2011 Annual Report
1a.Objectives (from AD-416)
Objective 1: Strategically expand the genetic diversity in genebank collections and improve associated information for priority cool season food and forage legume, turf and forage grass, native rangeland, oilseed, vegetable, medicinal, ornamental, and other specialty and industrial crop genetic resources.
Objective 2: Conserve and regenerate priority cool season food and forage legume, turf and forage grass, native rangeland, oilseed, vegetable, medicinal, ornamental, and other specialty and industrial crop genetic resources efficiently and effectively, and distribute samples and associated information worldwide.
Objective 3: Strategically characterize (“genotype”) and evaluate (“phenotype”) crop core subsets and other priority germplasm for molecular markers, morphological descriptors, and key agronomic or horticultural traits, such as general adaptation, phenology, and growth potential.
Objective 4: Develop genetically-enhanced populations of priority crops to broaden the genetic base of breeding genepools.
Objective 5: Conserve, regenerate, and distribute germplasm of specialty crops, current or potential bioenergy crops (e.g., Brachypodium, other cool-season grasses), and new stocks generated by genome sequencing and other genomic resarch with Brachypodium, Medicago truncatula, peas, and lettuce.
1b.Approach (from AD-416)
Plan and conduct both traditional as well as new and innovative activities to
acquire, store, regenerate, evaluate/characterize, and distribute plant germplasm
assigned to this project. Also, develop new conservation and preservation protocols that enable long-term genetic security. Prepare and publish appropriate articles, peer reviewed manuscripts and Internet (Germplasm Resources Information Network) data sets for the germplasm user community. Conduct research programs on molecular characterization of selected collections; the impact/use of insects as pests, pollinators and/or biological control agents; the interaction of fungi as plant disease organisms or plant mycosymbionts; and the physiological aspects of seed production relative to seed preservation and long-term storage. Replacing 5348-21000-020-00D (3/08) renumbered from 5348-21000-021-00D (5/08). This new number will be replacing 5348-21000-025-00D (5/29/08).
Plant genetic resources are critical to ensure continued genetic improvement of crop productivity. As of August 2, 2011, the germplasm collection at the Pullman Station included 89,077 accessions belonging to 3,877 species (4,317 taxa) in 851 genera. We continued to supply the global plant research community with high quality seed samples for both applied and basic research. Last year, a total of 22,212 seed packets were distributed to 739 requesters in 46 countries. We regenerated 2,908 accessions from a broad range of plant species with diverse breeding systems. A total of 2,392 accessions were shipped to the National Center for Genetic Resources Preservation (NCGRP), Fort Collins, CO, and 4,706 to the Svalbard Global Seed Vault, Longyearbyen, Norway for security backup.
Scientists and curators successfully acquired useful germplasm through their established collaboration with scientists around the world, particularly those in the CGIAR centers like the International Center for Tropical Agriculture (CIAT) in Columbia, and through the generous donations from the public researchers in the USA. The 3,524 new accessions acquired last year included 1,353 Phaseolus from CIAT, 1,249 native plant accessions from the Bureau Land Management (BLM) Seeds of Success (SOS) project, and 174 Lupinus from Germany. An international collection trip in Morocco for wild relatives of sugarbeet, a collection in California for wild sugarbeet, and a collection in Florida for wild Phaseolus helped close gaps in current collections.
Significant progress in evaluation and characterization of priority crop germplasm continued over the past year. Our curators uploaded to the GRIN database a total of 45,092 observation data points for 168 descriptors on 9,876 accessions. Six percent of the data were contributed by our collaborators and 94% were collected by unit personnel.
In FY 2011, the Research Agronomist correlated DNA marker polymorphism with habitat climatic variables in supina bluegrass germplasm collected across the Italian Alps. Supina bluegrass has potential for expanded use as a turf grass and this work showed added genetic variation in newly acquired germplasm. The Research Plant Pathologist isolated and confirmed by DNA sequencing the identity of a white rot pathogen from a garlic sample provided by a local grower. Necessary precautions have been implemented to prevent WRPIS regeneration nurseries from becoming infected, since WRPIS maintains germplasm of garlic and wild onions. The Research Geneticist in collaboration with University of California at Davis designed and tested a custom assay of 384 SNP (single nucleotide polymorphism) markers for high-throughput genotyping of lettuce germplasm. Experiments showed that this assay is capable of revealing sufficient levels of polymorphism among lettuce cultivars and is appropriate for rapid assessment of genetic diversity and population structure of the USDA lettuce collection.
Correlation of DNA marker polymorphism and climatic variables of supina bluegrass. Supina bluegrass (Poa supina Schrad.) has potential for expanded use as a turf grass, yet progress is limited due to access by germplasm for breeding as well as a lack of understanding in genetic variation. ARS researchers at Pullman collected a set of 46 supina bluegrass accessions across the Italian Alps, characterized them with AFLP markers and analyzed the correlation between molecular variation and climatic variables from collection locations. It was found that the collections were differentiated into three broad genetic groups, and climatic variables correlated with certain dimensions of the marker data, suggesting that differences in plant phenotypes vary with climate. Accessions are now being increased at WRPIS Pullman, WA, to make collections available for continued research on supina bluegrass.
Seedborne chickpea pathogens. Clonostachys rhizophaga was reported in 2009 as causing wilt and leading to 100% mortality in chickpea in Syria. ARS researchers at Pullman, WA, demonstrated that isolates identified as C. rhizophaga based on both morphology and DNA sequence commonly inhabit chickpea debris in the Pacific Northwest (PNW), yet it was found that this does not pose a threat to PNW chickpea production. PNW isolates, when inoculated to a cultivar of chickpea susceptible to the Syrian isolates, induced only mild, incidental and/or inconsistent effects, under temperatures typical of the PNW, or under elevated temperatures more typical of Syria. Thus, PNW isolates of C. rhizophaga do not appear to warrant regulatory concern.
A custom assay for high-throughput genotyping of lettuce germplasm. Lettuce is a commericially grown vegetable worldwide. The US lettuce germplasm collection is maintained in Pullman. ARS researchers at Pullman, WA, in collaboration with University of California at Davis designed and tested a custom assay for high-throughput genotyping of lettuce germplasm. This assay contains 384 SNP (single nucleotide polymorphism) markers derived from expressed genes of lettuce. Experiments showed that this assay is capable of revealing sufficient levels of polymorphism among lettuce cultivars of different horticultural types. This assay is being used to genotype the entire USDA lettuce germplasm collection. In addition, the assay is appropriate for rapid genetic diversity, population structure assessments of genetic diversity and population structure of the USDA lettuce collection.
Consistent quantitative trait loci (QTL) for marker assisted breeding of pea cultivars resistant to Aphanomyces root rot. Breeding for resistance to Aphanomyces root rot, one of the most important pea diseases, is difficult since many QTLs are involved and each QTL confers only a low level of resistance. ARS researchers at Pullman, WA, contributed to the discovery and confirmation of the seven QTLs useful for marker assisted selection of superior lines carrying high levels of partial resistance. Since the markers flanking the QTLs have been tested in multiple parentage populations, their application to marker assisted selection will greatly reduce the time for breeding and release of agronomically superior resistant cultivars.
Collecting wild/weedy beets in the Imperial Valley, CA. The Imperial Valley in California is the major sugar beet producing region. Since the first report in 1928, wild beets have extensively infested sugar beet fields in this area. ARS researchers from Pullman, WA, and Salinas, CA, made collections of wild beet populations from 27 commercial sugarbeet fields in the Imperial Valley. The collected seeds, tissue samples, herbarium specimens and associated locality data will be essential for studying the origin of the populations, determining species relationships, and exploring whether or not there may be gene flow between these wild beets and cultivated beet.
Evaluation and characterization of the U.S. teff germplasm collection. Teff is a crop produced predominantly in Ethiopia where it is a highly valued staple. Teff seeds produce gluten-free flour with high quality, complex nutrients as well as valued as high-quality forage crop. As a result, teff flour is in demand by Ethiopian immigrants in the United States and other countries and by people with Celiac disease. Characterization of the U.S. teff germplasm collection maintained at WRPIS will benefit U.S. and global stakeholders by providing genetic resources and associated information for improvement of teff productivity and quality. ARS researchers at Pullman, WA evaluated, in replicated field nursery trials, 368 teff accessions. Data for 12 descriptors was collected on 7,340 plants, and produced over 700 digital images were produced demonstrating the large amount of variation available within our teff collection for continued breeding and development.
Isolation and identification of white rot pathogen in garlic. White rot, caused by pathogen Sclerotium cepivorum, is a devastating disease for all Allium species including onions, garlic, leeks, chives and wild onions. It destroys the roots, kills the plant and then produces resting bodies that can last for many years in the soil. White rot is on quarantine lists of the agricultural departments of several states in the US. ARS researchers at Pullman isolated white rot from a garlic sample collected in Moscow, ID and confirmed the pathogen identification by DNA sequencing. Given the infected sample was only 12 kilometers from the Pullman Station, we have implemented necessary precautions to prevent our fields from becoming infected in order for our customers/growers to receive clean germplasm of garlic and wild onions.
Johnson, R.C., Johnston, W.J., Bertoli, F.L., Golob, C. 2011. Seed yield, Development, and Variation in Diverse Poa Pratensis Accessions. Crop Science. 50:337-344.
Pecetti, L., Johnson, R.C., Romani, M., Bassignana, M., Marianna, D.G. 2010. Ecological characterisation of supina bluegrass (Poa supina Schrad.) germplasm from the Italian Alps. Grass and Forage Science. doi: 10.1111/j.1365-2494.2010.00766.x.
Dugan, F.M., Hellier, B.C., Lupien, S.L. 2011. Resistance to Penicillium allii in accessions from a National Plant Germplasm System Allium collection. Crop Protection Journal. 30: 483-488.
Hellens, R.P., Moreau, C., Wang, K., Schwinn, K., Thomson, S., Fiers, M., Frew, T.J., Murray, S.R., Hofer, J., Jacobs, J., Davies, K.M., Allan, A.C., Bendahmane, A., Coyne, C.J., Timmerman, G.M., Ellis, N.T. 2010. Identification of Mendel's white flower character. PLoS One. 5 (10).
Smykal, P., Kenicer, G., Flavell, A.J., Kosterin, O., Redden, R.J., Ford, R., Coyne, C.J., Maxted, N., Ambrose, M.J., Ellis, T.N. 2010. Phylogeny, phylogeography and genetic diversity of Pisum genus. Plant Genetic Resources. 1-15 doi:10.1017/S147926211000033X.
Kisha, T.J., Cramer, C.S. 2011. Determining redundancy of short-day onion accessions in a germplasm collection using microsatellite and targeted region amplified polymorphic markers. Journal of the American Society for Horticultural Science. 136(2):129-134.
Dugan, F.M. 2011. Three new host-fungus records for Golovinomyces species in Montana and Washington. North American Fungi. 6(3): 1-7.
Skoglund, L. G., Harveson, R. M., Chen, W., Dugan, F., Schwartz, H. F., Markell, S. G., Porter, L., Burrows, M. L., and Goswami, R. 2011. Ascochyta blight of peas. Plant Health Progress DOI: 10.1094/PHP-2011-0330-01-RS
Mallikarjuna, N., Coyne, C.J., Cho, S., Rynearson, S., Rajesh, P., Jadhav, D.R., Muehlbauer, F. 2011. Cicer. Wild Crop Relatives: Genomic and Breeding Resources. Legume Crops and Forages. Springer, New York, N.Y. pp. 63-82.