2011 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, bioenergy crops, 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. Conserve and distribute genomic research genetic stocks including association mapping populations of sorghum and other crops. Regenerate, conserve, and distribute more than 88,000 accessions of specialty crops, bioenergy crops, and other 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.
A total of 90,942 accessions of 1,534 plant species were maintained in the Griffin plant genetic resources collection. Over 87.7% of accessions were available for distribution to users and over 97.1% were backed up for security at a second location. Bulk seed samples for 66,995 accessions were maintained at -18 C for long-term storage with seed of the remaining accessions stored at 4 C. A total of 28,308 seed and clonal accessions in 925 separate orders were distributed upon request to scientists and educators in 49 U.S. states and 47 foreign countries. Acquisitions made to the collection included 143 sorghum, 144 warm-season grass, 19 vegetable and 2 other accessions. A plant collection trip was conducted in Alabama, Florida, Georgia, and South Carolina for naturalized Sorghum halepense germplasm that is in demand for sorghum gene flow studies. Seed regenerations and characterization were conducted on 299 peanut, 131 cowpea, 46 warm-season grass, 60 pepper, 361 legume, new, and misc. crop, 91 annual clover, and 30 other vegetable accessions. Over 300 pepper accessions were grown in the field for regeneration, characterization and recording of digital images. Digital images of cowpea, sorghum, cucurbit, and watermelon accessions, and pepper capsaicin content, peanut core selection, sorghum, and sweet sorghum data were added to the Germplasm Resources Information Network (GRIN). Long-term maintenance of 241 wild peanut and 458 warm-season grass accessions was continued in the greenhouse. Over 30 warm-season grass accessions and 712 sweetpotato accessions were maintained in tissue culture with eight replications of each sweetpotato clone. Germination testing has been completed for 69,556 accessions (over 77% of collection) since 2002. In cooperation with vegetable industry plant pathologists, differential sets of four vegetable crops are being established and distributed to researchers for identification of disease races. Fatty acid content was determined for the entire U.S. castor bean (over 1,000 accessions) and sesame (over 1,200 accessions) collections and 98 okra accessions. Over 660 castor accessions were genotyped with 15 Simple Sequence Repeats (SSR) markers for further genetic classification. A population of over 1,900 mutant watermelon seeds were developed for a mutant Targeting Induced Local Lesions in Genomes (TILLING) study with ARS cooperators in Charleston, SC. Ploidy level was determined for the entire St. Augustine and seashore paspalum grass collections. Photoperiod-sensitive Neonotonia, Teramnus, and annual clover accessions were successfully regenerated in the greenhouse. A total of 92 peanut accessions were successfully evaluated under quarantine and disease-free seed was produced. In association with Kansas State University scientists, 1,000 biomass sorghum accessions will be evaluated for plant morphology, biochemical composition, and genotype.
Phenotyping and genotyping peanut genetic resources. The high oleic trait in peanut is an important seed quality trait caused by two key mutations in the ahFAD2 gene. The nine genotypes that can be produced by crossing normal oleic to high oleic peanuts have never been characterized because there was not a method developed to track all possible genotypes and link them to each phenotype. Therefore, a method was developed to detect all genotypes and the resulting phenotype (fatty acid composition) of each possible genotype was quantified in 500 individuals. This study demonstrated that the genetics of the trait were more complex than previously thought. Further, being able to detect all possible genotypes can now expedite the breeding process by allowing unwanted characteristics to be purged from the population at early stages and only maintaining and evaluating the plants with the desired traits. This data provided information on the genetics controlling the trait, a method to detect all possible genotypes, and linked a phenotype with each respective genotype.
Oil content in seed of watermelon species. Watermelon (Citrullus spp.) is cultivated primarily in Africa for its use as an oil seed crop with oil having industrial and nutritional value. ARS researchers at Griffin, GA, evaluated more than 1,000 accessions of various watermelon species for total oil content using nuclear magnetic resonance (NMR). Data indicated that total oil content varied from approximately 14% to >40%. Seed of egusi-type melons were notably higher in oil content than other types. This information will enable researchers to select watermelon accessions with potential for use as an oil seed crop.
Seashore paspalum salt tolerance and ploidy level. Plant breeders need to know the number of chromosome sets or ploidy level of accessions in order to produce fertile or sterile progeny. The ploidy level and salt tolerance of the entire U.S. seashore paspalum collection was determined. The ploidy level and salt tolerance data will enable plant breeders to efficiently use the proper accessions within their breeding program.
Capsaicin and Capsiate in Capsicum species. The sensory attributes (chemical composition) of vegetables can be an important factor in determining consumer acceptance and demand. The genetic basis for the preferential synthesis of capsiate rather than capsaicin was investigated in a mutant line of chile pepper (Capsicum annuum). Capsiate is a non-pungent analog of capsaicin with documented medicinal properties. Data indicated that the mutation is inherited as a single recessive gene. Portions of the gene were sequenced and the mutate allele characterized. This information will be of benefit to those developing pepper lines or varieties enhanced for either of these compounds.
Alternate utilization of non-viable peanut seeds. The USDA maintains a germplasm collection of Arachis species which contains cultivated and wild peanuts. However, due to the high oil content in these seeds, the germination rate is known to drastically decline after 10-15 years or more of cold storage. Low or zero viability (non-viable) seeds are often deemed useless in germplasm repositories. ARS scientists at Griffin, GA, demonstrated that high quality Deoxyribo Nucleic Acid (DNA) can be obtained from non-viable seeds in wild and cultivated peanuts. The extracted DNA can be successfully used to reveal differences among individuals. This study shows that non-viable seed can be successfully used in molecular research.
Fatty acid content of the U.S. sesame and castor bean collections. Plant accessions need to have not only high oil content, but proper fatty acid content to be utilized for biodiesel production. Oil content had previously been determined for the entire U.S. sesame and castor bean collections. ARS researchers at Griffin, GA, identified a sesame accession with both high oil and high oleic acid content, and a castor bean accession with high oil content and desirable fatty acid composition. These accessions will be useful for researchers developing crop cultivars suitable for biodiesel production from these plant species.
Morris, J.B., Wang, M.L., Morse, S.A. 2011. Ricinus. Wild Crop Relatives: Genomic and Breeding Resources. 3:251-260.
Morris, J.B., Wang, M.L. 2011. Evaluation for morphological, reproductive, anthocyanin index, and flavonol traits in ornamental and nutraceutical producing Hibiscus species. Ornamental Plants: Types, Cultivation and Nutrition. Hauppauge, NY: Nova Publishers. p.111-127.
Morris, J.B. 2011. Morphological, phenological, and peproductive trait analysis for the pasture species, Siratro [Macroptilium atropurpureum (DC.) Urb.]. Tropical Grasslands. 44:266-273.
Gremillion, S.K., Culbreath, A.K., Gorbet, D.W., Mullinix Jr, B.G., Pittman, R.N., Stevenson, K.L., Todd, J.W., Escobar, R.E., Condori, M.M. 2011. Field evaluations of leaf spot resistance and yield in peanut genotypes in the United States and Bolivia. Plant Disease. 95(3):263-268.
Barkley, N.L., Wang, M.L., Pittman, R.N. 2011. A real-time PCR genotyping assay to detect FAD2A SNPs in peanuts (Arachis hypogaea L.). Electronic Journal of Biotechnology. 14(1). Available: http://www.ejbiotechnology.info/index.php/ejbiotechnology/issue/view/65.
Jarret, R.L., Wang, M.L., Levy, I.J. 2011. Seed oil and Fatty acid content in okra (Abelmoschus esculentus) and related species. Journal of Agricultural and Food Chemistry. 59(8):4019-4024.
Chen, X., Wang, M.L., Holbrook Jr, C.C., Culbreath, A., Liang, X., Brennenman, T., Guo, B. 2010. Identification and characterization of a multigene family encoding germin-like proteins in cultivated peanut (Arachis hypogaea L.). Plant Molecular Biology Reporter. 29:389-403.
Antonious, G.F., Snyder, J.C., Burke, T., Jarret, R.L. 2010. Screening Capsicum chinense fruits for heavy metals bioaccumulation. Journal of Environmental Health. 45:562-571.
Wang, M.L., Morris, J.B., Pinnow, D.L., Davis, J., Raymer, P., Pederson, G.A. 2010. A survey of the castor oil content, seed weight and seed-coat colour on the United States Department of Agriculture germplasm collection. Plant Genetic Resources: Characterization and Utilization. 8:229-231.
Wang, M.L., Barkley, N.L., Chinnan, M., Stalker, T., Pittman, R.N. 2010. Oil content and fatty acid composition variability in wild peanut species. Plant Genetic Resources. 8:232-234.
Morris, J.B., Wang, M.L. 2011. Anthocyanin indexes, quercetin, kaempferol, and myricetin concentration in leaves and fruit of Abutilon theophrasti Medik. genetic resources. Plant Genetic Resources: Characterization and Utilization. 1:1-3.
Wang, M.L., Barkley, N.L., Chen, Z., Pittman, R.N. 2011. FAD2 Gene Mutations Significantly Alter Fatty Acid Profiles in Cultivated Peanuts (Arachis hypogaea). Biochemical Genetics. 49:748-759.
Wang, M.L., Sukumaran, S., Barkley, N.L., Chen, Z., Chen, C.Y., Guo, B., Pittman, R.N., Stalker, H., Holbrook Jr, C.C., Pederson, G.A., Yu, J. 2011. Population structure and marker-trait association analysis of the U.S. Peanut (Arachis hypogaea L.) mini-core collection. Journal of Theoretical and Applied Genetics. 123:1307-1317.