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United States Department of Agriculture

Agricultural Research Service


Location: Genomics and Bioinformatics Research

2009 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 Mid-South Area Genomics Laboratory (MGL) functions as a fully integrated component of the MSA which provides genomics service for an array of technologies. These services include, but are not limited to, high throughput DNA sequencing, gene expression analysis, bioinformatics, DNA marker development, BAC fingerprinting and high throughput genotyping with DNA markers. 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 service project, progress is measured by the service provided. For the reported time period these 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, B 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 Structure and Quality Research Unit, Service: D Crop Genetics and Production Research Unit, Service: D, G, B, M Crop Improvement and Protection Research Unit, Service: D Dale Bumpers National Rice Research Center Service: D Endemic Poultry Viral Disease Research Unit, Service: D,B Floral and Nursery Plants Research Unit, Service: M, G Genetics and Precision Agriculture Research, Service: D, B Natural Products Utilization Research Unit, Service: D Plant Genetic Resources, Genomics and Genetic Improvement, Service: D Southern Horticultural Laboratory, Service: G,M,B Southern Insect Management Research Unit, Service: D,G,B Southern Weed Science Research Unit, Service: D Soybean Genomics and Improvement, Service: D, B Subtropical Horticulture Research Station, Service: B,G,M Sugarcane Field Station, Service: D,G,M Sugarcane Research Unit, Service: G This project has a component of rice research which has been supported through various Specific Cooperative Agreements (6402-21310-002-07, Establishment of Marker Assisted Rice Breeding Programs in Mississippi and Missouri; 6402-21310-002-03, Mining Novel Blast Resistance Genes for Use in U.S. Breeding; 6402-21310-002-05, The Mississippi Rice Variety Acceleration Breeding Project). This research has revolved around mapping blast resistance, sheath blight resistance, and milling quality. In addition there has been a component for the integration of DNA markers into the Mississippi rice breeding program. In the past year this work was extremely important as it helped show that specific fields for Foundation seed production were not contaminated with “red rice”. A new component of single nucleotide polymorphism (SNP) discovery was incorporated into two of the SCAs. There is also a component in this project for biophotonics research which is handled through a Specific Cooperative Agreement with Mississippi State University (6402-21210-003-01S Biophotonics – The Application of Novel Imaging Methodologies to Livestock Production Research).

4. Accomplishments
1. Improvement in DNA Marker Development. DNA markers are a needed tool for many research problems of agriculturally important species; however, the methodology of marker development and validation is complex and cost prohibitive for many laboratories. Therefore, a better process is needed for DNA marker development. An improved methodology was developed for the isolation of Simple Sequence Repeats (SSRs) which is a specific class of DNA markers. This methodology overcame some obstacles in previous procedures and offers an economical method for the development of DNA markers for the Agency in an array of species. The process was further improved by the development of bioinformatic program that helps in the identification of markers that provide the most useful/diverse genetic information. All of this was achieved through the research efforts of a postdoc sponsored through ARS Headquarters Funded Postdoc Program. The methods have already been applied to Cercis canadiensis (redbud), Gossypium barbadense (cotton), Ipomoea batatas (sweet potato), Lolium multiflorum (ryegrass), Macrophomina phaseolina (Charcoal rot), Mangifera indica (mango), Puccinia kuehnii (orange rust, pathogen), Rotylenchulus reniformis (reniform nematode), Chionanthus retusus (fringetree, medicinal/ornamental), Cyperus rotundus (nutsedge, weed) and the markers are being applied by various scientists to further their research efforts.

Review Publications
Arias, R.S., Ballard, L.L., Scheffler, B.E. 2009. UPIC: How Many SSR Markers to Run. Bioinformation 3(8):352-360,

Wang, X., Wadl, P.A., Rinehart, T.A., Scheffler, B.E., Windham, M.T., Spiers, J.M., Johnson, D.H., Trigiano, R.N. 2008. A linkage map for flowering dogwood (cornus florida l.) based on microsatellite markers. Euphytica. 165:165-175.

Gutierrez, O.A., Stelly, D.M., Saha, S., Jenkins, J.N., McCarty Jr., J.C., Raska, D.A., Scheffler, B.E. 2009. Integrative placement and orientation of non-redundant SSR loci in cotton linkage groups by deficiency analysis. Molecular Breeding. 23:693-707.

Tucker, M.L., Puthoff, D.P., Neelam, A., Ehrenfried, M.L., Scheffler, B.E., Ballard, L.L., Campbell, K.B., Cooper, B. 2008. Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi. Phytopathology. 98:1126-1135.

Abdurakhmonov, I.Y., Saha, S., Jenkins, J.N., Buriev, Z.T., Shermatov, S.E., Scheffler, B.E., Pepper, A.E., Yu, J., Kohel, R.J., Abdukarimov, A. 2009. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica. 136:401-417.

Lee, J., Campbell, K., Scheffler, B.E., Feng, J., Naiman, D.Q., Garrett, W.M., Thibivilliers, S., Stacey, G., Tucker, M.L., Pastor Corrales, M.A., Cooper, B. 2008. Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus. Molecular and Cellular Proteomics. 8:19-31.

Dong, W., Wang, L., Thornton, C., Scheffler, B.E., Willett, K.L. 2008. Benzo(A)pyrene Decreases Brain and Ovarian Aromatase mRNA Expression. Aquatic Toxicology.

Ryan, P.L., Christiansen, D.L., Hopper, R.M., Bagnell, C.A., Vaala, W.E., Leblanc, M.M. 2009. Evaluation of Relaxin Blood Profiles of Horses as A Means of Assessing Placental Function in High-Risk Pregnancies And Responsiveness to Therapeutic Strategies. Annals of the New York Academy of Sciences. 1160:169-178.

Bowers, S., Gandy, S., Anderson, B., Ryan, P., Willard, S. 2009. Assessment Of Pregnancy in the Late Gestation Mare Using Digital Infrared Thermography. Theriogenology. 72(3):372-377.

Jung, S.Y., Willard, S.T. 2009. The Effect of Culture Methods and Serum Supplementation on Developmental Competence of Bovine Embryos Cultured In Vitro. Journal of Animal and Veterinary Advances. 8(1):67-74.

Jung, S.Y., Bowers, S.D., Willard, S.T. 2009. Simulated Microgravity Influences Bovine Oocyte In Vitro Fertilization and Preimplantation Embryo Development. Journal of Animal and Veterinary Advances 8(9):1807-1814.

Moulton, K., Ryan, P., Christiansen, D., Hopper, R., Klauser, C., Bennett, W., Rodts-Palenik, S., Willard, S. Hormonal Profiles of Late Gestation Ewes Following Intra-Uterine Inoculation With and Without Lux-Modified Escherichia Coli. Journal of Reproduction and Development 55(1):55-62.

Moulton, K., Ryan, P., Lay Jr, D.C., Willard, S. 2009. Postmortem Photonic Imaging of Lux-Modified Salmonella Typhimuium Within the Gastrointestinal Tract of Swine Following Oral Inoculation In Vivo. Journal of Animal Science 87:2239-2244.

Last Modified: 05/21/2017
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