2012 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.
Progress was made on all four objectives and their subobjectives, all of which fall under National Program 301, Plant Genetic Resources, Genomics, and Genetics Improvement. Progress on this project focuses on Problem Statement 1A: Efficiently and Effectively Manage Plant and Microbial Genetic Resources. Plant genetic resources are critical to ensure continued genetic improvement of crop productivity. During FY 2012, Western Region Plant Introduction Station (WRPIS) scientists and curators successfully acquired 3,103 new accessions to add to the collection. As of August 6, 2012, the WRPIS collection included 92,077 accessions belonging to 4,217 species (4,720 taxa) in 955 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 30,033 seed packets were distributed to 928 requesters in 45 countries and 50 US States. We regenerated/harvested 3,750 inventories of a broad range of plant species. The seeds were packed and stored and the quantity by weight was determined for 4,737 inventories. We shipped 2,246 seed inventories to the National Center for Genetic Resources Preservation, Fort Collins, Colorado, and 421 inventories to the Svalbard Global Seed Vault in Norway for secured backup.
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 35,499 observation data points for 161 descriptors in 19 crop species from 9,393 accessions. Eighty-eight percent of the data were collected by WRPIS staff and 12% by collaborators.
In FY 2012, ARS scientists demonstrated that fall planted winter-type safflower has the potential to substantially increase seed production compared to spring-types. The result of seven year-location combinations indicated 66% or more yield increase when the winter adapted safflower was fall planted. A map was developed and of 12 seed zones of Indian ricegrass based on phenology, production, and morphology traits measured over two years. This map is recommended to guide and broaden germplasm collection and utilization for Indian ricegrass restoration in the southwestern US. ARS scientists in collaboration with a laboratory at University of Arizona, identified new species and clarified some phylogenetic relationships of pathogenic fungi using DNA sequence information and morpho-cultural characteristics. An ARS scientist in collaboration with University of California at Davis, genotyped the cultivated lettuce germplasm collection with a high-throughput assay targeting 384 SNP (single nucleotide polymorphism) markers. The result will help the, WRPIS to eliminate redundancy in the US lettuce collection and save resources for storage, regeneration and data management in the future.
Updated characterization data of U.S. teff germplasm to help stakeholders select desirable material for their breeding program. Teff grain is in demand by Ethiopian immigrants in the United States and other countries and is of interest for people with Celiac disease. Teff straw is also valued for high-quality hay. The Western Region Plant Introduction Station (WRPIS) scientist collected and uploaded characterization data for 12 descriptors on 368 Eragrostis teff accessions to the GRIN (Germplasm Resources Information Network) database. This was the first large scale field evaluation on this species. This information for the U.S. teff collection, the only source of freely distributed Teff seed in the world, will help U.S. and global stakeholders select materials for their teff improvement programs.
DNA marker-trait association information in pea. To help nutritional enhancement in pea, ARS Western Region Plant Introduction Station (WPRIS) scientists in Pullman, WA, collaborated with scientists at the ARS, Children Nutrition Research Center in Houston, TX, and universities, analyzed the genetic diversity, population structure and genome-wide marker-trait association emphasizing seed nutrients of the USDA pea core collection. Three statistical procedures revealed 28 significant marker-trait associations for eight of the seed mineral nutrient concentrations, including Ca, Cu, K, Mo, Ni and P. This information is useful to breeders for implementing marker-assisted selection to expedite the process of breeding pea cultivars with improved mineral nutrients including calcium, copper, potassium, molybdenum, nickel and phosphorus.
Newly collected wild beet accessions widen the genetic variation of the US Beta germplasm collection. Wild sea beet is used as a pot herb, medicinal and as a donor of drought and salt tolerance in sugar beet breeding. Morocco is rich in Beta genetic resources which are not represented in the world genebanks. ARS researchers from Pullman, WA, and Fort Collins, CO, in collaboration with two Moroccan scientists made collections of 43 wild beet populations in the north of Morocco to add to the USDA National Plant Germplasm System and the Moroccan genebank Beta collections. The collected material filled some gaps of the US wild beet germplasm collection. This material will be made available to sugar beet breeders and researchers worldwide to explore the potential disease resistance and drought and salt tolerance of the accessions.
Genotyping of cultivated lettuce germplasm improves management efficiency. Lettuce is grown commercially as a vegetable worldwide. ARS researchers at Pullman, WA, in collaboration with University California Davis, genotyped the cultivated lettuce germplasm collection with a high-throughput assay targeting 384 SNP (single nucleotide polymorphism) markers. The data revealed that there are approximately 70 accessions present more than once; one butterhead cultivar was collected several times from different countries and at different time periods. The results will help ARS to eliminate redundancy in the US lettuce collection, saving resources for storage, regeneration and data management in the future.
Winter-type safflower yield advantage demonstrated. Safflower is a minor yet widely grown oil seed crop adapted to semi-arid regions. In regions where the winter-type safflower can be planted in the fall, this product developed by the Western Region Plant Introduction Station (WRPIS) will facilitate increased seed production. The combined results from the seven year-location trials showed that fall planted winter-type safflower yielded 66% more than spring planted safflower. Expanding the acreage of fall planted winter-type safflower has the potential to substantially increase safflower seed production.
Kwon, S.J., Truco, M., Hu, J. 2012. LSGermOPA, a custom OPA of 384 EST-derived SNPs for high-throughput lettuce (Lactuca sativa L.) germplasm fingerprinting. Molecular Breeding. Volume 29, Issue 4, Page 887-901.
Decarie, J., Coyne, C.J., Brumett, S., Shultz, J. 2011. Additional pea EST-SSR markers for comparative mapping in pea (Pisum sativum L.). Plant Breeding. DOI: 10,1111/j.1439-0523.2011.01917.x.
Hellier, B.C. 2011. Collecting in Central Asia and the Caucasus: US National Plant Germplasm System Plant Explorations. HortScience. Vol 46(11) p. 1438-1439.
Mcphee, K., Inglis, D., Gundersen, B., Coyne, C.J. 2012. Mapping QTL for Fusarium wilt Race 2 partial resistance in pea (Pisum sativum L.). Plant Breeding. pgs 1-7. doi:10.1111/j.1439-0523.2011.01938.x.
Dugan, F.M. 2012. Yippie Yi Yo Mycota Ki Yay! A mycologist’s fervently biased account of how the American western frontier was molded by spores and mycelium. Fungi. 5(1): 6-19. http://www.fungimag.com/.
Dugan, F.M., Nazaire, M. 2011. First Report of Rust of Sidalcea malviflora (Dwarf Checkerbloom)Caused by Puccinia sherardiana in Washington State. North American Fungi 6(15):1-5.
Iqbal, M.J., Mamidi, S., Ahsan, R., Kianian, S.F., Coyne, C.J., Hamama, A.A., Narina, S.S., Bhardwaj, H.L. 2012. Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping. Theoretical and Applied Genetics. DOI 10.1007/s00122-012-1850-6.
Dugan, F.M. 2012. First report of Erysiphe knautiae (Erysiphales) on Lomelosia caucasica (Caucasian pincushion flower) in North America. Plant Health Progress. Online doi:10.1094/PHP-2012-0227-01-BR.
Smykal, P., Aubert, G., Bustin, J., Coyne, C.J., Ellis, N., Flavell, A., Ford, R., Hybl, M., Macas, J., Mcphee, K., Redden, R., Rubiales, D., Weller, J., Warkentin, T. 2012. Pea (Pisum sativum L.) in the genomics era. Agronomy. 2(2), 74-115.
Kwon, S.J., Brown, A.F., Hu, J., Mcgee, R.J., Watt, C., Kisha, T.J., Timmerman-Vaughan, G., Grusak, M.A., Mcphee, K., Coyne, C.J. 2012. Genetic diversity, population structure and genome-wide marker-trait association analysis of the USDA pea (Pisum sativum L.) core collection. Genes and Genomics. 10.1007/s13258-011-0213-z.