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United States Department of Agriculture

Agricultural Research Service


Location: Genomics and Bioinformatics Research

2013 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 service in-house project, progress is measured by the service provided. For the five year in-house project cycle these ARS locations had significant amount of DNA sequencing (D), high throughput sequencing (HD), 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 Warmwater Aquaculture Research Unit, Service: D, B, G, HD, M 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, Services: D Cotton Fiber Bioscience Research Unit, Service: D, G Crop Genetics and Production Research Unit, Service: D, G, B, M Crop Improvement and Protection Research Unit, Service: D Crop Genetics and Breeding Research, Service: D, B, M, HD Crop Germplasm Research, Service: G Dale Bumpers National Rice Research Center: D, M, B Endemic Poultry Viral Disease Research Unit, Service: D, B Floral and Nursery Plants Research Unit, Service: M, G Food and Feed Safty Research Unit, Service: D Food Processing and Sensory Quality Research Unit, Service: D Formosan Subterranean Termite Research Unit, Service: G Genetics and Precision Agriculture Research, Service: D, B, G Natural Products Utilization Research Unit, Service: D, HD, M National Center for Cool and Cold Water Aquaculture, Service: HD National Peanut Research Lab, Service: D, G, B, M, HD Plant Genetic Resources, Genomics and Genetic Improvement, Service: D Plant Stress and Germplasm Development Unit, Service: B Poultry Microbiological Safety Research, Service: D Southern Horticultural Laboratory, Service: G, M, B Southern Insect Management Research Unit, Service: D, G, B, HD, M 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 Sunflower Research Unit, Service: D, HD Tropical Agriculture Research Station, Service: B, D, G, M Tropical Plant Genetic Resources and Disease Research Unit: G In addition, the in-house project was involved in several scientific efforts over the course of the project. These included but are not limited to: 1) Mapping of genes involved in sheath blight resistance and milling quality for rice; 2) Resequencing of rice lines that help lead to an advanced DNA marker format for rice breeders and identification of candidate genes for sheath blight resistance; 3) Contributed sequencing data to the completed genomes of cacao and cotton; 4) Characterization of ~2000 cotton germplasm accessions with ~100 DNA markers; 5) Developed, characterized and published on DNA markers for over 13 species; and 6) Generation of DNA sequences from ~98,779 long insert DNAs (BAC ends) of cotton for genome assembly.

4. Accomplishments
1. Release of a gold standard D genome of cotton. Knowing the genome sequence of species allows for advanced breeding techniques and gene discovery. In the case of cotton, the D genome represents a progenitor species that possibly contributed its genome to tetraploid (two genomes together) cultivated cotton. The genome assembly was conducted by a large number of international groups. ARS scientists in Stoneville, MS, in cooperation with Mississippi State University, contributed whole shotgun genome sequence of several related cotton species, which was important for comparative genome analysis. The whole group developed a high quality reference genome of a diploid cotton species. The data by ARS and cooperators provided insight into unexpected genome changes in tetraploid cotton. A reference genome is an invaluable tool for gene discovery and placement of genes within a genome. It also allows for easier DNA marker development with known locations. While this is only a progenitor diploid genome, the data is already being used by cotton scientists to improve cultivated cotton.

2. Providing critical DNA sequences to act as a scaffold for a tetraploid cotton genome. Assembling a genome of cultivated cotton is difficult because cotton is a tetraploid (two genomes from different species). Cotton DNA can be cloned as large fragments in Bacterial Artificial Chromosomes (BACs) and the ends of the DNA fragments then sequenced. An ARS scientist at Genomics and Bioinformatic Research Unit in Stoneville, MS, collaborated with a Clemson University scientist to generate a total of 197,559 iBAC end sequences. The BACs were also put into a physical map which is basically lining the BACs into the correct order covering the genome. The estimated distance between BAC ends is 12,276 bp. This will be critical information in assembling the cotton genome as these mapped sequences will act as a framework in which to align shorter DNA fragments into the correct orientation and location, thus making it possible to sequence and assemble a tetraploid cotton genome.

3. The complete cacao genome of the clone 'Matina 1-6' was released. Cacao represents an important crop to U.S.A. manufacturers in the area of confectionary products. However, cacao is produced in sub-tropical locations where it faces numerous challenges including disease pressure, production restraints, and quality issues. To improve cacao breeding efforts a high quality genome is needed. A team led by ARS scientists from Subtropical Horticulutre Research Unit, Miami, FL, and Genomics and Bioinformatic Reaearch Unit, Stoneville, MS, assembled, annotated and released the Matina 1-6 genome in a user friendly database. A 6,000 Single-nucleotide polymorphism (SNP) Illumina chip was designed and used on over 1,000 genotypes. Three fully saturated linkage maps were produced using the SNP and Simple Sequence Repeats (SSRs) markers and these were used to complement the genome assembly and to refine the quantitative trait loci for resistance to several diseases.

Review Publications
Nguyen, T., Collins-Silva, J.E., Macrander, J., Yang, W., Nazarenus, T.J., Nam, J., Jaworski, J.G., Lu, C., Scheffler, B.E., Mockaitis, K., Cahoon, E.B. 2013. Camelina seed transcriptome: Tool for meal and oil improvement and translational research. Plant Biotechnology Journal. pp. 1-11.

Paterson, A.H., Wendel, J.F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K.C., Shu, S., Udall, J., Duke, M.V., Scheffler, B.E., Scheffler, J.A. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 492:423-428.

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. Mycologia. 104(3):633-640.

Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2012. Genome-wide identification of differentially expressed genes under water deficit stress in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Plant Biology. Available:

Pastor, S., Sethumadhavan, K., Ullah, A.H.J., Gidda, S., Cao, H., Mason, C., Chapital, D., Scheffler, B., Mullen, R., Dyer, J., Shockey, J. 2013. Molecular properties of the class III subfamily of acyl-coenyzme A binding proteins from tung tree (Vernicia fordii). Plant Science. 203-204:79-88.

Fang, X., Thornton, C., Scheffler, B.E., Willett, K.L. 2013. Benzo[a]pyrene decreases global and gene specific DNA methylation during zebrafish development. Environmental Toxicology and Pharmacology. p. 40-50.

Silva, J., Scheffler, B.E., Sanabria, Y., De Guzman, C., Galam, D., Farmer, A., Woodward, J., May, G., Oard, J. 2012. Identification of Candidate Genes in Rice for Resistance to Sheath Blight Disease by Whole Genome Sequencing. Journal of Theoretical and Applied Genetics. 124(1):63-74.

Last Modified: 05/23/2017
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