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Research Project: Management of Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing Research

2014 Annual Report

Objective 1: Conserve, acquire, regenerate, back-up, and distribute genetic resources and associated information for cool season food and forage legumes, grasses, common beans, oilseeds, vegetables, beets, ornamentals, medicinal crops and related wild species. Objective 2: Conduct genetic characterizations and phenotypic evaluations of genetic resources of the preceding crops and related wild species for priority genetic and agronomic traits. Apply the preceding knowledge to genetic resource acquisition, management, and marker-trait association studies of selected taxa. Sub-objective 2A: Apply existing and newly developed DNA genetic marker technology to phylogenetic and genetic diversity analyses of priority crops, emphasizing core subsets of Phaseolus, Beta, Allium, Carthamus, Pisum, Vicia, Cicer, Lens, and temperate grass species. Incorporate characterization data into the Germplasm Resources Information Network (GRIN-Global) and/or other databases. Sub-objective 2B: Update and apply phenotypic descriptors for Allium, Beta, Lactuca, Pisum, Cicer, Phaseolus, Carthamus, and priority native and other cool season grasses. Incorporate phenotypic data into GRIN Global and/or other databases. Sub-objective 2C.1: Assess genetic (molecular) and phenotypic variation of reed canarygrass (Phalaris arundinacea, L.) and apply that information to curating the collection. Sub-objective 2C.2: Genecology of bottlebrush squirreltail, Thurber's needlegrass, and basin wildrye. Sub-objective 2D: Develop mapping populations and genomic resources of Pisum, Lens, Cicer and Vicia, for developing markers suitable for marker assisted selection of those crops. Objective 3: Identify pathogens causing emerging diseases associated with the preceding genetic resources, investigate interactions among these plant taxa and the pathogens, and devise and apply pathogen management strategies. Objective 4: Conduct initial pre-breeding programs for underutilized agronomic traits, and release genetically-enhanced populations for selected crops. Sub-objective 4A: Pre-breeding Safflower for improved oil concentration and high oleic fatty acids in winter safflower. Sub-objective 4B: Incorporate genes for improved nutritional content into faba bean pre-breeding populations.

Regenerate, conserve, and distribute more than 92,000 accessions of cool season food and forage legumes, grasses, common beans, oilseeds, vegetables, beets, ornamentals, medicinal crops and related wild species, and associated information by following the established protocols and procedures. Ship high quality seed samples to National Center for Germplasm Resources Preservation at Ft. Collins, CO and the Svalbard Global Seed Vault in Norway for long-term security back-up. Conduct collaborative plant expedition and collection trips to acquire samples to fill gaps in NPGS collections, and to meet stakeholder needs. Apply existing and newly developed genomic tools and technologies to characterize phylogenetic relationship and genetic diversity of priority crop collections. Evaluate the phenotypic variation of economic traits of specialty crops independently or collaboratively. Upload characterization/evaluation data into the Germplasm Resources Information Network (GRIN-Global) and/or other databases. Survey production fields, identify pathogens causing emerging diseases with morphological-cultural and molecular techniques, investigate interactions among these host plants and their pathogens, and devise and apply pathogen management strategies to maintain the health of the assigned genetic resources. Use both classical plant breeding methods and modern marker-assisted selection (MAS) to enhance the nutritional attributes and the resiliency to abiotic stress of safflower and faba bean. Publish research results and release improved germplasm to the user community.

Progress Report
During FY 2014, progress was made on all four objectives and their sub-objectives, 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. Plant Germplasm Introduction and Testing Research Unit (PGITR) scientists and curators successfully acquired 1,556 new accessions, and most of them are native plant materials from the Save Our Seeds (SOS) project and added to our collection. As of August 6, 2014, the Western Regional Plant Introduction Station (WRPIS) collection included 94,642 accessions belonging to 1,308 genera, 4,802 species, and 5,397 taxa. The global plant research community depends on National Plant Germplasm System (NPGS) genetic resources for both applied and basic research. Last year, a total of 38,022 packets of high quality seed samples were distributed to 1,220 requesters in 43 countries and 50 states in the U.S. This is the record high number of distributed sample packets by WRPIS in one year. We regenerated/harvested 1,280 inventories of a broad range of plant species. The seeds were packed and stored, and the quantity by weight was determined for 3,575 inventories. We continued the evaluation and characterization of priority crop germplasm over the past year. Our curators uploaded to the Germplasm Resources Information Network (GRIN) database a total of 25,969 observation data points on 12,618 accessions on 106 descriptors of 20 different crop species. We shipped 2,174 seed inventories to the National Center for Genetic Resources Preservation, Fort Collins, Colorado and 2,875 inventories to the Svalbard Global Seed Vault in Norway for secured backup. In FY 2014, the Research Agronomist completed an extensive common garden study in many locations of diverse climate environment and developed the restoration seed zones for another important native plant species, Sandberg bluegrass, based on expressed adaptive traits. The Research Plant Pathologist identified two species and characterized host range for several fungal causal agents of blue mold of edible and ornamental bulb crops in the Northwest. Results to date indicate greater taxonomic complexity and importance for these agents, all in the fungal genus Penicillium, than prior research had indicated, and so we are expanding our research accordingly. He also mapped the regional temporal and spatial distribution of the fungus causing white rot of onion and garlic in the Pacific Northwest and worldwide, and is closely monitoring its further expansion locally and regionally. The Research Geneticist, in collaboration with researchers at Washington State University, completed a two-year study quantifying the variation of L-DOPA (L-3,4-dihydroxy phenylalanine), the major ingredient of several prescription drugs used to treat Parkinson’s disease, in the leaf and flower tissues of several faba bean lines. The faba bean lines with high L-DOPA concentration in the leaves and flowers have potential to be developed as a functional food crop for patients with Parkinson’s disease.

1. Faba bean has potential to be developed into a functional food crop. Faba bean is one of the few plant species that can produce the medicinally important molecule, L-DOPA (L-3,4-dihydroxy phenylalanine), the major ingredient of several prescription drugs used to treat Parkinson’s disease. ARS scientists in Pullman Washington, in collaboration with researchers at Washington State University, revealed a high level of variation in L-DOPA concentration for leaf and flower tissues among six faba bean lines with common and rare flower colors in two consecutive years. The crimson flowered line had the highest L-DOPA concentration and the brown flowered line had high average L-DOPA concentrations in both flowers and leaves. Based on the results, the brown flower is the most promising genetic resource for developing faba bean as a functional food crop, as a potential natural remedy for improving the quality of life for the estimated seven to ten million patients with Parkinson’s disease worldwide.

2. Hexaploid reed canarygrass has potential in warm and dry areas as a forage crop and a bio-fuel feedstock. Reed canarygrass occurs commonly as a tetraploid and also as a much less common hexaploid. An ARS researcher in Pullman, Washington, studied the ploidy, origin, and adaptation of the species and found that ploidy showed strong interactions with growing environment. At a dryer, warmer site the hexaploids generally produced more, and at a wetter, cooler site, the tetraploids more. This result suggests that hexaploid reed canarygrass has an adaptive advantage for use as a forage crop and a potential bio-fuel feedstock in the expanding areas with warm, dry climates.

3. Seed zones for restoration developed for Sandberg bluegrass based on adaptive traits. Sandberg bluegrass is an important native plant species for restoration across the inter-mountain West. ARS researchers in Pullman, Washington, found extensive genetic diversity for plant adaptive traits among 130 collection locations across the inter-mountain West. Heat and drought stress adaptations such as earlier development, lower dry weight, and smaller, narrower leaves were found in accessions from generally warmer, dryer locations. Statistical models relating genetic variation and source climates resulted in 12 seed zones that were mapped using a Geographic Information System. Of the approximately 173 million acres mapped, four seed zones represented 92% of the area in typically semi-arid and arid regions. The link between genetic variability for Sandberg bluegrass and source climate suggested climate driven natural selection and evolution. As landscape disturbances such as fire and invasive weeds continue, these genetics-based seed zones are useful to guide successful restoration projects.

4. Resistance to stripe rust in an extensive collection of forage and range grass. Stripe rust is an important disease and causes substantial yield loss of wheat and barley in the Northwest U.S. ARS scientists in Plant Introduction and Testing Unit, Pullman, Washington, in collaboration with colleagues in the Wheat Genetics Research Unit at the same location, and Washington State University, documented degrees of resistance to stripe rust in a large collection of Basin wild rye (an important forage and range grass). Because new races of stripe rust continually appear, it is vital to have a "bank" of resistant germplasm, and even susceptible germplasms are of importance for genetic studies. All the evaluated accessions and associated data Germlines are conserved and will be available to the research community via the National Plant Germplasm System.

Review Publications
Konecná, E., Šafárová, D., Navrátil, M., Hanácek, P., Coyne, C.J., Flavell, A., Vishyakova, M., Ambrose, M., Redden, R., Smykal, P. 2014. Geographical gradient of the eIF4E alleles conferring resistance to potyviruses in pea (Pisum sp.) germplasm. PLoS One. 9(3):e90394. DOI: 10.1371/journal.pone.0090394.
Dugan, F.M. 2013. Yeasts: What's in a name? A brief reconnaissance and sampling of literature. Fungi. 6(4):45-46.
Syamaladevi, R.M., Lupien, S.L., Bhunia, K., Sablani, S.S., Dugan, F.M., Rasco, B., Killinger, K., Dhingra, A., Ross, C. 2014. UV-C light inactivation kinetics of Penicillium expansum on pear surfaces: Influence on physicochemical and sensory quality during storage. Postharvest Biology and Technology. 87:27-32.
Kumar, Y., Kwon, S.J., Coyne, C.J., Hu, J., Grusak, M.A., Kisha, T.J., Mcgee, R.J., Sarker, A. 2014. Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum l.) germplasm. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-014-0089-2.
Yang, T., Jiang, J., Burlyaeva, M., Hu, J., Coyne, C.J., Kumar, S., Redden, R., Sun, X., Wang, F., Chang, J., Hao, X., Guan, J., Zong, X. 2014. Large-scale microsatellite development in grasspea (Lathyrus sativus L.), an orphan legume of the arid areas. Biomed Central (BMC) Plant Biology. 14:65.
Johnson, R.C., Evans, M. 2014. Comparative growth and development of hexaploid and tetraploid reed canarygrass. Crop Science. 54:1062–1069.
Johnston, W.J., Johnson, R.C., Golob, C.T., Dodson, K.L., Silbernagel, D.D., Stahnke, G.K. 2014. Kentucky bluegrass (Poa pratensis L.) germplasm for non-burn seed production. p 43-48. In: Rakshit, A., editor. Technological advancement for vibrant agriculture. Athens, Greece:Atiner. p.43-48.
Dugan, F.M., Cashman, M.J., Chen, X., Johnson, R.C., Wang, M. 2014. Differential resistance to stripe rust (Puccinia striiformis) in collections of basin wild rye (Leymus cinereus). Plant Health Progress. 15:97-102.
Dugan, F.M., Lupien, S.L., Armstrong, C.M., Chastagner, G.A., Schroeder, B.K. 2014. Host ranges of North American isolates of Penicillium causing blue mold of bulb crops. Crop Protection Journal. 64:129-136.
Song, X., Deng, Z., Gong, L., Hu, J., Ma, Q. 2012. Cloning and characterization of resistance gene candidate sequences and molecular marker development in gerbera (Gerbera hybrida). Scientia Horticulturae 145:68–75.
Johnson, R.C., Petrie, S.E., Franchini, M.C., Evans, M. 2012. Yield and yield components of winter-type safflower. Crop Science. 52:2358-2364.
Gao, J., Radwan, M.M., Leon, F., Dale, O.R., Husni, A.S., Wu, Y., Lupien, S.L., Wang, X., Manly, S.P., Hill, R.A., Dugan, F.M., Cutler, H.G., Cutler, S.J. 2013. Neocosmospora sp.-derived resorcylic acid lactones with in vitro binding capacity for human opioid and cannabinoid receptors. Journal of Natural Products. 76:824-828.
Lawrence, D., Pryor, B., Dugan, F.M., Pryor, B. 2013. Characterization of Alternaria isolates from the infectoria species-group and a new taxon from Arrhenatherum, Pseudoalternaria arrhenatheria sp. nov. Mycological Progress. DOI: 10.1007/s11557-013-0910-x.
Sen Gupta, D., Thavarajah, D., Knutson, P., Thavarajah, P., Mcgee, R.J., Coyne, C.J., Kumar, S. 2013. Lentils (Lens culinaris L.), a rich source of folates. Journal of Agricultural and Food Chemistry. 61:7794-7799.