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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

2016 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
During FY 2016, progress was made on all four objectives and their sub-objectives, 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. Introduced plant genetic resources are critical to supply desirable genes for improving the current crops and developing new crops. Our curators and scientists successfully acquired 1,908 new accessions which includes 1,631 native plant accessions from the Seeds of Success (SOS) project and 277 accessions of common beans, cool season grasses and crop wild relatives. The common bean germplasm curator received a grant from Plant Exchange Office for the collection of Phaseolus polystachios (a wild relative of common bean) in the State and National Forests in Ohio. The collection trip proceeded in partnership with a botanist of the Smithsonian Institution and collected seven populations throughout Ohio, two populations in Indiana, two in Missouri and one in West Virginia. As of July 31, 2016, the Western Regional Plant Introduction Station (WRPIS) collection included 96,824 accessions belonging to more than 5,000 plant species. Of these, 71,998 accessions were available for distribution to requesters in the global plant research community, which uses genetics for both applied crop improvement and basic biological research. During FY 2016, a total of 28,031 packets of high quality seed samples were distributed to 1,171 requesters in 43 foreign countries and 50 domestic states. We packed and stored 1,213 newly regenerated/harvested inventories of a broad range of plant species. We determined seed quantities of 15,728 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 13,581 observation data points on 3,947 accessions on 169 established descriptors of 10 different crop species. We shipped 2,805 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. Up to date, 72,109 accessions of our collection were backed up. In FY 2016, we continued research on cool season food legumes, safflower, garlic and ornamental bulb crop diseases, native plants and grasses. This work supports small to medium scale growers in the U.S., especially in the Pacific Northwest. An ARS Research Geneticist quantified the low molecular weight carbohydrates with high performance liquid chromatography in the immature and mature seeds from 40 selected faba bean varieties and generated information useful to consumers as well as to plant breeders. An ARS Research Plant Pathologist, in collaboration with other ARS researchers in Peoria, Illinois, and scientists at Washington State University, identified a new (as yet unnamed) Fusarium fungus that is pathogenic to Hibiscus. This discovery will help disease management of the important ornamental hibiscus crops. An ARS Research Geneticist contributed to the collaborative research project in mapping a gene that confers high levels of resistance to bacterial leaf spot of lettuce. An ARS scientist contributed to a collaborative study in determining the genetic diversity of cultivated lentil and its relation to the world’s agro-ecological zones. The combined effort of researchers at ARS in Pullman, Washington, the International Center for Agricultural Research in the Dry Areas, Morocco, Washington State University, Pullman, and the University of Saskatchewan, Canada, generated useful information that will enable researchers to access needed genetic diversity in an efficient method for the lentil crop improvement.


Accomplishments
1. The low molecular weight carbohydrates in faba bean seed quantified. Faba bean is a valuable pulse crop for human consumption. The low molecular weight carbohydrates: glucose, fructose, sucrose and raffinose family oligosaccharides (RFO), raffinose, stachyose, and verbascose, in faba bean seeds contribute to the flavor and prebiotic nature of this edible bean. An ARS researcher in Pullman, Washington, quantified the low molecular weight carbohydrates with high performance liquid chromatography in the immature and mature seeds from 40 selected faba bean varieties across a wide range of seed sizes. Sucrose was the predominant constituent of low molecular weight carbohydrates of immature seeds ranging from 5.9 to 22.6% dry weight for cotyledons and 6.7 to 16.7% dry weight for seed coats, while total RFO averaged <1% dry weight across populations. The sucrose content of mature seeds was relatively stable across population with a mean of 2.4% dry weight, while RFO content ranged from 2.5 to 7.5% dry weight. This information is useful to consumers as well as to plant breeders for future faba bean quality improvement.

2. A new species of Fusarium pathogenic to Hibiscus. Hibiscus, a large genus in the mallow family with many species noticeable for their showy flowers, contributes $23 million annual sales to the American ornamentals industry. An ARS researcher in Pullman, Washington, in collaboration with other ARS researchers in Peoria, Illinois, and researchers at Washington State University, identified a new (as yet unnamed) Fusarium fungus that is pathogenic to Hibiscus. Phylogenetic analysis based on DNA sequences placed this new pathogen to an established clade with a known species that attacks other members of the same plant family. A clade is a group of organisms believed to have evolved from a common ancestor. This information will help developing disease management strategies for the important ornamental hibiscus crops.

3. Useful DNA variation information to help chickpea improvement. Chickpea production is increasing in acreage in the U.S. with expanding domestic and export markets. An ARS scientist in Pullman, Washington, in collaboration with researchers at the University of California, Davis, and at the International Crops Research Institute for the Sem-Arid Tropics, India, completed a research project determining the multiple post-domestication origins of large-seeded chickpea through DNA variation in a diversification-associated transcription factor for flower color. The research involved 322 accessions of wild and domesticated chickpea which were genotyped with 538 single nucleotide polymorphisms (SNP) markers. The data indicated a genetic bottleneck in cultivated lines and points to potentially useful genetic variation discovered in wild species of chickpea.

4. The acreage of lentil production increased more than 20% in 2016 in the U.S. in responding to an expanding export market demand. Expediting genetic improvement of lentil productivity requires information on genetic variation and the agro-ecological zones. An ARS scientist in Pullman, Washington, cooperated on a research project to determine the genetic diversity of cultivated lentil and its relation to the world’s agro-ecological zones. The research interrogated 352 with 1,194 polymorphic single nucleotide polymorphism (SNP) markers identifying three agro-ecological zones. The defined agro-ecological zones enable researchers to access needed genetic diversity in an efficient method for the lentil crop improvement.


ARS scientists in Pullman, Washington, manage the Western Regional Plant Introduction station (WRPIS)collection of garlic. This is the largest non-commercial collection in North America and intensely used by small-scale garlic farmers. Accordingly, garlic accessions are characterized by various traits, such as agronomic descriptors, microbial associates (including agents of disease), morphology, etc. that would be of interest to small-scale producers. The Horticultural Crops curator, through the Crop Germplasm Committee for Allium, keeps in touch with small-scale producer needs.


Review Publications
Van Oss, R., Abbo, S., Eshed, R., Sherman, A., Coyne, C.J., Vandemark, G.J., Zhang, H., Peleg, Z. 2015. Genetic relationship in Cicer Sp. expose evidence for geneflow between the cultigen and its wild progenitor. PLoS One. doi: 10.1371/journal.pone.0139789.
Landry, E.J., Coyne, C.J., Mcgee, R.J., Hu, J. 2016. Adaptation of autumn-sown faba bean germplasm to southeastern Washington. Agronomy Journal. 108:301–308.
Khazaei, H., Caron, C., Fedoruk, M., Diapari, M., Vandenberg, A., Coyne, C.J., Mcgee, R.J., Bett, K. 2016. Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world’s agro-ecological zones. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01093.
Dugan, F.M. 2016. Shakespeare, plant blindness and electronic media. Plant Science Bulletin. 62:2.
Wiseman, M., Dugan, F.M., Xiao, C. 2016. Potential hosts for Lambertella corni-maris and Phacidium lacerum within the family Rosaceae. Plant Health Progress. 17:128-129.
Wiseman, M.S., Kim, Y.K., Dugan, F.M., Rogers, J.D., Xiao, C. 2016. A new postharvest fruit rot in apple and pear caused by Phacidium lacerum. Plant Disease. 100:32-39. doi: 10.1094/PDIS-02-15-0158-RE.
Oss, R.P., Sherman, A., Zhang, H., Vandemark, G.J., Coyne, C.J., Abbo, S. 2015. Vernalization response of domesticated× wild chickpea progeny is subject to strong genotype by environment interaction. Plant Breeding. 135:102-110.
Desgroux, A., L'Anthoene, V., Roux-Duparque, M., Riviere, J., Aubert, G., Tayeh, N., Moussart, A., Mangin, P., Vetel, P., Pirio, C., Mcgee, R.J., Coyne, C.J., Burstin, J., Baranger, A., Manzanares-Dauleux, M., Bourion, V., Pilet-Nayel, M. 2016. Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea. BMC Genomics. 17:124.
Landry, E.J., Lafferty, J.E., Coyne, C.J., Pan, W.L., Hu, J. 2015. Registration of four winter-hardy faba bean germplasm lines for use in winter pulse and cover crop development. Journal of Plant Registrations. 9:367–370.
Penmetsa, R.V., Carrasquilla-Garcia, N., Bergmann, E.M., Vance, L., Castro, B., Kassa, M.T., Sarma, B.K., Datta, S., Farmer, A.D., Baek, J.M., Coyne, C.J., Varshney, R.K., Von Wettberg, E.B., Cook, D.R. 2016. Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor. New Phytologist. 211:1440-1451.
Dugan, F.M. 2015. Fungi. In: Beaudry, M.C., Bescherer Metheny, K., editors. Archaeology of Food: An Encyclopedia. Lanham, MD:Rowman & Littlefield. p.308-309.
Dugan, F.M. 2015. Fungi. In: Beaudry, M.C., Bescherer Metheny, K., editors. Archaeology of Food: An Encyclopedia. Lanham, MD:Rowman & Littlefield. p.231.
Idrissi, O., Udupa, S.M., De Keyser, E., Mcgee, R.J., Coyne, C.J., Saha, G., Muehlbauer, F., Van Damme, P., De Riek, J. 2016. Identification of quantitative trait loci controlling root and shoot traits associated to drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01174.
Ma, Y., Hu, J., Myers, J., Mazourek, M., Coyne, C.J., Main, D., Wang, M., Humann, J., Mcgee, R.J. 2016. Development of SCAR markers linked to sin-2, the stringless pod locus in pea (Pisum sativum L.). Molecular Breeding. doi: 10.1007/s11032-016-0525-4.