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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND BIOINFORMATICS RESEARCH IN AGRICULTURALLY IMPORTANT ORGANISMS

Location: Genomics and Bioinformatics Research Unit

2011 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 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 Research Unit, Service: D, G, B Crop Germplasm Research, Service: G Dale Bumpers National Rice Research Center: D Food Processing and Sensory Quality Research Unit, Service: D Formosan Subterranean Termite Research Unit: G Genetics and Precision Agriculture Research, Service: D Natural Products Utilization Research Unit, Service: D, Southern Insect Management Research Unit, Service: D,B 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 Tropical Agriculture Research Station, Service: B,D,G,M Tropical Plant Genetic Resources and Disease Research Unit: G

DNA marker development, validation, and utilization, has become an important output component of the unit. In the past year a rice breeders Single Nucleotide Polymorphism (SNP) chip was developed in an international effort in which Genomics and Bioinformatics Research Unit (GBRU) participated by providing resequencing data and validation of a chip designed for U.S.A. breeders in cooperation with the Dale Bumpers National Rice Research Center and Cornell University.

DNA markers can be used for many purposes and three major ones are for identification, classification of relationship or for associating a DNA marker with a physical trait. Three large studies are in progress that are near completion. One involves over 2,000 cotton accessions and almost 100 DNA markers. This work is joint effort with the Cotton Fiber Bioscience Research Unit and Crop Germplasm Research Unit and will represent the largest publically effort to characterize cotton germplasm. Another study involves the characterization of the U.S.A. germplasm collection of tropical bamboos and related species. This is done in conjunction with the Tropical Agriculture Research Station. A different study is examining the relationship of almost 400 accessions of breadfruit and jackfruit of which approximately half are in germplasm collections in the U.S.A. This is done in conjunction with the Tropical Agriculture Research Station, Tropical Plant Genetic Resources and Disease Research Unit, Northwestern University, the Chicago Botanic Garden and the National Tropical Botanical Garden.


4.Accomplishments
1. Development of an advanced DNA marker format for rice breeders. The development of new cultivars can be greatly enhanced through the use of DNA markers. If a DNA marker can be associated with a physical trait, like disease resistance, it can be used as a selection tool to make breeding efforts faster and more cost effective. DNA markers can also be used for the introduction of traits from exotic germplasm and assist with the rapid conversion of the material into desirable cultivars. A limitation in rice has been the availability of a rapid and cost effective DNA marker system. Using DNA resequencing data from a number of sources (the vast majority of the U.S.A. relevant rice data was provided by Genomics and Bioinformatics Research Unit (GBRU)) rice breeders’ Single Nucleotide Polymorphism (SNP) chips were developed, with Cornel University leading an international effort. Validation of the U.S.A. relevant SNP chip was conducted by ARS scientist at Stoneville, MS, GBRU unit with rice DNA provided by the Dale Bumpers National Rice Research Center. Having a rice breeder’s SNP chip can drastically increase the rate at which important traits can be associated with a DNA marker (a reduction of months to days) and with a price reduction of at least 50%. The use of the SNP chip in introgression efforts of important traits can reduce the timeline of breeding a new cultivar by years.

2. Release of the draft Cacao genome. Cacao is the tree that produces the bean used in chocolate production. While it is an economically very important plant, little has been done to develop advanced genomic tools for breeding purposes. This is very important as worldwide cacao production is threatened by emerging disease problems and there is a limit to worldwide production. ARS scientist at Stoneville, MS, in cooperation with a multi-institutional group (Subtropical Horticulture Research Station, MARS, IBM, Indiana University, Clemson University, National Center for Genomics Resources and HudsonAlpha) released a draft genome of cacao three years ahead of schedule. This effort represented a unique public and private industry effort to release a plant genome with no proprietary rights. The genome has already been used to develop a high density genetic map and to characterize some of the genomic regions associated with agronomically important traits. The availability of a cacao genome is already greatly enhancing breeding efforts to produce cultivars with superior traits and productivity.


Review Publications
Fang, X., Dong, W., Thornton, C., Scheffler, B.E., Willet, K. 2010. Benzo(A)pyrene induced glycine N-methyltransferase messenger rna expression in Fundulus heteroclitus embryos. Marine Environmental Research. 69:274-276.

Arias, R.S., Ray, J.D., Mengistu, A., Scheffler, B.E. 2011. Discriminating microsatellites from Macrophomina phaseolina and their potential association to biological functions. Plant Pathology. 60(4):709-718 DOI:10.1111/j.1365-3059.2010.02421.x.

Narina, S.S., Buyyarapu, R., Kottapalli, R., Sartie, A.M., Moahmed, A., Asiedu, R., Mignouna, H., Sayre, B., Scheffler, B.E. 2011. Generation and analysis of expressed sequence tags(ESTs) for marker development in yam (Dioscores alata L.). Biomed Central (BMC) Genomics. 1471-2164.

Wadl, P.A., Dean, D., Li, Y., Vito, L.M., Scheffler, B.E., Hadziabdic, D., Windham, M.T., Trigiano, R.N. 2011. Development and characterization of microsatellites for switchgrass rust fungus (Puccinia emaculata). Conservation Genetics. 3:185–188.

Arias, R.S., Techen, N., Rinehart, T.A., Olsen, R.T., Kirkbride, J.H., Scheffler, B.E. 2010. Development of simple sequence repeat markers for Chionanthus retusus (Oleaceae) and effective discrimination of closely related taxa. HortScience. 46(1):23-29.

Arias, R.S., Stetina, S.R., Scheffler, B.E. 2011. Comparison of whole-genome amplifications for microsatellite genotyping of Rotylenchulus reniformis. Electronic Journal of Biotechnology. DOI:10.2225/vol14-issue3-fulltext-13.

Han, K.M., Dharmawardhana, P., Arias, R.S., Ma, C., Busov, V., Strauss, S.H. 2011. Gibberellin-associated cisgenes modify growth, stature and wood properties in Populus. Plant Biotechnology Journal. 9(2):162-178.

Blanco, C., Portilla, M., Jurat-Fuentes, J., Sanchez, J.F., Viteri, D., Vega-Aquin, P., Teran-Vargas, A.P., Azuara-Dominguez, A., Lopez, J., Arias De Ares, R.S., Zhu, Y., Barrera, D., Jackson, R.E. 2010. Susceptibility of Spodoptera frugiperda (Lepidoptera: noctuidae) isofamilies to Cry1Ac and Cry1F proteins of Bacillus thuringiensis. Southwestern Entomologist. 35(3):409-415.

Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Identification of the family of aquaporin genes and their expression in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Plant Biology. 10:142.

Blacklock, B.J., Scheffler, B.E., Shepard, M.R., Jayasuriya, N., Minto, R.E. 2010. Functional diversity in fungal fatty acid synthesis. The first acetylenase from the Pacific Golden Chanterelle, Cantharellus formosus. Journal of Biological Chemistry. 287(37):28442-28449.

Brooks, J.P., McLaughlin, M.R., Scheffler, B.E., Miles, D.M. 2010. Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house. Science of the Total Environment. 408:4770-4777.

Day, J.M., Ballard, L.L., Duke, M.V., Scheffler, B.E., Zsak, L. 2010. Metagenomic analysis of the turkey gut RNA virus community. Virology Journal. 7:313.

Wang, X., Wadl, P.A., Cabrera, R.I., Pounders Jr, C.T., Scheffler, B.E., Pooler, M.R., Rinehart, T.A., Trigiano, R.N. 2011. Evaluation of genetic diversity and pedigree within crapemyrtle (Lagerstroemia spp.) cultivars using simple sequence repeat (SSR) markers. Journal of the American Society for Horticultural Science. 136(2):116-128.

Wang, X., Dean, D., Wadl, P., Hadziabdic, D., Scheffler, B.E., Rinehart, T.A., Trigiano, R. 2010. Development of microsatellite markers from Crape Myrtle (Lagerstroemia L.). HortScience. 45(5):842-844.

Rinehart, T.A., Trigiano, R., Wadl, P., Hadziabdic, D., Pooler, M.R., Scheffler, B.E. 2010. Characterization of twelve microsatellite markers for the native redbud tree (Cercis canadensis). Molecular Ecology Resources. 10(4):751-754.

Nelson, J.C., McClung, A.M., Fjellstrom, R.G., Moldenhauer, K.K., Boza, E., Jodari, F., Oard, J.H., Linscombe, S., Scheffler, B.E., Yeater, K.M. 2011. Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm. Theoretical and Applied Genetics. 122(2):291-309.

Tung, C., Zhao, K., Wright, M.K., Ali, M., Jung, J., Kimball, J.A., Tyagi, W., Thomson, M.J., McNally, K., Leung, H., Kim, H., Ahn, S., Reynolds, A., Scheffler, B.E., Eizenga, G.C., McClung, A.M., Bustamante, C.D., McCouch, S.D. 2010. Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice. 3:205–217.

Last Modified: 7/24/2014
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