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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

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families - (Peer Reviewed Journal)
Link, T.I., Lang, P., Scheffler, B.E., Duke, M.V., Graham, M.A., Cooper, B., Tucker, M.L., Van De Mortel, M., Voegele, R.T., Mendgen, K., Baum, T.J., Whitham, S.A. 2014. The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families. Molecular Plant Pathology. 15(4):379-393. DOI:10.1111/mpp.12099.
Global and gene specific DNA methylation changes during zebrafish development - (Peer Reviewed Journal)
Fang, X., Corrales, J., Thornton, C., Scheffler, B.E., Willett, K.L. 2013. Global and gene specific DNA methylation changes during zebrafish development. Comparative Biochemistry and Physiology. 99-108.
Isolation and characterization of microsatellite Loci for Cornus sanguniea (Cornaceae) 1 - (Peer Reviewed Journal)
Wadl, P.A., Hatmaker, A., Fussi, B., Scheffler, B.E., Trigiano, R.N. 2013. Isolation and characterization of microsatellite Loci for Cornus sanguniea (Cornaceae) 1. American Journal of Botany. 1(9):1300012. doi:10.3732/apps.1300012.
Microsatellites from Bipolaris sorokiniana: Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species - (Peer Reviewed Journal)
Fajolu, O.L., Wadl, P.A., Vu, A.L., Gwinn, K.D., Trigiano, R.N., Ownley, B., Scheffler, B.E. 2013. Microsatellites from Bipolaris sorokiniana: Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species Mycologia. 105/5:1164-1173.
Camelina seed transcriptome: Tool for meal and oil improvement and translational research - (Peer Reviewed Journal)
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.
Benzo[a]pyrene decreases global and gene specific DNA methylation during zebrafish development - (Peer Reviewed Journal)
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.
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres - (Peer Reviewed Journal)
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.
Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina - (Peer Reviewed Journal)
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.
High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform - (Peer Reviewed Journal)
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, C.J., Mauleon, R., Leung, H., Bustamante, C., Mccouch, S.R. 2011. High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform . Molecular Breeding. 29:875-886.
Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina - (Peer Reviewed Journal)
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.
Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)1 - (Peer Reviewed Journal)
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.
Development and characterization of sixteen microsatellite loci for Geosmithia morbida, the causal agent of thousand canker disease in black walnut (Juglans nigra) - (Peer Reviewed Journal)
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.
Identification of Candidate Genes in Rice for Resistance to Sheath Blight Disease by Whole Genome Sequencing - (Peer Reviewed Journal)
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.
Registration of "Rex" Southern Long-Grain Rice - (Peer Reviewed Journal)
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).
Comparison of whole-genome amplifications for microsatellite genotyping of Rotylenchulus reniformis - (Peer Reviewed Journal)
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.
Generation and analysis of expressed sequence tags(ESTs) for marker development in yam (Dioscores alata L.) - (Peer Reviewed Journal)
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.
Isolation and characterisation of the first microsatellite markers for Cyperus rotundus - (Peer Reviewed Journal)
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.
First microsatellites developed from Spodoptera frugiperda and their potential use for population genetics - (Abstract Only)
Arias De Ares, R.S., Blanco, C.A., Portilla, M., Snodgrass, G.L., Scheffler, B.E. 2011. First microsatellites developed from Spodoptera frugiperda and their potential use for population genetics. Entomology Society America Annual Meeting. 104(3):516-587.
First microsatellites from Spodoptera frugiperda (Lepidoptera: Noctuidae) and their potential use for population genetics - (Peer Reviewed Journal)
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.
Development of Mississippi cotton breeding lines resistant to reniform and root-koot nematodes via marker assisted selection - (Proceedings)
Wallace, T.P., Thaxton, P.S., Gutierrez, O.A., Scheffler, B.E., Stetina, S.R., Scheffler, J.A. 2011. Development of Mississippi cotton breeding lines resistant to reniform and root-koot nematodes via marker assisted selection. National Cotton Council Beltwide Cotton Conference. pp.742.
Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing - (Abstract Only)
Arias De Ares, R.S., Irish, B.M., Ballard, L.L., Duke, M.V., Liu, X.F., Simpson, S.A., Scheffler, B.E. 2010. Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing. Plant and Animal Genome. Abstract P089.
Discriminating microsatellites from Macrophomina phaseolina and their potential association to biological functions - (Peer Reviewed Journal)
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.
Development and characterization of microsatellites for switchgrass rust fungus (Puccinia emaculata) - (Peer Reviewed Journal)
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.
Functional diversity in fungal fatty acid synthesis the first acetylenase from the Pacific Golden Chanterelle Cantharellus formosus - (Peer Reviewed Journal)
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.
Gibberellin-associated cisgenes modify growth, stature and wood properties in Populus - (Peer Reviewed Journal)
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.
Characterization of twelve microsatellite markers for the native redbud tree (Cercis canadensis) - (Peer Reviewed Journal)
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.
Development of microsatellite markers from crape myrtle (Lagerstroemia L.) - (Peer Reviewed Journal)
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.
Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance - (Peer Reviewed Journal)
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.
Microsatellites Reveal Genetic Diversity in Reniform Nematode Populations - (Abstract Only)
Arias De Ares, R.S., Stetina, S.R., Tonos, J.L., Scheffler, J.A., Scheffler, B.E. 2010. Microsatellites Reveal Genetic Diversity in Reniform Nematode Populations. National Cotton Council Beltwide Cotton Conference, New Orleans, Louisiana, January 4-7, 2010
Optimized Construction of SSR-enriched Libraries - (Peer Reviewed Journal)
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
Benzo(A)pyrene induced glycine N-methyltransferase messenger rna expression in Fundulus heteroclitus embryos - (Peer Reviewed Journal)
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.
Fingerprinting the bad guys, SSR DNA-profiling of Nutsedge - (Abstract Only)
(25-Sep-09)
The Effect of Culture Methods and Serum Supplementation on Developmental Competence of Bovine Embryos Cultured In Vitro - (Peer Reviewed Journal)
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.
Hormonal Profiles of Late Gestation Ewes Following Intra-Uterine Inoculation With and Without Lux-Modified Escherichia Coli - (Peer Reviewed Journal)
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.
Evaluation of Relaxin Blood Profiles of Horses as A Means of Assessing Placental Function in High-Risk Pregnancies And Responsiveness to Therapeutic Strategies - (Peer Reviewed Journal)
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.
Ethanol Disrupts Chondrification of the Neurocranial Cartilages in Medaka Embryos without Affecting Aldehyde Dehydrogenase 1A2 (Aldh1A2) Promoter Methylation     Reprint Icon - (Peer Reviewed Journal)
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.
Simulated Microgravity Influences Bovine Oocyte In Vitro Fertilization and Preimplantation Embryo Development - (Peer Reviewed Journal)
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.
UPIC: Perl scripts to determine the number of SSR markers to run     Reprint Icon - (Peer Reviewed Journal)
Arias, R.S., Ballard, L.L., Scheffler, B.E. 2009. UPIC: How Many SSR Markers to Run. Bioinformation 3(8):352-360, http://www.bioinformation.net/003/007800032009.htm
Assessment of Pregnancy in the Late Gestation Mare Using Digital Infrared Thermography - (Peer Reviewed Journal)
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.
Postmortem Photonic Imaging of Lux-Modified Salmonella Typhimuium Within the Gastrointestinal Tract of Swine Following Oral Inoculation In Vivo - (Peer Reviewed Journal)
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: 9/1/2014
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