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United States Department of Agriculture

Agricultural Research Service


Location: Genomics and Bioinformatics Research

2012 Annual Report

1a. Objectives (from AD-416):
Utilization and development of bioinformatic and genomic tools/information to support structural analysis of plant and animal genomes. This includes the generation of DNA sequences and subsequent analysis. Development and implementation of DNA markers for development of superior cultivars (e.g., superior yield, improved quality, or resistance to the biotic or abiotic factors) or germplasm/population/species characterization. Both marker data and DNA sequences will be used for genome structure analysis.

1b. Approach (from AD-416):
The Genomics and Bioinformatics Research Unit conducts research in the area of genomics and bioinformatics for an array of species and topics. It also acts as a fully integrated component of the Mid South Area by providing genomics research support for an array of technologies and research projects. The support includes, but is not limited to high throughput DNA sequencing, gene expression analysis, bioinformatics, DNA marker development, BAC fingerprinting and high throughput genotyping with DNA marker. The centralization of these operations assures that all research projects in the MSA that could benefit from these genomic tools have access to the technology, that there is no unnecessary duplication of equipment within the Area, and there is maximum utilization and conservation of funding.

3. Progress Report:
As a research project, progress is measured by the service provided. For the reported time period these ARS locations had significant amount of DNA sequencing (D), genotyping (G), bioinformatics (B) and/or DNA marker development (M) processed through the Laboratory: Animal Waste Management Research Unit, Service: D Aquatic Animal Health Research Unit, Service: D Biological Control of Pests Research Unit, Service: D Catfish Genetics Research Unit, Service: D,B,G, Commodity Utilization Research Unit, Service: D Coastal Plains Soil, Water, and Plant Research Center, Service: D Corn Host Plant Resistance Research, Service: D,B Cotton Fiber Bioscience Research Unit. Service: D, G Crop Genetics and Breeding Research, Service: D, B, M Crop Genetics Research Unit, Service: D, G, B, M Crop Germplasm Research, Service: G Dale Bumpers National Rice Research Center: D, M Endemic Poultry Viral Disease Research Unit, Service: D,B Food Processing and Sensory Quality Research Unit, Service: D Genetics and Precision Agriculture Research, Service: D Natural Products Utilization Research Unit, Service: D, National Peanut Research Lab, Service: D, G, B, M Poultry Microbiological Safety Research, Service: d Southern Insect Management Research Unit, Service: D,B Soybean Genomics and Improvement, Service: D, B Subtropical Horticulture Research Station, Service: G, Sugarcane Field Station, Service: D,G, Sugarcane Research Unit, Service: G Sunflower Research Unit, Service: D Tropical Agriculture Research Station, Service: B,D,G,M Tropical Plant Genetic Resources and Disease Research Unit: G DNA marker development, validation, and utilization, is an important output component of the unit. This is often in conjunction with its service component and impact most of the major crops within the Mid-South Area like cotton and soybean. In the past year work was conducted on yam and tepary bean. Yam is a very important carbohydrate crop for many world agricultural systems. DNA markers were processed on a yam mapping population related to anthracnose resistance. Tepary bean is a plant native to southwest part of the USA and thus has important traits related to drought and heat tolerance. It is also known to be an excellent source of disease resistance genes for crop species like common bean. DNA markers were developed, validated and tested on small germplam collection illustrating they can be used on the larger U.S. collection. Another major output of the unit is DNA sequencing. In January a project was started to sequence the ends of 100,000 Bacterial Artificial Chromosomes (BACs) which will be useful for sequence the genome of upland cotton. The use of next generation DNA sequencing has greatly increased in the past year for cotton and insects. It is anticipated that this trend will only increase as more samples for other species are submitted, e.g. peanut, maize and soybean.

4. Accomplishments
1. Germplasm conservation of breadfruit and jackfruit through DNA markers. Germplasm conservation of breadfruit and jackfruit through DNA markers. Germplasm collections are hampered by the goal to preserve the maximum amount of genetic diversity with limited resources to maintain many accessions. DNA markers can be used to determine a general relationship of one accession to another and the preservation techniques and regeneration schedule can be prioritized based on this relationship. Using DNA markers, approximately 400 accessions of breadfruit and jackfruit, part of which constitute the U.S. collection, were characterized for genetic relationship.Breadfruit and jackfruit are important staple items in the diets of some cultures, and the information in this study should help in the preservation of the genetic resources of these species.

Review Publications
Arias, R.S., Molin, W.T., Ray, J.D., Peel, M., Scheffler, B.E. 2011. Isolation and characterisation of the first microsatellite markers for Cyperus rotundus. Weed Research. 51:451-460.

Nelson, J.C., Jodari, F., Roughton, A.I., McKenzie, K.S., McClung, A.M., Fjellstrom, R.G., Scheffler, B.E. 2012. QTL mapping for milling quality in elite western U.S. rice germplasm. Crop Science. 52:242-252.

Thomson, M.J., Zhao, K., Wright, M., McNally, K.L., Rey, J., Tung, C., Reynolds, A., Scheffler, B.E., Eizenga, G.C., McClung, A.M., Kim, H., Ismail, A.M., Ocampo, M., Mojica, C., Reveche, M., Dilla-Ermita, C.J., Mauleon, R., Leung, H., Bustamante, C., McCouch, S.R. 2011. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 29:875-886. doi: 10.1007/s11032-011-9663-x.

Dean, D., Wadl, P.A., Trigiano, R., Wang, X., Klingeman, W., Ownley, B.H., Rinehart, T.A., Scheffler, B.E. 2011. Screening and characterization of eleven novel microsatellite markers from Viburnum dilatatum. HortScience. 46(11):1456-1459.

Nelson, J., Oard, J.H., Groth, D., Utomo, H., Jia, Y., Liu, G., Moldenhauer, K.K., Correa-Victoria, F.J., Fjellstrom, R.G., Scheffler, B.E., Prado, G.A. 2012. Sheath-blight resistance QTLs and in japonica rice germplasm. Euphytica. 184:23-24. 10.1007/s10681-011-0475-1.

Solomon, W.L., Kanter, D.G., Walker, T.W., Baird, III, G.E., Scheffler, B.E., Lanford, L.S., Shaifer, S. 2012. Registration of "Rex" Southern Long-Grain Rice. Journal of Plant Registrations. 6(1).

Trigiano, R.N., Wadl, P.A., Dean, D., Hadziabdic, D., Scheffler, B.E., Runge, F., Telle, S., Thines, M., Ristaino, J., Spring, O. 2012. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. Mycological Society of America. 104(3):633-640.

Arias, R.S., Blanco, C.A., Portilla, M., Snodgrass, G.L., Scheffler, B.E. 2011. First microsatellites from Spodoptera frugiperda (Lepidoptera: Noctuidae) and their potential use for population genetics. Annals of the Entomological Society of America. 104(3):576-587.

Hadziabdic, D., Wadl, P.A., Boggess, S.L., Scheffler, B.E., Windham, M.T., Trigiano, R.N. 2011. Development and characterization of sixteen microsatellite loci for Geosmithia morbida, the causal agent of thousand canker disease in black walnut (Juglans nigra). Conservation Genetics. 4(2):287-289.

Wadl, P.A., Dattilo, A.J., Scheffler, B.E., Trigiano, R.N. 2011. Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)1. American Journal of Botany. 0:e1-e4.

Yu, J., Fang, D.D., Kohel, R.J., Ulloa, M., Hinze, L.L., Percy, R.G., Zhang, J., Chee, P., Scheffler, B.E., Jones, D.C. 2012. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica. 187(2):203-213.

Last Modified: 06/26/2017
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