Projects

CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES Appropriated (D)   Accession Number: 413173

GENOMIC RESOURCES TO ACCELERATE WESTERN CORN ROOTWORM RESEARCH Reimbursable (R)   Accession Number: 415033

ACCELERATED COMMERCIAL DEVELOPMENT OF HYDROTREATED RENEWABLE JET FUEL (HRJ) FROM REDESIGNED OILSEED FEEDSTOCKS SUPPLY CHAINS Reimbursable (R)   Accession Number: 424027

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

Integration of the draft sequence and physical map as a framework for genomic research in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.) - (Peer Reviewed Journal)

Ha, J., Abernathy, B., Nelson, W., Grant, D.M., Wu, X., Nguyen, H., Stacey, G., Wing, R., Shoemaker, R.C., Jackson, S. 2012. Integration of the draft sequence and physical map as a framework for genomic research in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.). Genes, Genomes, Genetics. 2(3):321-329.

SoyBase and the legume information system: accessing information about the soybean and other legume genomes - (Book / Chapter)

Cannon, S.B., Crow, J.A., Grant, D.M. 2012. SoyBase and the legume information system: accessing information about the soybean and other legume genomes. In: Wilson, R. editor. Designing Soybeans for 21st Century Markets. Urbana, IL: AOCS Press. p. 53-66.

Mobilizing the genome of Lepidoptera through novel sequence gains and end creation by non-autonomous Lep1 Helitrons - (Peer Reviewed Journal)

Coates, B.S., Hellmich II, R.L., Grant, D.M., Abel, C.A. 2012. Mobilizing the genome of Lepidoptera through novel sequence gains and end creation by non-autonomous Lep1 Helitrons. DNA Research. 19(1):11-21.

Changes in twelve conserved soybean genomic regions following three rounds of polyploidy - (Peer Reviewed Journal)

Severin, A.J., Cannon, S.B., Graham, M.A., Grant, D.M., Shoemaker, R.C. 2011. Changes in twelve conserved soybean genomic regions following three rounds of polyploidy. The Plant Cell. 23(9):3129-3136.

Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean - (Peer Reviewed Journal)

Bolon, Y.E., Haun, W.J., Xu, W.W., Grant, D.M., Stacey, M.G., Nelson, R., Gerhardt, D.J., Jeddeloh, J.A., Stacey, G., Muehlbauer, G.J., Orf, J.H., Naeve, S.L., Stupar, R.M., Vance, C.P. 2011. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiology. 156(1):240-253.

Fast neutron mutants database and web displays at SoyBase - (Abstract Only)

Grant, D.M., Bolon, Y.E., Nelson, R., Vance, C.P., Shoemaker, R.C. 2011. Fast neutron mutants database and web displays at SoyBase [abstract]. Plant and Animal Genome Conference. Poster 389.

Soybean transcriptome analysis using the SoyBase soybean metabolic database SoyCyc - (Abstract Only)

Nelson, R., Grant, D.M., Cannon, S.B., Chi, A., Zhang, P., Rhee, S., Shoemaker, R.C. 2011. Soybean transcriptome analysis using the SoyBase soybean metabolic database SoyCyc [abstract]. Plant and Animal Genome Conference. Poster 772.

Phenotypic and genomic analysis of a fast neutron mutant population resource in soybean - (Abstract Only)

Bolon, Y.E., Haun, W.J., Xu, W., Grant, D.M., Gerhardt, D.J., Albert, T.J., Richmond, T., Jeddeloh, J.A., Muehlbauer, G., Orf, J., Naeve, S., Stupar, R.M., Vance, C.P. 2011. Phenotypic and genomic analysis of a fast neutron mutant population resource in soybean [abstract]. XIX Plant and Animal Genome Conference Proceedings, January 15-19, 2011, San Diego, California. Abstract No. P390. Available: http://www.intl-pag.org/19/abstracts/P05f_PAGXIX_390.html.

Gene expression patterns are correlated with genomic and genic structure in soybean - (Peer Reviewed Journal)

Woody, J.L., Severin, A., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.T., Weeks, N.T., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2011. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 54(1):10-18.

Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean - (Peer Reviewed Journal)

Song, Q., Jia, G., Zhu, Y., Hwang, E., Hyten, D.L., Cregan, P.B., Grant, D.M., Nelson, R. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Science. 50:1950-1960.

Integration of draft sequence and physical map as framework for genomic research in soybean (Glycine max) - (Peer Reviewed Journal)

Ha, J., Abernathy, B., Grant, D.M., Wu, X., Nelson, W., Stacey, G., Shoemaker, R.C., Jackson, S. 2012. Integration of draft sequence and physical map as framework for genomic research in soybean (Glycine max). Biomed Central (BMC) Genomics. 2(3):321-329.

An integrative approach to genomic introgression mapping - (Peer Reviewed Journal)

Severin, A.J., Peiffer, G., Xu, W.W., Hyten, D.L., Bucciarelli, B., O'Rourke, J.A., Bolon, Y.E., Grant, D.M., Farmer, A.D., May, G.D., Vance, C.P., Shoemaker, R.C., Stupar, R.M. 2010. An integrative approach to genomic introgression mapping. Plant Physiology. 154(1):3-12.

Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences - (Peer Reviewed Journal)

Peto, M.F., Grant, D.M., Shoemaker, R.C., Cannon, S.B. 2010. Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences. Advances in Bioinformatics. DOI:10.1155/2010/976792.

RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome - (Peer Reviewed Journal)

Severin, A.J., Woody, J.L., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2010. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. Biomed Central (BMC) Plant Biology. 10:610.

SoyTEdb: A Comprehensive Database of Transposable Elements in the Soybean Genome - (Peer Reviewed Journal)

Du, J., Grant, D.M., Tian, Z., Nelson, R., Zhu, L., Shoemaker, R.C., Ma, J. 2010. SoyTEdb: A Comprehensive Database of Transposable Elements in the Soybean Genome. Biomed Central (BMC) Genomics. 11:113.

Genome Sequence of the Paleopolyploid Soybean (Glycine max (L.) Merr.) - (Peer Reviewed Journal)

Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Hyten, D.L., Song, Q., Mitros, T., Nelson, W., May, G.D., Gill, N., Peto, M.F., Shu, S., Goodstein, D., Thelen, J.J., Cheng, J., Sakurai, T., Umezawa, T., Shinozaki, K., Du, J., Bhattacharyya, M., Sandhu, D., Grant, D.M., Joshi, T., Libault, M., Zhang, X., Hguyen, H., Valliyodan, B., Xu, D., Futrell-Griggs, M., Abernathy, B., Hellsten, U., Berry, K., Grimwood, J., Yu, Y., Wing, R.A., Cregan, P.B., Stacey, G., Specht, J., Rokhsar, D., Shoemaker, R.C., Jackson, S. 2010. Genome Sequence of the Paleopolyploid Soybean (Glycine max (L.) Merr.). Nature. 463:178-183.

SSWAP: A Simple Semantic Web Architecture and Protocol for Semantic Web Services - (Peer Reviewed Journal)

Gessler, D.D., Schiltz, G.S., May, G.D., Avraham, S., Town, C.D., Grant, D.M., Nelson, R. 2009. SSWAP: A Simple Semantic Web Architecture and Protocol for Semantic Web Services. BMC Bioinformatics. 10:309doi:10.1186/1471-2105-10-309.

SoyBase, The USDA-ARS Soybean Genetics and Genomics Database - (Peer Reviewed Journal)

Grant, D.M., Nelson, R., Cannon, S.B., Shoemaker, R.C. 2009. SoyBase, The USDA-ARS Soybean Genetics and Genomics Database. Nucleic Acids Research. Doi: 10.1093/nar/gkp798.

Integrating Microarray Analysis and the Soybean Genome to Understand the Soybean's Iron Deficiency Response - (Peer Reviewed Journal)

O'Rourke, J.A., Nelson, R., Grant, D.M., Schmutz, J., Grimwald, J., Cannon, S.B., Vance, C.P., Graham, M.A., Shoemaker, R.C. 2009. Integrating Microarray Analysis and the Soybean Genome to Understand the Soybean's Iron Deficiency Response. Biomed Central(BMC)Genomics. 10:376. Available: http://www.biomedcentral.com/1471-2164/10/376.

Soybase and The Soybean Breeder's Toolbox: Updated Features and New Data - (Abstract Only)

Grant, D.M., Nelson, R., Cannon, S.B., Shoemaker, R.C. 2009. Soybase and The Soybean Breeder's Toolbox: Updated Features and New Data [abstract]. Plant and Animal Genome Conference. Poster No. P364.

SoyBase Soybean Ontologies: Pathways to Soybean Growth and Developmental Description - (Abstract Only)

Nelson, R., Grant, D.M., Cannon, S.B., Shoemaker, R.C. 2009. SoyBase Soybean Ontologies: Pathways to Soybean Growth and Developmental Description [abstract]. Plant and Animal Genome Conference. Poster No. P797.

SoyBase Simple Semantic Web Architecture and Protocol (SSWAP) Services - (Abstract Only)

Nelson, R., Grant, D.M., Gangwal, P., Shoemaker, R.C. 2009. SoyBase Simple Semantic Web Architecture and Protocol (SSWAP) Services [abstract]. Plant and Animal Genome Conference. Poster No. P798.

Identification of Candidate Signaling Genes Including Regulators of Chromosome Condensation 1 Protein Family Differentially Expressed in the Soybean - Phytophthora Sojae Interaction - (Peer Reviewed Journal)

Narayanan, N.N., Tasma, I.M., Grant, D.M., Shoemaker, R.C., Bhattacharyya, M.K. 2009. Identification of Candidate Signaling Genes Including Regulators of Chromosome Condensation 1 Protein Family Differentially Expressed in the Soybean - Phytophthora Sojae Interaction. Journal of Theoretical and Applied Genetics. 118(3):399-412.

The Soybean Breeder’s Toolbox: Updated Features and New Data - (Abstract Only) - (20-Jul-08)

Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps - (Peer Reviewed Journal)

Shoemaker, R.C., Grant, D.M., Olson, T., Warren, W.C., Wing, R., Yu, Y., Kim, H., Cregan, P.B., Joseph, B., Futrell-Griggs, M., Nelson, W., Davito, J., Walker, J., Wallis, J., Kremitski, C., Scheer, D., Clifton, S., Graves, T., Nguyen, H., Wu, X., Luo, M., Dvorak, J., Nelson, R., Cannon, S.B., Thomkins, J., Schmutz, J., Stacey, G., Jackson, S. 2008. Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps. Genome. 51:294-302.

BIOINFORMATIC RESOURCES FOR SOYBEAN GENETIC AND GENOMIC RESEARCH - (Book / Chapter)

Grant, D.M., Nelson, R., Graham, M.A., Shoemaker, R.C. 2008. Bioinformatic resources for soybean genetic and genomic research. In: Stacey, Gary, editor. Genetics and Genomics of Soybean. New York, New York. Springer. p. 141-162.

THE SOYBEAN BREEDER'S TOOLBOX: INTEGRATION OF GENETIC AND MOLECULAR DATA FOR SOYBEAN - (Abstract Only)

Nelson, R., Grant, D.M., Shoemaker, R.C. 2007. The soybean breeder's toolbox: integration of genetic and molecular data for soybean [abstract]. Plant and Animal Genome Conference. Paper No. P851.

THE SOYBEAN BREEDER'S TOOLBOX: A NEW RESOURCE FOR SOYBEAN GENETIC AND GENOMIC INFORMATION - (Abstract Only)

Nelson, R., Grant, D.M., Shoemaker, R.C. 2006. The soybean breeder's toolbox: a new resource for soybean genetic and genomic information [abstract]. Biennial Conference on Molecular and Cellular Biology of the Soybean. p. 4.

THE LEGUME INFORMATION RESOURCE (LIS): AN INTEGRATED RESOURCE FOR COMPARATIVE LEGUME BIOLOGY - (Peer Reviewed Journal)

Gonzales, M., Archuleta, E., Farmer, A., Gajendran, K., Grant, D.M., Shoemaker, R.C., Beavis, W., Waugh, M. 2005. The legume information resource (lis): an integrated resource for comparative legume biology. Nucleic Acids Research. 33:D660-D665.

PRELIMINARY ANALYSIS OF SINGLE NUCLEOTIDE POLYMORPHISMS IN SOYBEAN DETECTED B ESTMINER ANALYSIS - (Abstract Only)

Nelson, R., Grant, D.M., Shoemaker, R.C. 2005. Preliminary analysis of single nucleotide polymorphisms in soybean detected b estminer analysis. Plant and Animal Genome Abstracts. p. 433.

THE LEGUME INFORMATION RESOURCE (LIS): AN INTEGRATED INFORMATION RESOURCE FOR COMPARATIVE LEGUME BIOLOGY - (Abstract Only)

Gonzales, M.D., Beavis, B., Gajendran, K., Farmer, A., Archuletal, E., Grant, D.M., Nelson, R., Shoemaker, R.C., Waugh, M. 2005. The legume information resource (lis): an integrated information resource for comparative legume biology. Plant and Animal Genome Abstracts. p. 873.

ESTMINER: A SUITE OF PROGRAMS FOR GENE AND ALLELE IDENTIFICATION - (Peer Reviewed Journal)

Nelson, R., Grant, D.M., Shoemaker, R.C. 2004. Estminer: a suite of programs for gene and allele identification. Bioinformatics. 21(5):691-693.

MINING EST DATABASES TO RESOLVE EVOLUTIONARY EVENTS IN MAJOR PLANT SPECIES - (Peer Reviewed Journal)

Schlueter, J.A., Dixon, P., Granger, C., Grant, D.M., Clark, L., Doyle, J.J., Shoemaker, R.C. 2004. Mining EST databases to resolve evolutionary events in major plant species. Genome. 47:868-876.

SOYBEAN GENOMIC SURVEY: BAC-END SEQUENCES NEAR RFLP AND SSR MARKERS - (Peer Reviewed Journal) - (20-Apr-01)

GENOME ORGANIZATION IN DICOTS. II: ARABIDOPSIS AS A 'BRIDGING SPECIES' TO RESOLVE GENOME EVOLUTION EVENTS AMONG LEGUMES - (Peer Reviewed Journal) - (13-Jan-01)

GENOME ORGANIZATION IN DICOTS: I. GENOME DUPLICATION IN ARABIDOPSIS AND SYNTENY BETWEEN SOYBEAN AND ARABIDOPSIS - (Peer Reviewed Journal) - (01-Feb-00)

SOYBEAN GENOME EVOLUTION - (Abstract Only) - (05-Aug-99)

RFLP MAP OF SOYBEAN - (Book / Chapter) - (30-Jun-98)

USING THE WWW AS A GENOMIC INFORMATION RESOURCE - (Other) - (15-Jun-98)

ACCESSING SOYBASE AND OTHER GENOME DATABASES VIA THE INTERNET - (Proceedings) - (28-Feb-98)

MOLECULAR CHARACTERIZATION OF IRON DEFICIENCY CHLOROSIS IN SOYBEAN - (Proceedings) - (15-Feb-98)

QTL IN SOYBASE: A NEW PERSPECTIVE - (Proceedings) - (16-Jan-98)

NODULATION AND NITROGEN FIXATION IN SOYBASE, A SOYBEAN GENOME DATABASE - (Research Notes) - (08-May-97)

SOYBASE, A DATABASE FOR SOYBEAN GENOME AND GENETIC DATA - (Research Notes) - (14-Sep-96)

MOLECULAR HYBRIDIZATION - (Book / Chapter) - (30-Aug-96)

SOYBASE, A SOYBEAN GENOME DATABASE - (Research Notes) - (30-Jun-96)

THE UMC MAIZE RFLP MAP AND CORE MARKER SEQUENCES - (Abstract Only) - (15-Jan-96)