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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Research Project #424494

Research Project: Management of Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing Research

2015 Annual Report


Objectives
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.


Approach
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
This progress report addresses the work conducted in 2015 by the Plant Germplasm Introduction and Testing Research Unit at Pullman, Washington. During FY 2015, satisfactory 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. Our curators and scientists successfully acquired 1,698 new accessions including 1,403 native plant accessions from the SOS (Seeds of Success) project, 43 accessions from the country Georgia and 85 accessions of Miscanthus sacchariflorus received as live plants. As of July 24, 2015, the Western Regional Plant Introduction Station (WRPIS) collection included 96,739 accessions belonging to 1,100 genera and more than 5,000 species. The global plant research community depends on National Plant Germplasm System (NPGS) genetic resources for both applied crop improvement and basic biological research. Last year, a total of 33,536 packets of high quality seed samples were distributed to 1,269 requesters in 45 countries and 50 states in the U.S. This is the second highest number of distributed sample packets by WRPIS in one year. We packed and stored 1,280 newly regenerated/harvested inventories of a broad range of plant species. We determined seed quantities of 15,043 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 65,164 observation data points on 24,816 accessions on 157 established descriptors of 18 different crop species. We shipped 3,020 seed inventories to the National Center for Genetic Resources Preservation, Fort Collins, Colorado and 451 inventories to the Svalbard Global Seed Vault in Norway for secured backup. In FY 2015, ARS scientists in Pullman, Washington, are continuing research on cool season food legumes, safflower, garlic and ornamental bulb crop diseases, native plants and ornamental grasses. This work supports small scale growers in the U.S., especially in the Pacific Northwest. An ARS Research Geneticist released four enhanced winter hardy faba bean germplasm lines for pulse and cover crop development. These lines were developed through field selection in five consecutive winter seasons and had high percentage of survival through the harsh winter conditions in the Palouse. The Research Agronomist continued to advance the native plant research by evaluating and testing new plant materials. An ARS scientist conducted a collaborative study and mapped several chromosomal regions (also called QTL for quantitative trait loci) controlling high levels of genetic resistance to Fusarium root rot. The Research Plant Pathologist identified additional species and characterized host range for several fungal causal agents of blue mold of edible and ornamental bulb crops in the Northwest. The Research Plant Pathologist also isolated and documented the pathogens of Ascochyta blight and chocolate spot from faba bean plants for the first time in Washington State.


Accomplishments
1. Winter hardy faba bean germplasm lines for pulse and cover crop development. The U.S. pulse growers showed an increased interest in faba bean for its high capacity of fixing nitrogen and high protein content in the grain. An ARS Research Geneticist in Pullman, Washington, developed and released four winter-hardy faba bean accessions for pulse and cover crop development after five consecutive seasons of overwintering selection at three farms in two locations in the Palouse. The average increase in percent survival was 54% across the four accessions and the winter hardiness of the selected accessions was comparable to European materials. These four lines are potential reservoirs of useful diversity accessible for the development of a winter annual legume cover crop in the U.S. Pacific Northwest and other regions up to USDA plant hardiness zone 6b.

2. Genetic mapping of quantitative trait loci for resistance to fusarium root rot in pea. Genetic resistance to fusarium root rot has been sought to improve pea production worldwide. An ARS researcher in Pullman, Washington, conducted a collaborative study and successfully mapped several chromosome regions quantitative trait loci (QTL) conferring high levels of genetic resistance to Fusarium root rot using a recombinant inbred line population in a Fusarium root rot field disease nursery for three years. One of the top four QTL contributed to a significant portion of the resistance, from 22.1% up to 72.2% in the three years. User-friendly, co-dominate simple sequence repeat or microsatellite markers were found flanking the four QTL, which are useful in marker-assisted breeding for Fusarium root rot resistance to expedite pea improvement.

3. Identification of new genetic resource with high level of resistance to lettuce bacterial leaf spot (BLS). In collaborating with University of Florida we conducted a genome-wide association analysis for resistance to bacterial leaf spot of lettuce with SNP (single nucleotide polymorphism) markers. PI 358001-1 was identified as almost immune to the Florida isolate of BLS. This germplasm line is from the recently formed special pure-line collection based on 322 SNP marker genotypes. Our results indicated that the resistance gene is most likely on lettuce linkage group 2 since the phenotype has significant association with a mapped SNP QGB19C20.yg-1-OP5.This information will lead to a rapid development of user-friendly markers for marker-assisted selection for this valuable trait in lettuce.

4. Identification of additional agents of blue mold of Allium species. Blue mold, caused by various Penicillium species, on garlic and other bulb crops is an important disease in bulb storage and can lead to the death of planted cloves before emergence or distribution of diseased germplasm. An ARS Research Plant Pathologist in Pullman, Washington, assessed experimentally the pathogenicity of five Penicillium species belonging to different taxonomic series on garlic and two varieties of table onion. This project is the third in a series of research addressing identification and host range of agents of blue mold on bulb crops. The results provided useful information to growers for effective disease management.

5. Documented new fungal diseases of several National Plant Germplasm System (NPGS) crops. New crop diseases pose management challenges. An ARS Research Plant Pathologist at Pullman, Washington, identified a pathogen causing a problematic and novel disease of pome fruit crops in Washington State. Research results were published jointly with a researcher at Washington State University and an ARS Research Plant Pathologist at Parlier, California. Pathogens causing Ascochyta blight and chocolate spot were isolated for the first time in Washington State from faba bean, a potential new pulse crop in the Pacific Northwest. These results will have positive impact on disease management of the crops because identification and taxonomic placement of disease agents is critical for formulation of new management strategies or adaption of existing strategies.

6. Basin wildrye seed zones to guide germplasm selection for restoration. Basin wildrye is a widely distributed native grass useful for grazing and wildlife habitat. It is the largest native grass found in the arid to semiarid intermountain West region and exists in both hexaploid and octoploid forms. Its large size makes it particularly effective for wildlife cover and as a potential bio-fuel in semiarid regions. An ARS Research Agronomist in Pullman, Washington has found widespread genetic variation in phenology, morphology and production traits in both ploidy types. A seed zone map covering 673,258 square kilometers in the intermountain West was developed based on information of adaptive traits and seed source climates. This seed zone map is useful in guiding germplasm selection for restoration projects and for in situ conservation.


Review Publications
Smýkal, P., Coyne, C.J., Ambrose, M.J., Maxted, N., Schaefer, H., Blair, M.W., Berger, J., Greene, S.L., Nelson, M.N., Besharat, N., Vymyslický, T., Toker, C., Saxena, R.K., Roorkiwal, M., Pandey, M.K., Hu, J., Li, Y.H., Wang, L.X., Guo, Y., Qiu, L.J., Redden, R.J., Varshney, R.K. 2014. Legume crops phylogeny and genetic diversity for science and breeding. Critical Reviews in Plant Sciences. 34:43-104. doi: 10.1080/07352689.2014.897904.
Coyne, C.J., Pilet-Nayel, M., McGee, R.J., Porter, L., Smykal, P., Grunwald, N.J., Inglis, D. 2015. Identification of QTL controlling high levels of partial resistance to Fusarium solani f. sp. pisi in pea. Plant Breeding. 134:446-453.
Syamaladevi, R.M., Adhikari, A., Lupien, S.L., Dugan, F.M., Bhunia, K., Khingra, A., Sablani, S.S. 2015. Ultraviolet-C light inactivation of Penicillium expansum on fruit surfaces. Food Control. 50:297-303.
Wiseman, M.S., Dugan, F.M., Kim, Y.K., Xiao, C. 2015. A postharvest fruit rot of apple caused by Lambertella corni-maris in Washington State. Plant Disease. 99:201-206.
Greene, S.L., Kisha, T.J., Yu, L., Parra-Quijano, M. 2014. Conserving plants in gene banks and nature: Investigating complementarity with Trifolium thompsonii Morton. PLoS One. 9(8):e105145.
Dugan, F.M., Lupien, S.L., Osuagwu, A.N., Uyoh, E.A., Okpako, E., Kisha, T.J. 2015. New records of Lasiodiplodia theobromae in seeds of Tetrapleura tetraptera from Nigeria and fruit of Cocos nucifera from Mexico. Journal of Phytopathology. 164: 65–68. doi: 10.1111/jph.12384.