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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

2018 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 is the final report for this project which terminated February 28, 2018 and has been replaced by new Project 2090-21000-032-00D, “Management of Priority Legume, Oilseed, Vegetable, Forage Grass, Sugar, Ornamental, and Medicinal Plant Genetic Resources and Associated Information”. For additional information, please see the annual report for the new project. Objective 1: In the past five years ARS scientists at Western Regional Plant Introduction Station (WRPIS) in Pullman, Washington, carried out three international and four domestic plant explorations and collected targeted crop and crop wild relatives. A total of 7,574 new accessions of needed plant germplasm were acquired for the WRPIS collection through these explorations and other forms of germplasm exchange with collaborators. As of June 12, 2018, there were 100,471 accessions belonging to 4,633 species (5,285 taxa) in 1,057 genera. Most of these newly introduced resources are available to researchers and breeders. Viability data for 16,279 accessions were determined and entered into the Germplasm Resources Information Network (GRIN) Global Database. Over 10,539 accessions of diverse crop genetic resources were regenerated during the past five years. A total of 27,155 accessions of newly regenerated seed samples were shipped for security back-up at the National Laboratory for Genetic Resources Preservation, Ft. Collins, Colorado (13,605 accessions) and the Svalbard Global Seed Vault, Norway (13,550 accessions). The distributed seed samples for research and education purposes totaled 175,413 packets in the last five years and the germplasm requestors were from over 60 foreign countries and from each of the 50 domestic states. In the calendar year 2017, 42,484 seed packets were distributed to researchers worldwide. This number constituted a record in the history of this regional plant introduction station. The average annual distribution of the past five years (2013-2017; 35,082 packets) increased more than 19 percent from the previous five years (2008-2012; 29,377 packets). This data demonstrates an increased interest of the user community in the USDA plant germplasm collection. The distributed seed samples have been used in a wide range of research, education and breeding projects. Objective 2: During past five years, WRPIS staff uploaded 250,036 data points of plant germplasm evaluation to the GRIN-Global database. These data points were from 59,489 accessions in the Plant Germplasm Introduction and Testing (PGIT) Research Unit collection and comprise digital images and qualitative and quantitative values of the established crop specific descriptors. This accession-associated information facilitates germplasm requestors for accessions with specific traits. An ARS scientist in Pullman, Washington, found widespread genetic variation in phenology, morphology and production traits in both ploidy types of Basin wildrye. 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. Similar seed zone maps were developed for several native plant species such as bluebunch wheatgrass, tapertip onion, Sandberg bluegrass and Thurber’s Needlegrass. All of these species are important to ecosystem restoration in the Western U.S. These seed zone maps are useful in guiding germplasm selection for restoration projects and for in situ conservation. Another ARS scientist on the team analyzed the genetic diversity, population structure and genome-wide marker-trait association in a special collection of 298 lettuce lines. Each of these lines was derived from a single plant that had been identified as homozygotic at all 322 genetic loci. This special collection and its associated marker information will be useful to lettuce genetic improvement when they are validated in segregating populations. PGITR scientists conducted independent and cooperative research projects on several pulse crops including determining the genetic diversity of cultivated lentil and its relation to the world’s agro-ecological zones (in cooperation with the University of Saskatchewan, Canada). The research interrogated 352 germplasm samples with 1,194 polymorphic single nucleotide polymorphism (SNP) markers identifying three agro-ecological zones. The defined agro-ecological zones enable researchers and curators to access needed genetic diversity in an efficient method for crop improvement. We determined multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor for flower color (in cooperation with the University of California, Davis). The research involved 322 accessions of wild and domesticated chickpea which were genotyped with 538 single nucleotide polymorphisms (SNPs) markers. The data indicate a genetic bottleneck in cultivated lines and points to potentially useful genetic variation discovered in wild species of chickpea. The USDA Pea Single Plant Core Plus (410 accessions) was genotyped and 66,000 SNP markers were developed (in cooperation with Cornell University). The dataset was used for association mapping proof-of-concept to identify the gene that determines the white flower trait studied by Mendel. SNP markers associated with high levels of seed mineral nutrient content and concentrations were identified in pea accession PI 357292 using a recombinant inbred line population phenotyped in two environments (in cooperation with Washington State University). These markers are being tested for utility in the ARS pea breeding program for nutrient content improvement, and 5) evaluating 100 faba bean accessions with replicated small plots under organic environment with the support of a grant from the Food Legume Crop Germplasm Committee (in cooperation with the Lundberg Family Farms, Richvale, California). Evaluation data, such as biomass, plant height, days to flower and seed yield, were collected and uploaded into our GRIN-Global database. Objective 3: An ARS researcher in Pullman, Washington, assessed the pathogenicity of eleven Penicillium species belonging to different taxonomic series on garlic, two varieties of table onion, two other wild onion entries, and six ornamental bulb species. Penicillium species novel to North America and new host-fungus records were identified. The host range for several fungal causal agents of blue mold of edible and ornamental bulb crops in the Northwest were characterized. The results provided useful information to growers for effective disease management. ARS scientists quantified and published on resistance/susceptibility to stripe rust in over 100 germplasm lines of Great Basin wild rye. Brief 'first reports' or full-length articles on six fungal diseases of WRPIS or National Plant Germplasm System (NPGS) germplasm, and one report of dodder novel on WRPIS germplasm; one manuscript on mycobiota of stored white lupine seed, and one manuscript describing a new species of Alternaria from a WRPIS forage grass were published. ARS scientists 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 percent up to 72.2 percent 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. In collaboration with the University of Florida, An ARS researcher from Pullman, Washington, identified a lettuce accession PI 358001-1 that has the high level of resistance to bacterial leaf spot, caused by the Florida strain. We also mapped this resistant gene on linkage group 2 of the lettuce genome. This strong resistant gene should be readily transferred to adapted lettuce cultivars to battle the devastating bacterial leaf spot of lettuce. Objective 4: ARS scientists 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 survival was 54 percent 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. Many advanced breeding lines have been distributed to interested parties in ten domestic states under standard USDA-ARS Material Transfer Agreement (MTA). An ARS scientist in Pullman, Washington, collaborated with the International Center for Agricultural Research in the Dry Areas, Terbol, Lebanon and collected data for eight agronomic traits on a Generation Challenge Program (GCP) reference set of 140 faba bean accessions grown under high temperature at different locations in Lebanon and the U.S. We also genotyped the reference set with the genotyping by sequencing (GBS) technique which produced approximately 4 million reads per genotype on an Illumina HiSeq 2500 Sequencer. The single nucleotide polymorphism (SNP) marker, called pipeline Universal Network Enabled Analysis Kit (UNEAK), found 10,950 variant loci from the sequence data. The SNP genotype data discriminated the 140 entries from each other. A Genome-Wide Association Study (GWAS) was performed and four SNPs were identified that are significantly associated with plant height and 100 seeds weight.


Accomplishments
1. Quantified the polyphenolic compounds in 120 heirloom bean accessions. There is strong evidence that consumption of pulses (dry beans, pea, chickpea and lentil) has substantial health benefits such as reducing cardiovascular disease, preventing diabetes and even preventing certain types of cancer. Scientific research demonstrated that these benefits are associated with the antioxidant activity of an array of phytochemicals including polyphenolic compounds. However, there is little information on the variation of polyphenolic compounds among the accessions of heirloom beans in the Western Reginal Plant Introduction Station (WRPIS) collection. An ARS scientist in Pullman, Washington, in collaboration with researchers at Washington State University, analyzed extractable and non-extractable phenolics in 120 heirloom bean accessions exhibiting a wide array of colors and patterns of seed coat, and found that the phenolic content was not strictly correlated with seed coat color and that there were 2 to 3-fold differences even within market classes of Red and Black beans. This critical information will be useful for breeders to select desirable parental accessions in developing varieties with the optimal polyphenolic compound contents for consumers.

2. Pre-acclimation temperatures influence the freezing tolerance of faba bean germplasm. Autumn-sown winter-type faba bean has been shown to have a yield advantage over spring sowing. Still, adoption of this overwintered pulse crop remains limited in temperate locations, due to inadequate winter hardiness. To understand how the prevailing temperature during emergence and seedling development, that is pre-acclimation, influences freezing tolerance, ARS scientists in Pullman, Washington, used seedlings grown under controlled “warm”, 17 to 12 degrees Centigrade, and “cold”, 12 to 5 degrees Centigrade, pre-acclimation environments. The team found that the seedlings under “warm” treatment were less freeze tolerant than those grown under “cold” treatment, and that there was a genotype specific response of above-ground tissues to pre-acclimation treatment. It was concluded that both above, and below ground tissues should be tested across a range of pre-acclimation temperatures when screening faba bean germplasm for freeze tolerance.


Review Publications
Dugan, F.M., Lupien, S.L., Hu, J. 2017. Fungal plant pathogens associated with emerging crops in North America: An emerging challenge for plant health professionals. Plant Health Progress. 18:221-229.
Thavarajah, D., Abare, A., Mapa, I., Coyne, C.J., Kumar, S., Pushparajah, T. 2017. Selecting lentil accessions for global selenium biofortification. Plants. 6(3):34. https://doi.org/10.3390/plants6030034.
Hu, J., Chen, W., McGee, R.J. 2017. Three faba bean (Vicia faba L.) breeding lines appear naturally resistant to Pythium damping-off. Plant Disease Management Reports. 11:V008.
Kim, W., Park, J., Dugan, F.M., Gang, D., Vandemark, G.J., Peever, T., Chen, W. 2017. Production of the antibiotic secondary metabolite solanapyrone A by the fungal plant pathogen Ascochyta rabiei during fruiting body formation in saprobic growth. Environmental Microbiology. 19(5):1822-1835. https://doi.org/10.1111/1462-2920.13673.