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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND BIOINFORMATICS RESEARCH IN AGRICULTURALLY IMPORTANT ORGANISMS
2010 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 research 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 Fiber Bioscience Research Unit. Service: G Crop Genetics Research Unit, Service: D, G, B, M Crop Germplasm Research, Service: G Dale Bumpers National Rice Research Center Service: 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: G Natural Products Utilization Research Unit, Service: D, M Plant Stress and Germplasm Development Unit, Service B Southern Horticultural Laboratory, Service: G,M,B Southern Insect Management Research Unit, Service: D,G,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 DNA marker development and validation, in the form of microsatellites, have become an important output component of the unit and in the past year, markers have developed for over 18 species ranging from fungi, plants to insects. This in-house research project has a component of rice research which has been supported through various cooperative agreements (6402-21310-003-03, Mining Novel Blast Resistance Genes for Use in U.S. Breeding Programs; 6402-21310-003-04, The Mississippi Rice Variety Acceleration Breeding Project). This research has revolved around mapping novel blast resistances and the integration of DNA markers into the Mississippi rice breeding program. DNA markers, using technology advancement reported in last’s years annual report, were developed for 10 tropical tree species that are curated at the Tropical Agriculture Research Station, Mayaguez, Puerto Rico. Species for which markers were developed: Nephelium lappaceum (Rambutan) (1,362 designed markers), Manilkara zapota (sapodilla)(2,292 designed markers), Pouteria sapota (sapote)(1,124 designed markers), Litchi chinensis (lychee)(2,722 designed markers), Melicoccus bijugatus (Spanish lime) (630 designed markers), Annona reticulate and Annona squamosa (Custard apple, sugar apple) (996 designed markers), Dimorcarpus longan (longan) (3,670 designed markers), Averrhoa carambola (star fruit) (3,707), Garcinia mangostana and Garcinia cochinchinensis (mangosteen) (600 designed markers), Bambusa vulgaris var. vittata and Guadua angustifolia (bamboo) (420 designed markers).


4.Accomplishments
1. Development of DNA Markers for Germplasm Conservation. Germplasm conservation is an important but expensive and difficult endeavor. This is especially true when trees are the species of interest. The USDA, ARS has germplasm collections for tropical trees but lacks the tools to characterize the genetic diversity, which is important when deciding which accessions to add to or eliminate from a collection. The unit has developed tools and procedures to cost effectively develop and validate DNA markers. DNA markers using this technology were developed for 10 species that are curated at the Tropical Agriculture Research Station, Mayaguez, Puerto Rico. The molecular markers developed in this project are now being used to characterize the germplasm of the corresponding species in three different collections (Hawaii, Florida and Puerto Rico). This should help confirm the identity of replicated accessions and determined the relative genetic diversity in the collections.


Review Publications
Wubben, M., Callahan, F.E., Scheffler, B.E. 2010. Transcript Analysis of Parasitic Females of the Sedentary Semi-Endoparasitic Nematode Rotylenchulus reniformis. Molecular and Biochemical Parasitology. 172:31-40.

Hu, Y., Willett, K.L., Khan, I.A., Scheffler, B.E., Dasmahapatra, A.K. 2009. Ethanol Disrupts Chondrification of the Neurocranial Cartilages in Medaka Embryos without Affecting Aldehyde Dehydrogenase 1A2 (Aldh1A2) Promoter Methylation. Comparative Biochemistry and Physiology. 150(4):495-502.

Oard, J.H., Moldenhauer, K.K., Fjellstrom, R.G., Nelson, J., Linscombe, S.D., Silva, J., May, G.D. 2010. Registration of the MY2 Cypress/LaGrue rice recombinant inbred line mapping population. Journal of Plant Registrations. 4(3):1-5.

Yuan, J.S., Abercrombie, L., Cao, Y., Halfhill, M.D., Zhou, X., Peng, Y., Hu, J., Rao, M.R., Heck, G.R., Larosa, T.J., Sammons, R.D., Wang, X., Ranjan, P., Johnson, D.H., Wadl, P.A., Scheffler, B.E., Rinehart, T.A., Trigiano, R.N., Stewart, Jr, C.N. 2010. Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance. Weed Science. 58:109-117.

Wang, X.W., Good, L.L., Wadl, P.A., Johnson, D.H., Panthee, D., Scheffler, B.E., Rinehart, T.A., Stewart, N.R., Yuan, J., Stewart, N.C., Trigiano, R.N. 2009. Microsatellites from Conyza canadensis (horseweed). Molecular Ecology Resources. 9(5):1375-1379.

Tremblay, A., Li, S., Scheffler, B.E., Matthews, B.F. 2009. Laser capture microdissection (LCM) and expressed sequence tag analysis of uredinia formed by Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Physiological and Molecular Plant Pathology. 73(6):163-174.

Thibivilliers, S., Joshi, T., Campbell, K., Scheffler, B., Borerma, R., Xu, D., Cooper, B., Nguyen, H.T., Stacey, G. 2009. Generation of Phaseolus vulgaris ESTs and investigation of the regulation upon Uromyces appendiculatus infection. Biomed Central (BMC) Plant Biology. 9:46.

Arias, R.S., Stetina, S.R., Tonos, J.L., Scheffler, J.A., Scheffler, B.E. 2009. Microsatellites Reveal Genetic Diversity in Rotylenchulus reniformis Populations. Journal of Nematology. 41(2): 146-156.

Techen, N., Pan, Z., Scheffler, B.E., Kahn, I.A. 2009. Detection of Illicium anisatum as Adulterant of Illicium verum. Planta Medica. 75:392–395.

Kelley, R.Y., Williams, W.P., Mylroie, J.E., Boykin, D.L., Hawkins, L.K., Windham, G.L., Brooks, T.D., Bridges, S.M., Scheffler, B.E., Wilkinson, J.R. 2009. Genomic Profile of Maize Response to Aspergillus flavus Infection. Toxin Reviews. 28:129-141.

Rinehart, T.A., Scheffler, B.E., Reed, S.M. 2010. Ploidy Variation and Genetic Diversity in Dichroa. HortScience. 45:208-213.

Buriev, Z.T., Saha, S., Abdurakhmonov, I.Y., Jenkins, J.N., Abdukarimov, A., Scheffler, B.E., Stelly, D.M. 2010. Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 120:587-606.

Simko, I., Pechenick, D.A., Mchale, L.K., Truco, M.J., Ochoa, O.E., Michelmore, R.W., Scheffler, B.E. 2010. Development of molecular markers for marker-assisted selection in lettuce (Lactuca sativa). Acta Horticulture Proceedings, Year 2010, volume 859, pages 401-408.

Simko, I., Pechenick, D.A., Mchale, L.K., Truco, M.J., Ochoa, O.E., Michelmore, R.W., Scheffler, B.E. 2009. Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1.. Biomed Central (BMC) Plant Biology, Year 2009, volume 9, article number 135.

Joshi, V., Techen, N., Scheffler, B.E., Khan, I.A. 2009. Identification and Differentiation Between Hoodia gordonii Masson) Sweet ex Decne., Opuntia ficus indica (L.) P. Miller and Other Related Hoodia Species by Microscopy and PCR Methods. Journal of Herbs, Spices and Medicinal Plants. 15(3)253-264

Techen, N., Arias De Ares, R.S., Glynn, N.C., Pan, Z., Khan, I.A., Scheffler, B.E. 2010. Optimized Construction of SSR-enriched Libraries. Molecular Ecology Resources. 10(3)508-515

Last Modified: 10/30/2014
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