core subsets with established descriptors and key agronomic or horticultural traits; assess the value for use in research and production, and enhance environmental resiliency and nutritional traits of selected crops.
Comments: States participating: WA, ID, CA, OR
Apply available molecular tools and techniques to assess genetic diversity, identify taxa that were difficult to classify with morphological characteristics, and associate DNA polymorphism with variations of important economical traits in selected crops.
Comments: States participating: WA, ID, CA, OR
Expand the genetic diversity in the WRPIS collection and improve strategically associated information for common bean, pea, chickpea, lentil, alfalfa, lettuce, sugar beet, safflower, turf and forage grasses, native rangeland plants and other specialty and industrial crop genetic resources.
Comments: States participating: WA, ID, CA, OR
Document the usage of plant genetic resources in the western 13 states, interact with user communities, and follow through with suggestions and recommendations to improve the operation of WRPIS in management and utilization of plant genetic resources and associated information.
Comments: States participating: WA, MT, OR, NM, CA, CO, ID, UT, ARS/WA
The US Department of Agriculture, ARS provides approximately 86% of the WRPIS’ annual budget including salaries of federal employees at the station, general operations, and certain facilities and equipment. The remaining 14% of the WRPIS’ budget is covered by the W6 funds supporting six full-time employees working on the farms, in the greenhouses and laboratories, which are critical to the operation of the project. In addition, Washington State University contributes substantial in-kind support of farm land, greenhouse, laboratory, and office spaces to the project. Eight scientists (five curators and three research scientists) and 21 supporting staff members are working diligently and collaboratively towards accomplishing the mission of this multi-state project at the WRPIS. The WRPIS germplasm collection of approximately 97,000 accessions is divided into crop groups and assigned to five individual curators with respective responsibilities. The research scientists conduct mission-related research in agronomy, plant pathology and genetics to help the curators effectively and efficiently manage the assigned genetic resources.
1. Our priority is to conserve our germplasm collections in proper storage conditions and keep them accessible to researchers and breeders worldwide. Our active plant genetic resources collections are maintained in the seed storage facility on the WSU Pullman campus. The storage conditions are set at 4 °C for temperature and 28% for relative humidity. These conditions are not for long-term preservation of the seed samples but allowing people to go in and out of storage when filling orders. The original samples and multiple samples waiting for regeneration are stored at -18 C separate from the distribution samples. Regeneration and seed increase are critical to ensure viability, availability and backup samples. Original collections arriving at genebanks normally have low seed quantity and must be regenerated or increased before they can be made available for research. As seed viability or supply declines, periodic regeneration and seed increase are also required (Clark et al., 1997; Jarret, 2006). Particular emphasis will be placed on regeneration of accessions that have never been regenerated, those with low germination, those with few seeds, and those that have not yet been duplicated at a back-up site. Each winter we will generate a priority list of accessions to be regenerated by querying updated inventory data in the GRIN database. The National Center for Genetic Resources Preservation (NCGRP) at Ft. Collins, CO is our central back-up facility. Currently, where approximately 71% of the entire collection is backed-up, nearly 100% of the accessions assigned PI numbers are backed up. In addition, we have shipped 11,524 accessions and will continue to ship samples to the Svalbard Global Seed Vault in Norway for long-term back-up. Our five-year goal is to back-up at least 75% of the WRPIS collection at an alternative NPGS site.
The goal of NPGS germplasm distribution is to provide the genetic materials needed to support research and education for enhancing US and world agricultural productivity and ensuring an abundant, high-quality, safe supply of food, fiber, feed, industrial products, and other economically important commodities. Following the NPGS Distribution Guidelines approved by the Plant Germplasm Operations Committee in 2013, this project distributes germplasm free-of-charge and without restrictions for research, breeding, and education. The germplasm requests come in various ways: 1) completed request forms on the GRIN web page for REQUEST GERMPLASM, 2) an email from the requestor to the maintenance site or to: orders@ars-GRIN-Global.gov, and 3) phone, fax, e-mail, or regular mail from requestors directly to the curator with specific responsibility for the crop. We routinely fill and ship samples by regular US mail within 7-10 working days for all regular requests. Requestors can provide a courier account number for an expedited shipment of germplasm.
2. Regeneration protocols vary greatly from species to species. We will follow our established practical procedures to regenerate germplasm accessions and take every necessary measure to safeguard against physical and genetic mixing of accessions, natural/artificial selection, genetic drift, and genetic shift (Frankel et al. 1995, FAO, 2014). In most cases, seeds will be planted in the greenhouse in March–April to ensure germination and the seedlings will be transplanted to the field in April–May. For highly heterogenic and wind pollinated cool season grass accessions, we use an isolation distance of at least 50 m to limit unintended outcrossing (Johnson et al., 1998). Some accessions in the Horticultural Crops Program are regenerated in four established nurseries which are spatially isolated; only one accession per species will be grown per nursery, unless self-pollination with no out-crossing is documented for that species such as Scorpiurus (Heyn and Raviv, 1966). For wind pollinated, out-crossing cultivated and wild beet accessions, we will regenerate them in isolation (one accession per greenhouse room or if grown in the field, they will be isolated in pollen proof cages or by distance). At the recommendation of the CGC, all Phaseolus accessions are regenerated in greenhouses to prevent infection by Bean Common Mosaic Virus (BCMV), a seed-borne, aphid-vectored potyvirus. Day-length neutral accessions are increased during the long-day season and day-length sensitive accessions are grown during the short-day season. The greenhouses are provided with supplemental lighting to improve the quality and quantity of seed harvested.
Insect pollinated food and forage legumes and wild onions will be regenerated in the field under insect-proof cages to maintain the genetic integrity of the accessions. To maximize space use efficiency, we regenerate four food legume accessions; each is a different species (these species will not inter-cross) in one cage. Pollinators such as honey bees, leaf cutter bees, and blue bottle flies will be provided to increase seed set of the plants in the enclosure. Safflower is generally self-pollinating, but insect activity may promote outcrossing if plants are not caged (Li and Mündel, 1996). Accessions being regenerated in the field will be caged with fiberglass screen immediately prior to flowering to exclude insects. We recently started to cage alternate rows (due to limited cage supply) in our lettuce regeneration plots to reduce the possibility of cross pollination by insects since a low percentage of outcrossing has been reported for lettuce (Lebeda et al., 2007) and we had observed and rogued off-type plants in our recent lettuce evaluation nurseries.
Effective population size (Ne) is the key parameter for predicting genetic drift associated with germplasm regeneration. Research at the WRPIS has indicated that along with a large plant population, obtaining a proportional sample (that is, an equal number of inflorescences per plant from regeneration plots), is a practical way to maintain Ne (Johnson et al., 2004). We will continue this approach in regenerating all grass accessions. The target population size is 100 plants for each accession. Accessions will be harvested by hand, usually by cutting with a rice harvesting knife. We will harvest a proportional sample for a regeneration sample, and in addition, harvest a separate bulk sample for distribution. This is a practical method of maintaining genetic diversity while making a large number of accessions available to stakeholders (Bradley, 2010). The target population sizes for heterogeneous (outcrossing or partially outcrossing) and homogeneous (self-pollinating or inbreeding) accessions are 100 and 30 plants, respectively. After cleaning, seeds of newly regenerated accessions will be added to our active collection for distribution and selected quality seed samples will be sent to NCGRP at Fort Collins, CO for security back-up if needed.
Disease agents will be monitored in the WRPIS collection (including alternative weedy hosts) by the unit pathologist inspecting crops in the field and the submitted samples from WRPIS curators and other staff. Some accessions of food legumes and lettuce carry seed-borne, aphid-vectored potyvirus. Unless labeled as virus free, accessions being regenerated will be tested for these viruses with ELISA (enzyme-linked immunosorbent assay) at the seedling stage prior to being transplanted to the field/greenhouse. Additionally, we monitor local commercial fields plus botanical gardens and arboreta (which contain representatives of numerous plant families, including those of importance to WRPIS) for plant diseases. Causal agents are identified by standard methods (Dugan, 2006; Pappu et al., 2008) for fungi, viruses and parasitic plants such as dodder. We extract DNA, then amplify and sequence phylogenetically informative regions (e.g., ITS with flanking regions, beta-tubulin, elongation factor, etc.) and via Blast searches compare these sequences with data in GenBank. We emphasize the utility of GenBank deposits originating from type material (holotype, neotype, etc., depending on availability), authentic material (not type, but determination of the specimen was by the author of the species), or representative material (neither type nor authentic, but determination of the specimen was by an authority with a pertinent publication record on the relevant taxon). Confirmation of pathogenicity for pathogens with saprophytic capability is via Koch's postulates.
3. To meet the challenge of an ever increasing demand from the user community for genetic resources and associated information, we will continue to conduct independent and collaborative characterization, evaluation and enhancement studies and generate useful phenotypic data which add value to collections. We will collect evaluation data of established descriptors from representative plants of accessions being regenerated. The descriptor list for a particular crop is developed with the input from experts working with the respective crop, especially the respective CGC members. These traits are highly heritable characters ranging from morphological, physiological or agronomical features, including agrobotanic traits such as plant height, leaf morphology, flower color, seed traits, phenology, and overwintering ability for perennials. We will also collaborate with researchers and breeders to collect data on important agronomical traits such as disease resistance, drought tolerance and nutritional composition. All data will be uploaded into our GRIN database, some will be presented at conferences or published in journals to assure their maximum use for customers and stakeholders.
Native plant species for ecosystem restoration will be selected to study their genecology in separate common gardens at diverse sites in three states, Nevada, Oregon and Washington. The basic design for each garden will be randomized complete blocks with six replications at each garden site. Plants will be established in the greenhouse and transplanted to field sites. A single plant from each collection location will be the experimental unit. Proc mixed using restricted maximum likelihood estimates in SAS will be used for data analysis in multi-location trials as outlined by Littell et al. (1996). Garden sites, accessions, and the accession by site interaction will be fixed effects and the block within site and residual error will be random. Canonical correlation (Proc Cancorr in SAS) will be used to relate significant (P<0.01) and non-redundant common garden plant traits with climate at collection locations similar to St Clair et al. (2005) and Johnson et al. (2012a). Climate data will be 30-year averages (1971-2000) derived from Climate WNA (http://www.genetics.forestry.ubc.ca/cfcg/ClimateWNA/ClimateWNA.html) using PRISM spatial models (Daly et al., 2008; http://www.ocs.orst.edu/prism) at a grid resolution of 30-arcsec (≈ 800 m).
Multilinear regression modeling, completed with the significant canonical variates (P<0.01) as the dependent variable, will be regressed on monthly temperature and precipitation variables at source locations using SAS Proc Reg. The objective will be to find models with the highest predictive value combined with the fewest number of model parameters to minimize over parameterization (Draper and Smith, 1998). Within Proc Reg the maximum R2 improvement (MAXR) option will be used to maximize predictive power and the Mallows Cp statistic (Mallows, 1973) to minimize over parameterization. The model selected will be the maximum R2 model when the Cp statistic, which initially declines with increasing variables, starts to increase (Mallows, 1973), which is the point when adding variables only marginally improves the R2 and the model. Mapping of canonical variates predicted from multilinear regression models will be completed using the grid algebra function (raster calculator) of the ArcGIS 9.3 Spatial Analyst extension (ESRI, 2008). Each environmental variable will be multiplied by its respective regression coefficient and the results summed. The mapped area will correspond to the Omernik ecoregions (Omernik, 1987) where germplasm collections were made. A mapping contour interval corresponding to the 95% confidence interval will be calculated from the regression model error term. Seed zones delineating areas of similar plant trait variation will be delimited by classifying rasters for canonical variates into high, medium, or low categories over the range of the canonical variate scores, and then overlaying the resulting rasters, similar to St Clair et al. (2005), Johnson et al. (2010), and Johnson et al. (2012a).
We will incorporate genes governing low vicine/convicine content into USDA faba bean germplasm. Two crosses were made between winter hardy lines with the low vicine/convicine line (2370) with the genotype vc-vc- (Duc et al., 1989), introduced from a collaborator in the INRA Research Station at Dijon, France. Following the published protocol (Gutierrez et al., 2006), we conducted an HPLC analysis on the seeds harvested from several F2 plants and revealed that the contents of vicine/convicine were segregating. We will use the reported DNA markers linked to the above genes (Gutierrez et al., 2006; 2007 and 2008) for marker assisted selection (MAS) procedures to expedite the process. PCR primers and the amplification conditions from the above reference will be used in the laboratory to amplify the DNA markers. Laboratory quantification of vicine/convicine content using HPLC will be performed with the standard methods to confirm the phenotype of the selected lines based on marker genotype. Homozygous breeding lines will be tested in field conditions at two locations in Washington State prior to public release.
For combining the winter hardy trait with desirable oil content and fatty acid composition, the procedures of emasculation and pollination described by Knowles (1980) were used in making the crosses of the winter-type safflower accessions (PI 651878, PI 651879, and PI 651880) released by Johnson and Li (2008) and a high oil and high oleic fatty acid cultivar, Olé (PI 537695). Seed oil content and fatty acid composition of individual F2 plants will be determined at the University of Idaho Oilseed Chemistry Service Lab. The 10 F2 populations with the highest oil content will be selected for oleic and linoleic fatty acid determinations. Those with high oleic fatty acids will be grown in the greenhouse to the F3 generation for freezing tests. After acclimation at 4°C for 3 weeks, freezing tests will be completed in a specially designed chamber (Skinner and Bellinger, 2011). Surviving plants will be advanced to the F4 generation (F2:F4) and evaluated for oil and fatty acid composition. Promising selections advanced for field testing and improved germplasm will be released and registered in the public domain.
4. Molecular characterization of accessions in any given plant germplasm collection will provide an additional and valuable tool for collection management. These data will be important in both measuring genetic diversity among accessions, as well as helping to identify duplicates within the collections. Research, and the subsequent information generated, will facilitate the identification of universal marker sets for future characterizations of new accessions added to the collections. With the advance in DNA sequencing technology, more and more sequence information is being used for germplasm characterization, particularly the use of high-through put platforms which can reveal thousands of SNP (single nucleotide polymorphism) markers. We will continue to collaborate with researchers working on respective crops and seek extramural funds to support the genotyping work. We will focus on linking SNP markers with phenotypic variation in the core collections (a subset of accessions representing the entire collection of the crop) of chickpea, lentil and alfalfa through genome-wide association studies (GWAS). The laboratory genotyping will be carried out at UC Davis or Cornell University and data analyses will be done through our established collaborators in the Main Lab Bioinformatics group at Washington State University. The detected differences in the allele and genotype frequencies between the different plant groups with contrasting phenotypes indicate that the genes or the genomic regions are involved in controlling the trait of interest. This marker-trait information will expedite the breeding process in developing new cultivars. We will upload the information and publish the research results.
5. Because of the diversity of environments and needs in the Western Region, this project will make acquisition of new plant germplasm an ongoing process to satisfy the needs of plant breeders and other researchers. Due to the limitation of fiscal and physical resources, acquisition is not the highest priority. However, we will endeavor to strategically expand our collection and fill the gaps identified by researchers and the CGCs. Emphasis is on the species that offer critically needed traits to support current and future breeding and research. New germplasm is obtained through exchanges with foreign national programs, international centers and donation from general public including university researchers and the W6 participating state representatives. The curators are responsible for obtaining new accessions and, with every effort made to obtain complete passport data of new accessions, entering them into GRIN. We will continue to seek funds from the ARS Plant Exchange Office, to acquire cultivated and wild relative species from the limited foreign countries and areas accessible to fill gaps in our collection, emphasizing traits of biotic and abiotic stress resistances.
6. It is important to document the germplasm distribution and the use of the distributed materials. For each germplasm request we assign an order number and record the contact information of the requestor including name, affiliation, address, phone number and email address and the general purpose of the requested germplasm. All the information is entered into our GRIN database, which tracks progress from the time a request for germplasm is received until the germplasm is distributed. We also request feedback from germplasm recipients to improve our service and to meet the needs of germplasm users in the scientific community. In January, our database manager will generate a list of germplasm requestors residing in each of the 13 Western states and transmit to the respective state representatives, who will contact each germplasm recipient via email to solicit information regarding the NPGS service and germplasm usage. Some germplasm recipients provide answers to the questions on the condition of the requested material on arrival, the germination, the growth and development and other observations; the usefulness of the material, how the material was used (e.g. evaluation for adaptation, or used as donor parent in breeding or future plan to use) and the outcome derived from the material including news items and publications. Upon receiving the information the state representative will compile a summary report for the state. The highlights of NPGS germplasm usage will be shared at the annual Reginal Technical Advisory Committee (RTAC) meeting. A written report is submitted by individual state representatives and each NPGS germplasm projects to the RTAC and discussed at the meeting. The participants of the meeting include the Administrative Advisor of this project, the ARS National Program Leader, the ARS Pacific West Area Associate Area Director, the Research Leader/Station Coordinator and representative staff members of this project and from other NPGS germplasm management projects in the Western Region. The RTAC assesses the service and research, analyzes customer needs and makes recommendations to administrators as well as to the station.
Measurement of Progress and Results
- 1. The most important output of this project is the continued provision of quality genetic resources and information on common beans, cool season food legumes, forage grasses, oilseeds, vegetables, beets, ornamentals, medicinal crops, temperate forage legumes and related wild species to researchers in the Western Region, in the U.S. and around the world. The utilization of this germplasm in basic research will result in the advancement of plant sciences by documenting genetic variation, elucidating the mechanism of plant-environment interaction, and associating DNA sequence information with phenotypic variation. Breeders in applied research will incorporate novel genes into locally-adapted cultivars with enhanced pest resistance, improved end-user quality and increased productivity in variable environments.
- 2. The genetic variation within an accession will be maintained with the established and refined regeneration protocols based on research and information on pollination biology and population genetics of the respective species. Maximizing effective population size during regeneration of heterogenetic species and accessions is critical. This may also be applied to germplasm collecting to promote representative field sampling.
- 3. More phenotypic data associated with priority accessions will be available to U.S. and worldwide breeders and researchers who use our germplasm. The data include digital images, morphological descriptors, and important agronomical or horticultural traits such as disease and insect resistance, nutrition, general adaptation and growth habit. All the data collected will be uploaded to the GRIN database that can be accessed by the public through the Internet. Enhanced germplasm will be released for use in breeding programs.
- 4. Our molecular characterization program will generate information on molecular diversity and population structure of selected crop species and wild relatives. Application of this information to germplasm management will increase our overall efficiency and effectiveness by eliminating duplicated (redundant) accessions and monitoring allele frequencies to maintain genetic integrity during regeneration. Information on DNA markers associated with economic traits will be published in peer-reviewed journals, enabling breeders to incorporate novel traits into elite lines via marker-assisted selection in their cultivar development efforts.
- 5. New critically needed accessions of priority crop species will be added to the WRPIS collection for distribution. These new accessions will fill existing gaps in our collection as revealed by morphological variation or geographical origin. The acquisition will be accomplished by collection trips and germplasm exchange between WRPIS personnel and their international collaborators.
- 6. Criteria for identification (descriptive keys, DNA sequences etc) of important taxa of seed-associated fungi and bulb-rotting fungi will be published in peer-reviewed journals, as will discovery of new diseases or new disease agents. Control measures, including assessment of resistance, will be similarly published in collaboration with plant pathologists, curators and/or breeders. Plant and microbial germplasm of benefit to breeders and pathologists will be identified, preserved and distributed to bone fide researchers.
Outcomes or Projected Impacts
- Anticipated impacts and products of the proposed research: This project will continue to supply needed plant genetic resources to breeders and researchers in the western region, in the U.S. and around the world for use in basic scientific studies and in applied plant breeding to improve disease resistance, environment resilience and end-user quality traits of agricultural plants. Accessions of priority plant genetic resources will be secured and the genetic gaps in the collections will be filled through acquisition. Germplasm will be more efficiently and effectively conserved, monitored for seed quality and health, and distributed upon request worldwide. Methods will be developed and refined for regenerating germplasm collections. Accessions of priority genetic resources will be evaluated (“phenotyped”) for key traits related to adaptation, yield components, and host-plant resistance to diseases and insects. Diseases and their etiological agents will be identified and characterized from selected crops and native plants, and/or indigenous or endemic regional plants hosting diseases of WRPIS crops. Management of diseases will be enhanced with increase in germplasm quality. Genotypic and phenotypic (evaluation) datasets for key genetic, agronomic, and/or horticultural traits will be incorporated into GRIN and/or other databases, thereby expanding worldwide access to critical data.
• Regenerate 1,800-2,000 priority germplasm accessions including 450-500 cool season food legumes, 350-400 beans , 300-350 grasses, 100-120 safflowers, 350-360 horticultural crops (250 Alliums, 40 ornamentals and 20 Beta), and 250-300 temperate forage legumes. Obj 1
• Collect descriptor data and images on 500 regenerated accessions for uploading into the GRIN-Global database. Obj 1 and Obj 3
• Organize W6 Technical Advisory Committee annual meeting in June to review the status of the plant genetic resources collection and assess the impact of the germplasm usage in the Western Region. Obj 6
• Assay selected Allium sativum accessions for pathogenic fusaria. Obj 2
• Complete research and submit for publication on taxonomy and host range of Penicillium spp. causing blue mold of bulb crops. Obj 2
• Screening for drought tolerant alfalfa plants in 200 NPGS accessions. Obj 3
• Collect wild kidney bean throughout Southern Ohio. Obj 5
• Determine appropriate vernalization period to produce heads in Miscanthus sacchariflorus in the Greenhouse. Obj 2
• Evaluate the Patellifolia (a relative of Beta) collection for morphologic and phenologic characteristics and determine ploidy. Obj 3
• Release a selection of Eragrostis tef for ornamental use. Obj 3
• Submit a manuscript on fusaria in Allium sativum. Obj 2
• Assay samples of Vicia faba from eastern and western Washington State for pathogenic fungi, conduct Koch's postulates and submit for publication. Obj 2
• Assay samples of Camassia quamash from eastern Washington State for pathogenic fungi and conduct Koch's postulates. Obj 2
• Release winter safflower germplasm with enhanced oil characteristics and content. Obj 3
• Phenotype chickpea core collection for seed quality (protein, starch, oil, fatty acids) traits. Obj 3
• Evaluate 100 bean accessions for nutrient traits (Protein, polyphenols, total anti-oxidant activity, phytate, and fiber) Obj 3
• Mapping genes associated with resistance to Verticillium wilt in alfalfa. Obj 4
• With cooperators, genotype the chickpea kabuli core collection using SNP markers. Obj 4
• Add the ICRISAT sequenced Chickpea Reference set to the W6 collection. Obj 5
• With cooperators, characterize with molecular markers the Patellifolia collection. Obj 4
• Submit for publication results of research on pathogenic fungi in Camassia quamash. Obj 2
• Release Sandberg bluegrass and basin wildrye populations for restoration based on adaptive seed zones. Obj 3
• Screen alfalfa progeny for drought tolerance in the field and greenhouse. Obj 3
• Phenotype faba bean collection for seed quality traits (protein, starch, oil, polyphenolds). Obj 3
• Identify markers closely linked to the drought resistance gene loci in alfalfa. Obj 4
• With cooperators, genotype the lentil core collection using SNP markers. Obj 4
• Complete genome-wide association study on the chickpea kabuli core to associate SNP markers with seed quality traits (protein, starch, oil, fatty acids). Obj 4
• Report on nutrient traits of selected beans at an international meeting or publish in a journal. Obj 4
• Test bean inoculation with Rhizobium for more healthy plants and greater yield during regeneration in the greenhouse. Obj 2
• Release two winter-hardy vegetable-type faba bean breeding lines. Obj 3
• Phenotype pea collection for seed quality traits (protein, starch). Obj 3
• Validate markers associated with drought and Verticillium wilt resistance in different populations of alfalfa. Obj 4
• Genotype 100 faba bean accessions using SNP markers Obj 4
• Conduct genome-wide association study on the lentil core to associate SNP markers with seed quality traits (protein, starch, folate). Obj 4
• Submit a proposal to collect Allium tricoccum Aiton, ramps, from the central to western extent of the species range for addition to the wild Allium collection. Obj 5
• Release new low vincine/convicine faba bean germplasm line. Obj 3
• Advance breeding circles and carry out drought tolerant alfalfa variety tests. Obj 3
• Phenotype lentil core collection for seed quality traits (protein, starch). Obj 3
• With cooperators, release bean germplasm lines with enhanced nutritive traits. Obj 3
• Develop strategies for marker-assisted selection of alfalfa with improved resistance to Verticillium wilt and drought/salt stresses. Obj 4
• With cooperators, genotype the chickpea desi core collection using SNP markers. Obj 4
• Complete genome-wide association study on the pea core to associate SNP markers with seed quality traits (protein, starch). Obj 4
Projected ParticipationView Appendix E: Participation
W006 participants use all available opportunities for outreach by introducing plant genetic resource issues and accomplishments to the public, including students at all levels (primary, secondary, and college), and participants of local, regional, national and international meeting and conferences. Information, development and research results are presented as oral presentations, posters and written publications targeted for scientific, industrial, and popular audiences, documenting and thus promoting understanding of the service, research achievements, and impact of NPGS. WRPIS is located on the Pullman campus of Washington State University and has a strong academic association and a close collaborative relationship with WSU. WRPIS staff frequently provide tours and lectures for WSU students and visitors from other U.S. and international institutions. WRPIS scientists also advise graduate students, offer internships and participate in collaborative research partnerships. Due to the labor-intensive nature of its operation, WRPIS hires up to 40 needed, short-term (from two weeks to three months), seasonal workers (mostly WSU students) to help in the lab, in the greenhouse and on the farm.
We will continue to update the Germplasm Resource Information Network (GRIN) database on germplasm accessions maintained in WRPIS. GRIN is the NPGS’ public database that can be accessed from anywhere in the world via the Internet. In addition, our scientists/curators will transfer information and research results to the user community by publishing papers in peer-reviewed publications, presenting poster and oral presentations at professional conferences and commodity meetings. These publications and presentations lead to personal interaction with scientists from around the world, and subsequent additional germplasm utilization occurs.
The recommended Standard Governance for multi-state research activities includes the election of a Chair, a Chair-elect, and a Secretary for the Technical Advisory Committee (TAC). The TAC comprises state representatives from the western 13 states and meets annually to assess service and research progress, analyze customer needs and make recommendations to the station. Currently, Dr. Joe Kuhl of the University of Idaho serves as the Chair, Dr. Carol Miles of Washington State University the Chair-elect, and Dr. Jack Martin of Montana State University the Secretary of the W6 TAC. Dr. Shawn Mehlenbacher of Oregon State University was the past Chair. All officers are to be elected for a two-year term to provide continuity. Administrative guidance will be provided by an assigned Administrative Advisor (Dr. James Moyer of WSU) and a NIFA Representative (Dr. AnnMarie Thro). Over the next five years we will use internal benchmarks and accountability systems to assess progress and determine future needs. In addition to the input from the W6 Technical Advisory Committee, we will use the ARS National Program 301 review process, input from the CGCs, germplasm recipient feedback, and suggestions from external review, as appropriate.
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