W006: Plant Genetic Resource Management, Preservation, Characterization and Utilization
Statement of Issues and JustificationPlant genetic resources (germplasm) are vital for safeguarding the future of U.S. and global agriculture. Germplasm is the raw material that underpins the maintenance and development of crops for food, feed, and fiber production. Always needed for traditional plant breeding, these resources are rapidly becoming increasingly important for biofuel production, plant biotechnology, and for the development of industrial products. The USDA-ARS, National Plant Germplasm System (NPGS) is responsible for maintaining diverse germplasm collections in the U.S. for researchers and breeders. A major NPGS germplasm repository is the Western Regional Plant Introduction Station (WRPIS) at Washington State University, Pullman, Washington, which has long been part of the W-6 Regional Research Project. This project, a cooperative endeavor between the USDA-ARS and the Western State Agricultural Experiment Stations (SAESs), provides access to a wide range of plant genetic resources for scientists and stakeholders in the U.S., with emphasis on scientists and stakeholders in the 13 western states and land-grant universities. The W-6 Project (Plant Genetic Resource Management, Preservation, Characterization and Utilization) funds one of four Plant Introduction (PI) Stations in the NPGS, and like the other three PI projects, the W-6 project focuses on germplasm acquisition, conservation, regeneration, evaluation, documentation, and distribution. The renewal of this project is critical to supplying the genetic resources needed to maintain and develop food and fiber crops important to the Western Region and the entire U.S. The project will extend the availability of native species needed for revegetation, enhance the application of molecular marker technologies in key collections such as lettuce, and support disease and pest management in threatened collections such as garlic and chickpea.
Most agricultural crops are not native to the U.S. Thus, a continued supply of new, exotic germplasm is needed for ongoing genetic improvement of crops to support U.S. agriculture. Germplasm is required to provide the necessary genetic traits for U.S. food security, agricultural profitability, and competiveness (Duncan, 1995; Qualset and Shands, 2005; Day-Rubenstein and Heisey, 2006). The WRPIS holds approximately 80,000 germplasm accessions representing diverse crop species and their wild relatives. These species can be roughly divided into ten groups: 1) forage and turf grasses, 2) cool season food legumes (pea, lentil, chickpea, fava bean, lupine, etc.), 3) forage legume crops, 4) beans, 5) lettuce, 6) safflower, 7) garlic and onion relatives, 8) sugar beet, 9) selected ornamentals, and 10) medicinal plant species. The WRPIS holdings account for 15.5% of 509,000 accessions in the NPGS, which comprises 25 seed and clonal repositories including the related Regional Research Projects (North Central [NC-7] at Ames, IA; Northeastern [NE-9] at Geneva, NY; and Southern [S-9] at Griffin, GA). Most WRPIS accessions are maintained as seed, with a small proportion (garlic and relatives and some ornamentals) vegetatively-propagated.
Scientists affiliated with western U.S. Agricultural Experiment Stations (SAESs) and land-grant universities conduct research and extension projects that involve most of the crop species at the WRPIS. For example, forage and turf grass accessions are utilized for improving pasture and turf and for restoration of public and private lands in the western U.S. Lettuce is the leading vegetable crop in the U.S. with an annual value totaling more than $2 billion in 2004, and two western states, California and Arizona, account for more than 90 percent of U.S. lettuce production. Cool season food legumes (chickpea, pea, and lentil) are major crops in North Dakota, Washington and Idaho, with additional substantial acreage in California, Montana and elsewhere. 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 forage and turf grasses throughout the Midwest and Atlantic states. The continuation of the W-6 project will ensure that needed crop genetic resources are maintained as high quality, healthy and viable plant germplasm for researchers and breeders in the western U.S. and elsewhere.
Scientists and curators at the WRPIS utilize current methods and information to accomplish the major functions of acquiring, preserving, regenerating, evaluating, documenting and distributing germplasm accessions In addition, the two CRIS projects at the WRPIS (Plant Germplasm Introduction and Testing Research Unit, Pullman, Washington; National Temperate Forage Legume Genetic Resources Unit, Prosser, Washington) provide locations for re-generating germplasm under vastly different environmental conditions to serve the needs of crop species maintained by the WRPIS. Moreover, accomplishing this work requires that WRPIS scientists and curators cooperate with faculty and extension personnel in agronomy, horticulture, plant pathology, entomology, genetics, and plant physiology at Washington State University (WSU) and other western land-grant universities. For example, the WRPIS entomologist cooperates with scientists in the Plant, Soil and Entomological Sciences at the University of Idaho in evaluating cool season food legume germplasm for insect resistance, and the WRPIS agronomist collaborates with scientists of BLM (Bureau of Land Management) and in identifying suitable genotypes of native plant species for public land revegetation in the Great Basin. The WRPIS plant pathologist cooperates with WSU and other ARS scientists on biological and chemical control of Ascochyta blight of chickpea, and on identification and taxonomy of powdery mildew species on cool season legumes. Similarly, the WRPIS agronomy curator has a long history of cooperating with stakeholders at several forage grass seed companies in Oregon and elsewhere.
Collaborative projects also exist with scientists at international centers (e.g., ICRISAT- India; Biodiversity International, Rome, Italy; Centraalbureau voor Schimmelcultures, Utrecht, Netherlands), foreign institutes (John Innes, England), foreign national programs and foreign companies (AgResearch, New Zealand). The WRPIS Cool Season Food Legumes curator, working with scientists in ICARDA has acquired 1368 pea accessions of the Vavilov Institute Pisum collection. WRPIS accession holdings have increased at a rate of approximately 2,000 per year over the past five years (Attachment Figure 1: Growth in WRPIS Germplasm Collections). These collaborative activities highlight the importance of WRPIS in promoting the acquisition and utilization of new and existing germplasm.
The plant researchers in both public and private sectors frequently request germplasm from NPGS. Over the past seven years scientists from the Western Region, requested and received a total of 266,627 packets of seed samples from NPGS, and 46,843 packets were distributed from WRPIS. Most of these requests were from scientist at SAES Universities. Each year WRPIS sent out more than 20,000 seed packets to requesters worldwide, approximately 64% went to US users and 36% went to foreign countries. This germplasm is highly utilized. For example, over a five year period, 11% of germplasm distributed internationally had already been incorporated into breeding programs. This is well above the success rate typical for most "bioprospecting" endeavors.
Seed stocks at the WRPIS that are low in viability or supply must be regenerated. Advice from Crop Germplasm Committees, stakeholders, as well as the knowledge and experience of curators guide decisions concerning the timing and methodology of regenerations for specific seed collections. For this activity, priority is given to accessions that have not been regenerated, those with few seeds and/or low seed germination, and those that have not been duplicated at a back-up site (Clark et al., 1997; Jarret, 2006). Low quantity and quality seed arriving at the WRPIS and other genebanks must be regenerated before distributions to stakeholders can occur.
The biggest challenge for a regeneration program is to maintain the genetic integrity of the original collection. The first requirement for high quality regeneration is to understand the breeding systems of diverse taxa and design appropriate protocols that safeguard against physical and genetic mixing of accessions and natural selection and genetic drift (Frankel et al., 1995). From the limited literature on specific germplasm conservation (Pincker et al., 1987, Roath 1989, Rowe 1986), some general rules can be deduced and applied. In this context, WRPIS scientists and curators have developed seed-regeneration programs to safeguard the genetic integrity of specific collections. For insect pollinated taxa, the choices for insect pollinators and controlled pollination systems are critical (Clement et al., 2006; Clement et al., 2007a, 2007d). Indeed, there is a requirement for continued research on the pollination systems of many of the 2700 taxa in WRPIS collections because these taxa exhibit a wide diversity of breeding systems in the plant kingdom. Pollen isolation, effective population size, genetic drift, and unintended selection are important considerations for self-incompatible, outcrossing, entomophilous, and wind pollinated accessions (Clement et al., 2007; Johnson et al., 1996; Johnson et al., 2004). Based on genetic and statistical analyses, Marshall and Brown (1975) proposed a theoretical population size (sample size stored in collections and for sample size distributed) that would conserve at least one copy of each allele occurring at a frequency of >0.05 at the 0.95 probability level. However, limited budgets and human resources, as well as low numbers of seeds, can lead to low numbers of plants for some accessions in regeneration nurseries. This practice could potentially result in a loss of alleles that exist at very low frequencies. Also, there are few published guidelines on the regeneration of the wild relatives of several crop species (Kaiser et al., 1997 Muehlbauer et al., 1994), and none for many of the "new crop" species. For example, Russian dandelion germplasm is needed in breeding programs to fulfill a Federal mandate to develop a domestic source of natural rubber. The WRPIS horticulture curator collected from seed and root samples from Kazakhstan in 2008. However, no information on the reproductive biology is available for this species. These 'regeneration challenges' illustrate the requirement for continuous development of new regeneration protocols for the many germplasm holdings in the WRPIS (Johnson et al., 2004).
Biotic stresses (i.e. insect and disease) that adversely affect WRPIS germplasm maintenance efforts must be controlled to ensure the production of high quality seed for distribution to stakeholders. At WRPIS, research to assess etiologies of diseases and positive or negative interactions between arthropods and host plants have been an important part of the W-6 evaluation program for many years (Clement et al., 1990, 1991, 1993, 1997, 1999, 2002, 2005, 2007, Coyne et al., 2008, Dugan 2007, Dugan and Peever 2002, Dugan and Glawe 2006, 2007, Dugan and Newcombe 2007, Dugan et al., 2003, 2005, 2007, 2008). This type of research will continue as new problems develop, exemplified by recently discovered disease infections and mite infestations involving the WRPIS garlic collection. Additionally, knowledge of the relationships between insect vectors and plant pathogens (viral, bacterial, fungal), and plant- beneficial microbe associations (e.g., Clement et al., 2008), is essential for optimal seed regeneration and preservation for accomplishing the overall mission of WRPIS. Positive (symbiotic) associations between WRPIS germplasm (chiefly grasses) and various endophytes, some of which have proven commercially valuable, are also researched and documented (Dugan et al., 2002, Tadych et al., 2007).
The advent of high throughput DNA sequencing technology has generated tremendous amount of DNA sequence information. These include the draft whole genome sequences of two model plant species (Arabidopsis and Brachypodium) and several important crop plants (rice, soybean, sorghum, poplar) and massive numbers of ESTs (expressed sequence tags) of many plant species. This important resource is potentially useful for gene discovery in germplasm since genomics analyses with bioinformatics tools revealed substantial conservation across distantly related species at the DNA sequence level. Technologies are available to assess DNA sequence variation in large numbers of plant accessions to identify different forms (alleles) of a gene. These methods are increasingly robust and speedy, generating data from tiny amounts of plant tissue at any developmental stage unaffected by environmental conditions. DNA-based markers are becoming a key part of plant germplasm management. However, as pointed out by Bretting and Widrlechner (1995), molecular markers should be considered a complement to, not a replacement of, managerial experience with plant germplasm. WRPIS has built a substantial capacity of assessing genetic diversity of germplasm collections with a large number of different molecular techniques that are presently available such as Random Amplified Polymorphic DNA or RAPD (Williams et al., 1990), Amplified Fragment Length Polymorphism or AFLP (Vos et al., 1995), Simple Sequence Repeat or SSR (Diwen et al., 1997) and Target Region Amplification Polymorphism or TRAP (Hu and Vick, 2003). Several projects have been completed in analyzing genetic diversity and relationships among the accessions maintained at WRPIS (Johnson et al., 2002, 2007), in mapping quantitative trait loci (Loridon et al., 2005), in fingerprint the core subsets of pea (Coyne et al., 2005) and in developing markers tightly linked to important economic trait such as disease resistance (Okubara et al., 2002, Coyne et al., 2008). This information will be very useful to geneticists and breeders for genetic improvement of crops.
Morphological characterization of accessions and subsequent documentation also substantially increases the value of germplasm collections. Since the information will be entered into the GRIN database that can be accessed by scientists worldwide, it is necessary to develop and utilize adequate plant character descriptors that reflect national and international standards.
Global agriculture will need to be more productive to meet the nutrition requirements of a growing world population. State-of-the-art technologies that define plant biotechnology will help meet this need. But factors such as climate change, urbanization and environmental degradation are making both genetic resources and arable land increasingly limited. The availability of conserved plant germplasm for research and breeding will be the foundation for sustaining agricultural production into the future. Therefore, the WRPIS with its 80,000 conserved accessions of major American and global crops will assume an even greater role in sustaining 21st century agriculture in the Western Region and other regions of the world.
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