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United States Department of Agriculture

Agricultural Research Service

Research Project: CONSERVATION, CHARACTERIZATION, AND EVALUATION OF CROP GENETIC RESOURCES AND ASSOCIATED INFORMATION

Location: Plant Genetic Resources Conservation Unit

2009 Annual Report


1a.Objectives (from AD-416)
Strategically expand the genetic diversity in genebank collections and improve associated information for priority vegetable, sorghum, peanut, subtropical/tropical legume, and warm-season grass genetic resources. Conserve and regenerate priority vegetable, sorghum, peanut, subtropical/tropical legume, new crop, and warm-season grass genetic resources efficiently and effectively, and distribute pathogen-tested samples and associated information worldwide. Strategically characterize (“genotype”) and evaluate (“phenotype”) priority vegetable, sorghum, peanut, subtropical/tropical legume, and warm-season grass genetic resources for molecular markers, morphological descriptors, and key agronomic or horticultural traits such as biochemical content and product quality. Conserve, regenerate, and distribute germplasm of specialty crops, current or potential bioenergy crops (e.g., sweet sorghum, switch grass, and Miscanthus), and new genetic stocks generated by genomic research (e.g., assocition mapping projects) with sorghum and other crops.


1b.Approach (from AD-416)
Acquire samples of native warm-season grasses, subtropical legumes, Ipomoea species, chile pepper, and annual clovers to fill current gaps in NPGS collections. Survey existing holdings of sorghum genetic stocks, identify material that would fill gaps in NPGS collections, and begin acquiring and characterizing them. Regenerate and conserve more than 86,000 accessions of priority genetic resources and associated information. Increase the number of sweetpotato and warm-season grass clonal accessions maintained in tissue culture. Increase to 95 percent the proportion of the collection backed up at second sites. Develop superior regeneration methods for seed and clonally-propagated crops. Assay stored genetic resources for vigor, viability, and health. Distribute on request accessions and information that meet the specific needs of researchers and breeders. Develop and apply new genetic markers for phylogenetic and genetic diversity analyses of priority crops. Update and apply phenotypic descriptors for vegetables, peanuts, warm-season grasses, and subtropical/tropical legumes. Develop, enhance, and/or apply high performance liquid chromatography (HPLC) procedures for analyzing variation in flavonoids, antioxidants, capsaicin, and other key phytochemicals in accessions. Incorporate characterization, phenotypic, and biochemical data into GRIN and/or other databases.


3.Progress Report
A total of 89,451 accessions of 1,529 plant species were maintained in the Griffin plant genetic resources collection. Over 87% of accessions were available for distribution to users and over 96% were backed up for security at a second location. Bulk seed samples for 60,269 accessions were maintained at -18 C for long-term storage with seed of the remaining accessions stored at 4 C. A total of 30,883 seed and clonal accessions in 881 separate orders were distributed upon request to scientists and educators in 47 U.S. states and 45 foreign countries. Acquisitions made to the collection included 94 switchgrass, 230 pearl millet, 67 finger millet, 31 Hibiscus, and 30 vegetable accessions. Seed regenerations and characterization were conducted on 587 peanut, 150 warm-season grass, 323 legume, new, and misc. crop, 106 annual clover, and 10 cucurbit accessions. New regeneration techniques were developed for two Hibiscus, several cucurbits, and one sweetpotato species. Over 600 pepper accessions were grown in the field for characterization and recording of digital images. Digital images of watermelon seed and characterization data for big bluestem were added to the Germplasm Resources Information Network (GRIN). A new tablet PC was used to facilitate collection of peanut descriptor data. Long-term maintenance of 525 wild peanut and 398 warm-season grass accessions was continued in the greenhouse. Over 30 warm-season grass accessions and 750 sweetpotato accessions were maintained in tissue culture with eight replications of each sweetpotato clone. Virus screening was conducted on the warm-season grass clonal collection (for maize dwarf mosaic and johnsongrass mosaic viruses) and sweetpotato collection (for sweetpotato leaf curl virus). Tomato spotted wilt virus was found on peanut and clover species in the greenhouse and accessions were evaluated for virus infection by field, lab, and molecular techniques. Germination testing has been completed for 54,054 accessions (over 60% of collection) since 2002. A genotyping technique was developed to detect high oleic acid peanuts and will be useful in evaluating segregating populations to identify progeny with the desirable high oleic acid trait. In collaboration with other ARS scientists, 800 sorghum mutant lines were evaluated by tilling by ten candidate genes and gene function for brown midrib mutants was identified. In collaboration with university and ARS scientists, 96 sweet sorghum accessions were genotyped with 95 markers to determine their genetic diversity and population structure. These accessions will be used as a panel for association mapping in sweet sorghum. The oil content and fatty acid composition was determined for 48 castor bean and 200 peanut accessions. To determine nutritional value of peanut accessions, over 130 peanut accessions or breeding lines were evaluated for resveratrol and isoflavonoid content, and ratio of oleic/linoelic acid. Genetic variability for mineral, flavonoid, and anthocyanin index were determined for lablab, roselle, and perennial soybean accessions. Genetic relatedness was determined among species of pepper and among species of sweetpotato.


4.Accomplishments
1. Documenting Trait Diversity in Chile Pepper Species. A key factor in the selection and utilization of vegetable crop germplasm is extent and accuracy of the morphological data available. At the present time, little or only limited phenotypic data are available on many vegetable crop accessions. We continued our efforts to characterize vegetable crops germplasm using morphological descriptors and to supplement the documentation of this diversity using digital images that capture key morphological characteristics in 600 accessions of chile pepper (Capsicum annuum) grown in Griffin, GA and Woodland, CA. Several thousand data points and hundreds of digital images have been uploaded into the publicly accessible database. The acquisition of these data will permit a more accurate assessment of the extent of morphological diversity already present in the collection, and will benefit the scientific user community in facilitating the selection of material appropriate for specific research projects.

2. Technique Developed to Detect High Oleic Acid Peanuts. Peanut seeds and peanut oil are composed of several chemically unique fats such as oleic and linoleic fatty acids. The flavor and quality of the seed or the extracted oil is dependent on the ratio of these two fatty acids. Historically, the only method to determine the fatty acid composition was to chemically analyze finely ground up seeds. This research developed a molecular method to rapidly assess peanut accessions or breeding lines for high oleic acid from either the seeds or leaf tissue. This new molecular method is fast and does not destroy the seed, which allows peanut breeders to utilize the plants for breeding purposes or screening for other agronomic traits such as disease resistance. Breeders can rapidly identify the trait of interest and remove undesirable plants in large populations, which ultimately saves time and valuable resources.

3. Acquisition and Availability of Warm-Season Grass Accessions. The warm-season grass collection did not contain adequate numbers of diverse accessions native to the U.S. to meet the needs of requesters. The portion of the warm season grass collection considered native to the U.S. was enhanced by acquiring new material and improving existing material. The switchgrass collection was increased through the addition of 94 accessions collected from areas in the U.S. previously underrepresented including Florida and New York. Availability of material was increased for several native warm season grass species including big bluestem, indiangrass, little bluestem, and side-oats grama through seed increases. Collection site data was obtained from historical data for 1098 big bluestem accessions and made available online. Together, these efforts have increased the availability, broadened the diversity, and enhanced associated information for the native warm season grasses.

4. Flavonoid Variability in Two Hibiscus species. Limited to non-existent data regarding flavonols are available for many Hibiscus species. The flavonols, quercetin and kaempferol, were detected in leaves of two Hibiscus species (H. diversifolius and H. mutabilis) for the first time. These two species can now be used by breeders or other scientists in the development of new flavonol-containing products which may aid human health value as anticancer compounds.

5. Genotyping Diverse Accessions in the U.S. Sweet Sorghum Collection. Sweet sorghum is an important biofuel crop that has not been genotyped, thereby limiting its usefulness to researchers. A panel of 96 sweet sorghum accessions was genotyped with 95 molecular markers to determine the population structure and genetic diversity within this group of accessions. Genotyping of these sweet sorghum accessions will enable sorghum breeders to better develop sweet sorghum cultivars for bioethanol production.

6. Capsiate in Chile Pepper species. The sensory attributes (chemical composition) of vegetables can be an important factor in determining consumer acceptance and demand. The occurrence and concentration of capsiate in chile pepper species was investigated. This compound is related to capsaicin – the compound that confers pungency (heat) to pepper fruit. Data indicated that the levels of capsiate range from not present to moderate when compared to concentrations of capsaicin. Capsiate was present in all of the tested chile pepper species. This information will be of benefit to the study of the biosynthesis of this compound. These data will facilitate efforts to commercially produce capsiate-producing fruit and also to enhance capsiate concentrations in cultivated chile pepper species.

7. Sweetpotato Leaf Curl Virus (SPLCV) in the Sweetpotato Germplasm Collection. The occurrence of virus-infected sweetpotato clones within the germplasm collection poses a risk to sweetpotato growers/researchers who unknowingly receive infected plant materials. Real-time PCR and techniques developed previously were utilized to screen the collection for the occurrence of SPLCV. Approximately 7% of the sweetpotato germplasm collection was found to be infected with SPLCV. This information will be used to restrict distribution of selected clones and modify sweetpotato germplasm distribution policies.

8. Biochemically Evaluate the U.S. Peanut Mini-Core Collection. The U.S. peanut mini-core collection has not been evaluated for biochemical traits that may be useful for improving peanut nutrition. A total of 107 diverse peanut accessions within the mini-core collection were evaluated for oil content, fatty acid composition, and antioxidant compounds. The biochemical information obtained will be very useful to peanut researchers developing highly nutritious peanut cultivars.

9. Using the Waxy Locus to Identify Members of the Capsicum annuum Complex. Certain species of pepper (Capsicum species) can be difficult to identify based on their morphological characteristics. Specific DNA sequence changes within the waxy locus have shown promise in assisting in the identification of these species. Approximately 500 accessions of Capsicum (C. annuum, C. chinense & C. frutescens) were analyzed for variability at this locus. In most, but not all instances, the sequence data supported the existing classification. In some instances, it resulted in a reclassification. Proper classification ensures that distributed plant materials meet the requirements of the requestor.

10. Regeneration of Perennial Hibiscus Species. Some Hibiscus species, including H. ponticus and H. lasiocarpus, are perennial and require special regeneration techniques to produce seed under Georgia conditions. Hibiscus lasiocarpus produced quality seed during the first year, but H. ponticus flower production was too late to produce viable seed in the first year. During the second year of growth, H. ponticus flower production began much earlier and substantial seed quantities were produced. Quality seed are now available to customers for use in their research projects.

11. Sweetpotato Leaf Curl Virus (SPLCV) in the Sweetpotato Germplasm Collection. The occurrence of virus-infected sweetpotato clones within the germplasm collection poses a risk to sweetpotato growers/researchers who unknowingly receive infected plant materials. Real-time PCR and techniques developed previously were utilized to screen the collection for the occurrence of SPLCV. Approximately 7% of the sweetpotato germplasm collection was found to be infected with SPLCV. This information will be used to restrict distribution of selected clones and modify sweetpotato germplasm distribution policies.


Review Publications
Antonious, G., Berke, T., Jarret, R.L. Pungency in Capsicum Chinense: Variation Among Countries of Origin. 2009 Journal of Environmental Science and Health. 44(B)(2): 179-184.

Wang, M.L., Barkley, N.L., Gillaspie, A.G., Pederson, G.A. 2008. Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing.. Genetical Research. 90(6):467-480.

Barkley, N.L., Pinnow, D.L., Wang, M.L., Pederson, G.A. 2009. First Report of Tomato Spotted Wilt Virus Infecting African Clover (Trifolium tembense) in Georgia. Plant Disease. 93(2):202.

Singh, S., Jarret, R.L., Russo, V.M., Majetich, G., Shimkus, J.M., Bushway, R., Perkins, L.B. 2009. Determination of capsinoids by HPLC-DAD in Capsicum species. Journal of Agricultural and Food Chemistry. 57:3452-3457.

Jarret, R.L., Berke, T., Baldwin, E.A., Antonious, G. 2009. Variability for free sugars and organic acids in Capsicum Chinense. Chemistry and Biodiversity. 6:138-145.

Morris, J.B. 2009. Characterization of sesame (Sesamum indicum L.) germplasm regenerated in Georgia, U.S.A.. Genetic Resources and Crop Evolution. 56(7):925-936.

Morris, J.B. 2008. Characterization of regenerated butterfly pea (Clitoria ternatea L.) accessions for morphological, phenology, reproductive and potential nutraceutical, pharmaceutical trait utilization.. Genetic Resources and Crop Evolution. 56:421-427

Morris, J.B., Pederson, G.A., Quesenberry, K., Wang, M.L. 2009. Clover. In R.J.Singh (ed). Genetic Resources, Chromosome Engineering, and Crop Improvement: Forage Crops. p.207-228.

Naeem, M., Khan, M., Morris, J.B. 2009. Agrobotanical attributes, nitrogen-fixation, enzyme activities and nutraceuticals and tyrosinase enzyme of hyacinth bean (Lablab purpureus L.) - a bio-functional medicinal legume.. American Journal of Plant Physiology. 4:58-69.

Jarret, R.L. 2008. DNA Barcoding in a Crop Genebank: Resolving the Capsicum annuum Species Complex.. The Open Biology Journal. 1:35-42.

Wang, M.L., Pinnow, D.L., Barkley, N.L., Pittman, R.N. 2009. Plant Resistance to TSWV and Seed Accumulation of Resveratrol within Peanut Germplasm and Its Wild Relatives in the US Collection. Plant Pathology Journal ISSN 1812-5387 . 8(2):53-61.

Xin, Z., Wang, M.L., Burow, G.B., Burke, J.J. 2009. An induced sorghum mutant population suitable for bioenergy research. BioEnergy Research. 2(1-2):10-16.

Zhenbang, C., Wang, M.L., Waltz, C., Raymer, P. 2009. Genetic Diversity of Warm-Season Turfgrass: Seashore Paspalum, Bermudagrass, and Zoysiagrass Revealed by AFLPs. FLORICULTURE, ORNAMENTAL AND PLANT BIOTECHNOLOGY. Online ISSN 1749-0308 3:1 p.20-24.

Weimer, P.J., Morris, J.B. 2009. Grasses and Legumes for Bio-Based Products. In: Wedin, W.F., Fales, S.L. editors. Grassland: Quietness and Strength for a New American Agriculture. Madison, WI: American Society for Agronomy/Crop Science Society of America/Soil Science Society of America. p. 221-233.

Last Modified: 8/29/2014
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