2013 Annual Report
1a.Objectives (from AD-416):
1. Conserve, regenerate, back up, and distribute genetic resources and associated information for sorghum, peanut, vegetables, warm-season grasses, vigna, clover, tropical/subtropical legume crops and related wild species.
• 1.A. Conserve more than 91,000 accessions of priority genetic resources and periodically assess these stored genetic resources for vigor, viability, trueness to type, and health.
• 1.B. Regenerate and develop alternative regeneration techniques for priority genetic resources, and back up more than 95% of the collection at secondary sites.
• 1.C. On request, distribute accessions of plant genetic resources and their associated information to meet specific needs of the research and educational communities.
2. Acquire genetic resources to fill ecogeographical, taxonomic, and/or genetic gaps and to expand the genetic diversity available from genebank collections of the preceding crops and related wild species.
3. Conduct genetic characterizations and phenotypic evaluations of the preceding crops and related wild species for priority genetic and agronomic traits.
• 3.A. Develop and apply nuclear magnetic resonance (NMR), high performance liquid chromatography (HPLC), and gas chromatography (GC) procedures to analyze variation in oil, protein, sugar content, fatty acid composition, flavonoids, and other key phytochemicals in the preceding crops and related wild species. Incorporate biochemical data into the Germplasm Resources Information Network (GRIN-Global) of the National Plant Germplasm System (NPGS).
• 3.B. Update and obtain phenotypic descriptors and evaluate priority agronomic or horticultural traits for the preceding crops and crop wild relatives. Incorporate phenotypic descriptors and agronomic or horticultural trait data into GRIN-Global.
• 3.C. Develop DNA markers from existing genomic resources to assess phylogenetic relationships, genetic diversity, and population structure of priority crops and crop wild relatives. Incorporate DNA genetic marker characterization data into GRIN-Global or other databases (such as GenBank).
1b.Approach (from AD-416):
Conserve over 91,000 accessions of priority species with the majority of seed maintained at -18 C for improved longevity. Conduct germination tests of newly-regenerated seed and seed in storage to establish regeneration priorities. Identify duplicate or redundant accessions through evaluation of passport data or by genotyping suspected duplicates using a reference set of DNA markers. Conduct plant pathogen testing of peanut quarantine accessions for seed-borne virus infection, field or greenhouse plants for diseases, and verification of plant or seed health for satisfying import permits. Conserve clonal accessions of warm-season grasses and wild peanuts in the greenhouse, bamboo in the field, and sweetpotato in tissue culture. Conduct regenerations of seed-producing accessions each year locally or with cooperators at remote locations. Select accessions for regeneration based on low seed viability, low seed numbers, original seed only, age of seed, and demand by users. Utilize and modify regeneration methods to reduce genetic drift, inbreeding depression, and loss of unique alleles. Conserve more than 95% of crop seed accessions and the sweetpotato in vitro culture collection at a second location at Ft. Collins, CO. Cooperate with Ft. Collins scientists to increase cryopreservation of warm-season grass and sweetpotato clonal accessions for safety backup. Inform the research and educational communities of these genetic resources for their traditional and non-traditional uses. Distribute plant genetic resources and associated information to users worldwide in response to requests received. Distribute clonal accessions of sweetpotato as in-vitro cultures or plantlets and vegetative material of accessions which do not produce seed as bare-rooted cuttings. Acquire germplasm through plant collecting trips, germplasm exchanges, donations, existing breeding programs, or purchase. Acquisitions will focus on germplasm from specific locations, with specific traits, or to fill taxonomic gaps in the NPGS collection. Measure seed oil content and fatty acid composition on peanut, sesame, Desmodium, and Teramnus accessions using a nuclear magnetic resonance (NMR) analyzer and a gas chromatograph (GC). Measure crude protein content in cowpea and mung bean accessions. Determine sugar and organic acid content in fruits of chili pepper accessions. Obtain phenotypic data and digital images from peanut, vegetable, tropical/subtropical legumes, cowpea, annual clover, warm-season grasses, and other accessions grown for seed regeneration. Use genotyping and morphological descriptor data to develop a castor core collection. Identify desirable accessions from genotyping by sequencing, morphological data, and biomass chemical composition of sorghum accessions. Assess genetic diversity by genotyping Cucurbita, sweetpotato, seashore paspalum, chili pepper, and eggplant accessions and the watermelon collection using DNA markers. Develop functional DNA markers for oleic acid in sesame, tannin in sorghum, and oil metabolism in peanut accessions.
This report documents progress for Project Number 6607-21000-011-00D “Conservation, Characterization, and Evaluation of Plant Genetic Resources and Associated Information” which started in March 2013 and continues research from Project Number 6607-21000-010-00D, entitled “Conservation, Characterization, and Evaluation of Crop Genetic Resources and Associated Information”. A total of 92,180 accessions of 1,553 plant species were maintained in the Griffin plant genetic resources collection. Over 87.9% of accessions were available for distribution to users and over 96.6% were backed up for security at a second location. Bulk seed samples for 67,806 accessions were maintained at -18 C for long-term storage with seed of the remaining accessions stored at 4 C. A total of 40,465 seed and clonal accessions in 1,081 separate orders were distributed upon request to scientists and educators in 48 U.S. states and 41 foreign countries. Acquisitions made to the collection included 49 warm-season grass, 30 peanut, 10 vegetable, and 10 other accessions. A plant collection trip in Georgia, North Carolina, and South Carolina added 30 switchgrass, indiangrass, little bluestem, and naturalized Sorghum halepense accessions to the collection. Seed regenerations and characterizations were conducted on 900 peanut, 110 cowpea, 65 warm-season grass, 55 pepper, 65 watermelon, 284 legume, new, and misc. crop, 120 annual clover, and 78 other vegetable accessions. Peanut accessions were regenerated with cooperators in Georgia, Florida, North Carolina, Oklahoma, and New Mexico. A total of 200 pepper accessions were grown in Georgia and California for seed increase, characterization and recording of digital images. Long-term maintenance of 259 wild peanut and 308 warm-season grass clonal accessions was continued in the greenhouse with 46 napiergrass and 15 miscanthus accessions maintained in the field. The clonal grass collection is being reduced by removing redundant accessions, forming crossing blocks to obtain seeds from closely related clonal accessions, and removing clonal accessions that have existing seed in the collection. A total of 12 bermudagrass and 738 sweetpotato accessions were maintained in tissue culture. Germination testing has been conducted on 76,698 accessions (over 84% of collection) since 2002. Photoperiod-sensitive Neonotonia, Hibiscus, and annual clover accessions were regenerated in the winter greenhouse. Seed oil content and fatty acid composition was determined for accessions of Macrotyloma, Teramnus, Hibiscus, and castor species. With cooperators in Kansas and Puerto Rico, 280 sweet sorghum accessions were phenotypically evaluated in the field at two locations and 96 accessions were genotyped. Genotyping-by-sequencing (GBS) was conducted on 125 Vigna and 72 peanut accessions to evaluate genomic diversity, relationships among individuals, and develop new SNP markers. A new cowpea accession was acquired that can be used for fiber production. Accessions were identified with high oil content (peanut), high quercetin content (peanut), high leaf protein (bamboo), and sesamin content (sesame).
Purification of the U.S. peanut mini-core. Many of the lines in the U.S. peanut mini-core were variable within each accession which can be problematic for certain types of research such as genomics work. ARS researchers at Griffin, Georgia, purified each accession in the mini-core by eliminating rogue plants in the field and only allowing uniform plants to produce seeds. The resulting purified seeds were deposited into the germplasm collection as a separate inventory within the peanut collection to provide a consistent seed source for peanut genomics research.
Genetic relationships among tetraploid sweetpotato varieties. The genetic relationships of several tetraploid varieties of sweetpotato to each other and to the cultivated hexaploid sweetpotato are largely unknown. However, these tetraploid varieties may contain genes of importance for the crop’s improvement. Sequencing their plastid chloroplast genomes by ARS researchers at Griffin, Georgia, revealed that the tetraploid varieties were closely related to the cultivated sweetpotato and also to the diploid species Ipomoea trifida. All three tetraploid varieties intercrossed among themselves. This information is of use in targeting future germplasm acquisitions and suggests that these tetraploid varieties may provide a source of genes for introgression into cultivated sweetpotato via conventional or novel breeding methods.
Seed and corm regeneration in aeroponics. Several photoperiod-sensitive legumes do not produce adequate seed numbers for distribution to researchers using traditional field or greenhouse seed regeneration procedures. Also, Chinese water chestnuts have extensive corm rot when grown in traditional flooded sand systems. ARS researchers at Griffin, Georgia, produced high quality seed and corm production of these species by using an aeroponic system. This technique has produced adequate seed and corm numbers so that these accessions are now available for distribution and use by researchers.
Switchgrass collection on Atlantic Coast. Reduced genetic diversity of switchgrass germplasm limits the ability of plant breeders to develop improved cultivars for bioenergy production. ARS researchers at Griffin, Georgia, collected a total of 27 switchgrass accessions from diverse habitats and geographic locations in Georgia, South Carolina, and North Carolina, and processed these accessions into the U.S. switchgrass collection. These collections will provide valuable germplasm needed for switchgrass breeding and research programs.
Seed germination testing. Prior to 2002, little germination testing was conducted on accessions in the U.S. germplasm collections maintained at Griffin, Georgia, and regeneration priorities were based on seed age. ARS researchers have now completed germination testing on almost all of the available accessions maintained at this location. These data allow crop curators to set regeneration priorities based on these germination data and result in known higher seed quality in accessions distributed to researchers and educators.
Oil and antioxidant content of the U.S. peanut mini-core. The U.S. peanut mini-core of 108 accessions was developed to represent the majority of the genetic diversity in the entire peanut germplasm with little redundancy. The variability in compounds such as oil and antioxidants which are important seed quality traits has not been previously evaluated. ARS researchers at Griffin, Georgia, quantified the oil content and antioxidants in the peanut mini-core and assessed year to year variability by evaluating the accessions over a two year period. This information will provide breeders with a range of variation in oil and antioxidants in accessions of the mini-core that they can utilize to make improved selections in their breeding programs.
Barkley, N.L., Isleib, T.G., Wang, M.L., Pittman, R.N. 2013. Genotypic effect of ahFAD2 on fatty acid seed profiles in six segregating peanut (Arachis hypogaea L.) populations. BioMed Central (BMC) Genetics. doi: 10.1186/1471-2156-14-62 14:62.
Barkley, N.L., Wang, M.L. 2013. Oleic Acid: Natural variation and potential enhancement in oilseed crops. In: Silva, L, editor. Oleic Acid: Dietary Sources, Functions, and Health Benefits. Hauppauge, NY:Nova Publishers. p.29-44.
Austin, D., Jarret, R.L. 2013. Roots as a source of food. In: Eshel, A. and Beeckman, T., editors. Plant Roots: The Hidden Half. 4th Edition. CRC Press. Chapter 30.
Barkley, N.L., Wang, M.L. 2013. Revealing gene function and genetic diversity in plants and animals via TILLING and EcoTILLING.In: Neri, C. of Advances in Genome Science Changing Views on Living Organisms. Volume 1. Oak Park, IL: Bentham Science Publishers. p.316-351.