Location: Plant Germplasm Introduction and Testing Research
2019 Annual Report
Objectives
Objective 1: Efficiently and effectively acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority legume, oilseed, vegetable, forage grass, sugar, ornamental, and medicinal genetic resources and associated information.
1A: Acquire samples of priority plant genetic resources (including crop wild relatives) from the U.S. and/or other countries to fill current gaps in NPGS collections of these priority crops.
1B: Conserve and distribute WRPIS plant genetic resources and their associated information.
1C: Regenerate accessions of priority plant genetic resources, emphasizing accessions with low germination, few seeds in storage, or those not yet backed-up at secondary sites.
Objective 2: Develop more effective genetic resource maintenance, evaluation, or characterization methods and apply them to priority legume, oilseed, vegetable, forage grass, sugar, ornamental, and medicinal genetic resources. Record and disseminate evaluation and characterization data via Germplasm Resources Information Network (GRIN)-Global and other data sources.
2A: With collaborators, apply next generation DNA sequence technology to genotype selected accessions of priority crops for assessing genetic diversity and analyzing genome-wide association among DNA sequence variants and traits of economic importance, emphasizing core subsets of priority genetic resources. Incorporate characterization data into the GRIN-Global and/or other databases.
2B: With collaborators, characterize with NIR spectroscopy the major nutritional component content of food legume genetic resources.
2C: Screen germplasm accessions, and/or candidates for accessions, for disease resistance. Identify disease agents by current taxonomic criteria. Disseminate research results in peer-review venues with citations in GRIN-Global.
2D: With collaborators, characterize the fatty acid composition and oil content of selected safflower germplasm accessions with gas chromatography.
Objective 3: With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for priority legume, oilseed, vegetable, forage grass, sugar, ornamental, and medicinal genetic resource and information management.
3A: Working with respective Crop Germplasm Committees and curators at other locations, update Crop Vulnerability Statements for Food Legumes, Pisum, Grass, Leafygreen Vegetables, Phaseolus Bean, Root and Bulb (allium) and sugarbeet.
3B: Update WRPIS Operations Manual on Germplasm Management and Research.
Objective 4: Develop selected populations of priority genetic resources which are genetically enhanced for potentially higher yields, tolerance to environmental extremes, host-plant resistance to diseases and pests, and/or increased nutritional quality.
4A: Identify markers associated with resilience to temperature extremes by conducting a genome wide association study of faba bean using SNP markers and field evaluation data.
4B: Develop a Pisum recombinant inbred population in order to elucidate the genetic basis of economically important traits.
Approach
Conserve, regenerate, evaluate and distribute approximately 98,000 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 closely the National Plant Germplasm System Distribution Policy and the established protocols and procedures. Keep our active plant genetic resource collections in the seed storage facilities with adequate conditions for proper conservation of seed samples for short and medium term storage and for people entering the storage space to take samples for distribution and for viability tests. Monitor seed viability by periodic germination tests at variable intervals depending on the species. Ship high quality seed samples to National Laboratory for Germplasm Resources Preservation at Ft. Collins, Colorado and the Svalbard Global Seed Vault in Norway for long-term security back-up.
Conduct collaborative plant expedition/collection trips and germplasm exchange to acquire samples to fill gaps in NPGS collections, and to supply critically needed traits to support current and future breeding and research. Evaluate the phenotypic variation of economic traits of specialty crops independently or collaboratively. Use laboratory equipment to characterize major nutritional components of food crop germplasm such as using near infrared (NIR) spectroscopy to quantify the major nutritional component content of food legume genetic resources and gas chromatography to characterize the fatty acid composition and oil content of selected safflower germplasm accessions. Apply existing and newly developed genomic tools and technologies such as the Next Generation DNA sequencing to characterize genetic diversity, phylogenetic relationship and marker-trait association of priority crop collections. 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.
Publish research results and release improved germplasm to the user community. Update the pertinent section of Operations Manual with reference to changes in collection holdings, management technologies and practices, diagnostic procedures, roles of personnel and any other relevant changes. Work with relevant crop germplasm committees to update the Crop Vulnerability Statements of the crops under our management.
Use both classical plant breeding methods and contemporary marker-assisted selection (MAS) to enhance the nutritional attributes and the resiliency to abiotic stress of faba bean.
Progress Report
This report documents progress for the project 2090-21000-032-00D, "Management of Priority Legume, Oilseed, Vegetable, Forage Grass, Sugar, Ornamental, and Medicinal Plant Genetic Resources and Associated Information."
Progress is being made towards all four objectives and their sub-objectives, all of which fall under National Program 301, Crop Genetic Improvement. This project focuses on Problem Statement 1A: Efficiently and Effectively Manage Plant and Microbial Genetic Resources. Introduced plant genetic resources are critical for improving the current crops and developing new crops.
In support of Objective 1, approximately 2,800 new accessions were added, most of which were crop wild relatives collected by the Seeds of Success (SOS) project, to our collection. SOS is a national native seed collection program, led by the Bureau of Land Management in partnership with a variety of non-federal organizations and federal agencies including ARS. As of August 7, 2019, there were over 100,000 accessions belonging to 4,531 species (5,179 taxa) in 1,047 genera. Most of these newly introduced resources are available to researchers and breeders. During the past year, we distributed a total of 44,659 packets of seed samples to 835 requestors with addresses in each of the 50 domestic states and 44 foreign countries. The plant exploration proposal to collect faba bean landraces to fill the gaps in our collection was selected for funding by the Plant Exchange Office. The research geneticist communicated with his collaborators in Morocco and arranged a plant collecting trip with drive routes mapped to growers’ fields for seed collecting at harvest time. However, the international travel arrangements did not go through due to the critical vacancy in the research unit. The plant exploration trip has been postponed to next year.
For Objective 2, 2,218 inventories of diverse plant germplasm were regenerated on a farm or in greenhouses. Quality fresh seed samples of 1,994 and 120 inventories were shipped to the National Laboratory for Genetic Resource Preservation (NLGRP), Fort Collins, Colorado, and to the Svalbard Global Seed Vault, Svalbard, Norway, respectively, for secured backup. A total of 8,830 digital images including 5,787 seed images of 6,153 accessions were uploaded into the GRIN-Global database that is accessible via the internet by researchers, educators and the general public worldwide. All ongoing germplasm regeneration, seed increase, characterization and evaluation research experiments are progressing well, and evaluation data are being collected.
In support of Objective 3, germplasm curators have been working with the members serving in various Crop Germplasm Committees on updating the crop vulnerability statement. Updating the operations procedures is in progress.
In support of Objective 4, the planned project of developing a recombination inbred line population progressed well. Several thousand seeds harvested from the F1 hybrid plants in May 2019 segregated for seed coat color of yellow and green in the expected three to one ratio. The Single Seed Descent (SSD) method will be employed to advance the generation to F6 in our greenhouse. Since the two parental varieties are used for pea reference genome sequences, our resulting recombination inbred line population will be useful in studying genetic basis of agronomically-important traits.
Accomplishments
1. Identified three significant quantitative trait loci associated with cold tolerance in chickpea. Fall-sown chickpea has substantial yield advantage over those of spring-sown chickpea in regions with mild winter climates. Towards developing cold-tolerant chickpea for expansion of its current geographic range and for improvement of productivity, researchers in Pullman, Washington, identified the quantitative trait loci (QTL) associated with cold tolerance in chickpea using a recombinant inbred line population of 129 lines derived from an interspecific cross between ICC 4958, a cold-sensitive desi type cultivar, and PI 489777, a cold-tolerant chickpea wild relative. With the phenotype data for cold tolerance of both in the field and under controlled conditions and a genetic linkage map consisting 747 single nucleotide polymorphism (SNP) markers generated with genotyped using genotyping-by-sequencing and spanning 393.7 cM, three significant QTL were found on linkage groups (LGs) 1B, 3, and 8. The QTL on LGs 3 and 8 were consistently detected in six environments and explained 7.15 to 48.4 percent of the phenotypic variance. The QTL-associated single nucleotide polymorphism (SNP) markers will be useful for breeding increased cold tolerance in chickpea.
2. Characterizing the phenotypic diversity of the W6 table beet collection. The National Plant Germplasm System (NPGS) cultivated beet collection has 1,845 accessions with material from four beet types including sugar beet, fodder beet, leaf beet, and table beet. Table and leaf beets are minor vegetable crops in the U.S., but their annual planted acreage has been increasing in recent years. Over the past 30 years, the sugar beet accessions have been extensively evaluated and little data was collected on table beet accessions in the collection. To fill this gap, researchers in Pullman, Washington, completed collecting descriptor data of table beet including plant, plot, and root images. These useful phenotypic data and images have been uploaded into our Germplasm Research Information Network (GRIN)-Global database for breeders to use when selecting desirable parental accessions in developing varieties to satisfy consumers.
Review Publications
Dugan, F.M., Strausbaugh, C.A. 2019. Catalog of Penicillium spp. causing blue mold of bulbs, roots, and tubers. Mycotaxon. 134(1):197-213. https://doi.org/10.5248/134.197.
Mugabe, D., Coyne, C.J., Piakowski, J., Zheng, P., Ma, Y., McGee, R.J., Main, D., Vandemark, G.J., Zhang, H., Abbo, S. 2018. Quantitative trait loci for cold tolerance in chickpea. Crop Science. 59(2):573–582. https://doi.org/10.2135/cropsci2018.08.0504.
Harrison, M.L., Bradley, V.L., Casler, M.D. 2019. Native grass species for forage and turf. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. New York, NY: Springer, Cham. Volume 2, p. 579-605.
Pinhasi Van-Oss, R., Gopher, A., Kerem, Z., Sherman, A., Zhang, H., Coyne, C.J., Vandemark, G.J., Reamy, O., Abbo, S. 2018. Independent selection for seed free tryptophan content and vernalization response in chickpea domestication. Plant Breeding. 137(3):290-300. https://doi.org/10.1111/pbr.12598.
Beharav, A., Hellier, B.C., Richardson, K.L., Lebeda, A., Kisha, T.J. 2018. Genetic relationships and structured diversity of Lactuca georgica germplasm from Armenia and the Russian Federation among other members of Lactuca L., subsection Lactuca L., assessed by TRAP markers. Genetic Resources and Crop Evolution. 65(7):1963-1978. https://doi.org/10.1007/s10722-018-0669-7.
