Projects

Functional and Structural Genetic Analysis of Soybean and Other Legumes Appropriated (D)   Accession Number: 413378

Curation and Development of the Soybean Breeder's Toolbox and Its Integration with Other Plant Genome Databases Appropriated (D)   Accession Number: 413173

A Strategy for Responding to the Whole-Genome Shotgun Sequence of the Soybean Genome Reimbursable (R)   Accession Number: 412038

Development of High-Throughput Dna-Based Gene Silencing Technology for Soybeans Reimbursable (R)   Accession Number: 418114

Toward Cloning Rps3 and Rps8, Effective Resistance Genes for Phytophthora Sojae for the New Millennium Reimbursable (R)   Accession Number: 415160

Iron Deficiency Chlorosis: Getting to the Root of the Problem (Part Ii) Reimbursable (R)   Accession Number: 417036

Iron Deficiency Chlorosis: Getting to the Root of the Problem Reimbursable (R)   Accession Number: 412601

Database of Repetititve and Transposable Elements in Soybean: Genome Annotation Specific Cooperative Agreement (S)   Accession Number: 412307

Relational Legume Genome Database: the Breeder's Toolbox Specific Cooperative Agreement (S)   Accession Number: 409553

A Strategy for Responding to the Whole Genome Shotgun Sequence of the Soybean Genome - Purdue Assembly Specific Cooperative Agreement (S)   Accession Number: 412045

High Throughput Sequencing for Asian Soybean Rust and Phytophthora Specific Cooperative Agreement (S)   Accession Number: 413367

Publications

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.

Retrotransposons in the intergenic regions of syntenic blocks between soybean and Medicago truncatula and their contribution to local genome evolution - (Peer Reviewed Journal) - (27-May-09)

Soybean Comparative Genomics - (Book/Chapter) - (03-Mar-09)

Identification and Analyses of Candidate Genes for Rpp4 Mediated Resistance to Asian Soybean Rust in Soybean (Glycine max) - (Peer Reviewed Journal)

Meyer, J.D., Silva, D.C., Yang, C., Van De Mortel, M., Pedley, K.F., Hill, J.H., Shoemaker, R.C., Abdelnoor, R., Whitham, S.A., Graham, M.A. 2009. Identification and Analyses of Candidate Genes for Rpp4 Mediated Resistance to Asian Soybean Rust in Soybean (Glycine max). Plant Physiology. 150:295-307.

Genomic Studies in Soybean: Toward Understanding Seed Oil and Protein Production - (Abstract)

Bolon, Y.E., Joseph, B., Cannon, S.B., Diers, B., Farmer, A., Graham, M.A., May, G., Muehlbauer, G., Specht, J., Tu, Z., Weeks, N., Xu, W., Shoemaker, R.C., Vance, C.P. 2008. Genomic Studies in Soybean: Toward Understanding Seed Oil and Protein Production [abstract]. IV International Conference on Legume Genomics and Genetics, December 7-12, 2008, Puerto Vallarta, Mexico. Abstract No. W28. p. 101 and Abstract No. P57, p. 63.

Establishment of a soybean (Glycine max L. Merr.) transposon-based mutagenesis repository - (Peer Reviewed Journal)

Mathieu, M., Winters, E., Kong, F., Wan, J., Want, S., Eckert, H., Donovan, C., Somers, D., Wang, K., Nguyen, H., Shoemaker, R.C., Stacey, G., Clemente, T. 2008. Establishment of a Soybean (Glycine max L. Merr.) Transposon-based Mutagenesis Repository. Planta. 229:279-289.

Identification of regulatory genes for active defense responses induced immediately following Phytophthora sojae infection in soybean - (Peer Reviewed Journal)

Narayanan, N.N., Tasma, I.M., Grant, D.M., Shoemaker, R.C., Bhattacharyya, M.K. 2009. Identification of Regulatory Genes for Active Defense Responses Induced Immediately Following Phytophthora Sojae Infection in Soybean. Journal of Theoretical and Applied Genetics. 118(3):399-412.

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

Identification of Candidate Genes for the Rpp4 Asian Soybean Rust Resistance Locus in Soybean - (Abstract) - (20-Jul-08)

Targeted Sequencing and Analyses of the Rpp4 Asian Soybean Rust Resistance Locus in Soybean - (Abstract) - (20-Jul-08)

Targeted Sequencing of the Rpp2 Asian Soybean Rust Resistance Locus - (Abstract) - (20-Jul-08)

High-throughput genotyping with the GoldenGate assay in the highly complex genome of soybean - (Peer Reviewed Journal)

Hyten, D.L., Song, Q., Choi, I., Yoon, M., Specht, J.E., Matukumalli, L.K., Shoemaker, R.C., Young, N.D., Cregan, P.B. 2008. High-throughput genotyping with the GoldenGate assay in the highly complex genome of soybean. Theoretical and Applied Genetics. 116:945-952.

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.

Sequence Level Analysis of Recently Duplicated Regions in the Soybean [Glycine max (L.) Merr.] Genome - (Peer Reviewed Journal)

Van, K., Kim, D., Mei Cai, C., Young Kim, M., Shin, J., Graham, M.A., Shoemaker, R.C., Choi, B., Yang, T., Lee, S. 2008. Sequence Level Analysis of Recently Duplicated Regions in the Soybean [Glycine max (L.) Merr.] Genome. DNA Research. 15:93-102.

Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes Across Glycine max, Medicago truncatula and Arabidopsis thaliana - (Peer Reviewed Journal)

Schlueter, J.A., Scheffler, B.E., Jackson, S., Shoemaker, R.C. 2008. Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes Across Glycine max, Medicago truncatula and Arabidopsis thaliana. Journal of Heredity.

Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines - (Peer Reviewed Journal)

O'Rourke, J.A., Charlson, D.V., Gonzalez, D.O., Vodkin, L.O., Graham, M.A., Cianzio, S.R., Grusak, M.A., Shoemaker, R.C. 2007. Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. Biomed Central (BMC) Genomics. 8:476.

Gene expression profiling of soybean near-isogenic lines contrasting in seed protein and oil - (Abstract)

Bolon, Y.E., Diers, B., Graham, M.A., Muehlbauer, G., Shoemaker, R.C., Specht, J., Vance, C.P. 2008. Gene expression profiling of soybean near-isogenic lines contrasting in seed protein and oil [abstract]. XVI Plant and Animal Genome Conference Proceedings, January 12-16, 2008, San Diego, California. Abstract W481.

Cel_interrogator: a Free and Open Source Package for Affymetrix Cel File Parsing - (Abstract)

Nelson, R., Shoemaker, R.C. 2008. Cel_interrogator: a free and open source package for affymetrix cel file parsing [abstract]. Plant and Animal Genome Conference. Paper No. P867.

Gene Duplication and Paleopolyploidy in Soybean and the Implications for Whole Genome Sequencing - (Peer Reviewed Journal)

Schlueter, J., Lin, J., Schlueter, S., Vasylenko-Sanders, I., Deshpandem, S., Yi, J., O'Bleness, M., Roe, B., Nelson, R., Scheffler, B.E., Jackson, S., Shoemaker, R.C. 2007. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. Biomed Central (BMC) Genomics. 8:330.

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.

Soybean Genome Structure and Organization - (Book/Chapter)

Shoemaker, R.C., Schlueter, J.A., Jackson, S. 2008. Soybean genome structure and organization. In: Stacey, G. editor. Genetics and Genomics of Soybean. Series:Plant Genetics and Genomics:Crops and Models 2. New York, NY: Springer-Verlag. p. 125-140.

Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations - (Peer Reviewed Journal)

Hyten, D.L., Choi, I., Song, Q., Shoemaker, R.C., Nelson, R.L., Costa, J.M., Specht, J.E., Cregan, P.B. 2007. Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations. Genetics. 175:1937-1944.

A Soybean Transcript Map: Discovery and Mapping of Single Nucleotide Polymorphisms in Soybean Genes - (Peer Reviewed Journal)

Choi, I., Hyten, D.L., Matukumalli, L.K., Song, Q., Chaky, J.M., Quigley, C.V., Chase, K., Lark, K.G., Reiter, R.S., Yoon, M., Hwang, E., Yi, S., Young, N.D., Shoemaker, R.C., Van Tassell, C.P., Specht, J.E., Cregan, P.B. 2007. A soybean transcript map: discovery and mapping of single nucleotide polymorphisms in soybean genes. Genetics. 176:685-696.

Recovering from Iron Deficiency Chlorosis in Near Isogenic Soybeans: a Microarray Study - (Peer Reviewed Journal)

O'Rourke, J., Graham, M.A., Vodkin, L., Gonzalez, D., Cianzio, S., Shoemaker, R.C. 2007. Recovering from iron deficiency chlorosis in near isogenic soybeans: a microarray study. Plant Physiology and Biochemistry. 45:287-292.

Chromosome Levelhomeology in Paleopolyploid Soybean (Glycine Max) Revealed Through Integration of Genetic and Chromosome Maps - (Peer Reviewed Journal)

Walling, J., Shoemaker, R.C., Young, N., Mudge, J., Jackson, S. 2006. Chromosome levelhomeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics. 172:1893-1900.

The Soybean Breeder's Toolbox: Integration of Genetic and Molecular Data for Soybean - (Abstract)

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.

Toward Reference Sequence of the Soybean Genome: a Multi-Agency Effort - (Peer Reviewed Journal)

Jackson, S.A., Rokhsar, D., Stacy, G., Shoemaker, R.C., Schmutz, J., Grimwood, J. 2006. Toward reference sequence of the soybean genome: a multi-agency effort. The Plant Genome. 1:55-61.

Recovering from Iron Deficiency Chlorosis in Near Isogenic Soybeans: a Microarray Study - (Abstract)

O'Rourke, J.A., Graham, M.A., Cianzio, S.R., Shoemaker, R.C. 2007. Recovering from iron deficiency chlorosis in near isogenic soybeans: a microarray study [abstract]. Iron Nutrition and Interactions in Plants Symposium. Paper No. S6-P-21.

The Fad2 Gene Family of Soybean:insights into the Structural and Functional Divergence of a Paleopolyploid Genome - (Peer Reviewed Journal)

Schlueter, J.A., Sanders, I.F., Deshpande, S., Yi, J., Seigfried, M., Roe, B.A., Schlueter, S.D., Scheffler, B.E., Shoemaker, R.C. 2006. The fad2 gene family of soybean:insights into the structural and functional divergence of a paleopolyploid genome. The Plant Genome. 1:14-26.

Genetic Bottlenecks and Soybean Genetic Variability and Vulnerability - (Abstract)

Cregan, P.B., Hyten, D.L., Song, Q., Zhu, Y., Choi, I., Nelson, R.L., Costa, J.M., Shoemaker, R.C., Specht, J.E. 2006. Genetic Bottlenecks and Soybean Genetic Variability and Vulnerability [abstract]. Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting. Paper No. 23301. Available: http://a-c-s.confex.com/crops/2006am/techprogram/P23301.htm.

Impacts of Genetic Bottlenecks on Soybean Genome Diversity - (Peer Reviewed Journal)

Hyten, D.L., Song, Q., Zhu, Y., Choi, I., Nelson, R.L., Costa, J., Specht, J.E., Shoemaker, R.C., Cregan, P.B. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proceedings of the National Academy of Sciences. 103:16666-16671.

An Initial Assessment of Genome-wide Linkage Disequilibrium in Soybean - (Abstract)

Hyten, D.L., Choi, I., Yoon, M., Song, Q., Specht, J.E., Nelson, R., Chase, K., Young, N., Lark, G., Shoemaker, R.C., Cregan, P.B. 2006. An Initial Assessment of Genome-wide Linkage Disequilibrium in Soybean [abstract]. Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting. Paper No. 23311. http://a-c-s.confex.com/crops/2006am/techprogram/P23311.htm.

Soybean Genetics - (Book/Chapter)

Palmer, R.G., Shoemaker, R.C. 2008. Soybean Genetics. In: Miladinovic, J., Hrustic, M., Vidic, M., editors. Novi Sad, Serbia: Soybean Institute of Field and Vegetable Crops Publisher. p. 77-129.

Identification and Analysis of Gene Families from the Duplicated Genome of Soybean Using EST Sequences - (Peer Reviewed Journal)

Nelson, R., Shoemaker, R.C. 2006. Identification and Analysis of Gene Families from the Duplicated Genome of Soybean Using EST Sequences. Biomed Central (BMC) Genomics. 7:204.

Characterization of Flowering Time and Ssr Marker Analysis of Spring and Winter Type Brassica Napus L. Germplasm - (Peer Reviewed Journal)

Cruz, V.V., Luhman, R., Rife, C.L., Shoemaker, R.C., Marek, L.F., Brummer, E., Gardner, C.A. 2007. Characterization of flowering time and SSR marker analysis of spring and winter type Brassica napus L. germplasm. Euphytica. 153:43-57.

The Soybean Breeder's Toolbox: a New Resource for Soybean Genetic and Genomic Information - (Abstract)

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.

Analysis of Bulked and Redundant Accessions of Brassica Germplasm Using Assignment Tests of Microsatellite Markers - (Peer Reviewed Journal)

Cruz, V.V., Nason, J.D., Luhman, R., Marek, L.F., Shoemaker, R.C., Brummer, E., Gardner, C.A. 2006. Analysis of bulked and redundant accessions of Brassica germplasm using assignment tests of microsatellite markers. Euphytica. 152:339-349.

Soybean Unigenes ¿ Using Snps to Determine Their Genetic Map Position - (Abstract)

Choi, I., Song, Q.J., Hyten, D.L., Reiter, R., Lee, M.S., Hwang, E.Y., Costa, J.M., Shoemaker, R.C., Chase, K., Lark, K.G., Specht, J.E., Cregan, P.B. 2006. Soybean unigenes ¿ using snps to determine their genetic map position [abstract]. Annual International Plant & Animal Genome Conference, January 13-17, 2006, San Diego, CA. p.189.

Paleopolyploidy and Genome Duplication in Soybean and Other Legumes - (Peer Reviewed Journal)

Shoemaker, R.C., Schlueter, J., Doyle, J. 2006. Paleopolyploidy and genome duplication in soybean and other legumes. Current Opinion in Plant Biology. 9:104-109.

Genome Studies and Molecular Genetics: Exploring the Structure Function and Evoluti0n of Legume Genomes - (Review Article)

Young, N.D., Shoemaker, R.C. 2006. Genome studies and molecular genetics: exploring the structure function and evolution of legume genomes. Current Opinion in Plant Biology. 9:1-16.

Domestication, Founding Effects and Artificial Selection - Genetic Bottlenecks and Soybean Genetic Variability - (Abstract)

Cregan, P.B., Hyten, D.L., Zhu, Y., Song, Q., Choi, I., Nelson, R.L., Costa, J., Specht, J.E., Shoemaker, R.C. 2006. Domestication, founding effects and artificial selection - genetic bottlenecks and soybean genetic variability [abstract]. Annual International Plant & Animal Genome Conference. January 13-17, 2006, San Diego, CA. W148.

Genetic Association Analysis for the Detection of Genetic Factors Controlling Seed Protein Concentration in Soybean - (Abstract)

Hwang, E., Song, Q., Joseph, B., Shoemaker, R.C., Costa, J., Specht, J., Cregan, P.B. 2006. Genetic association analysis for the detection of genetic factors controlling seed protein concentration in soybean [abstract]. International Plant and Animal Genome IX Conference. January 13-17, 2006, San Diego, CA, p.167.

Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations. - (Abstract)

Hyten, D.L., Song, Q., Choi, I., Shoemaker, R.C., Nelson, R.L., Costa, J., Specht, J., Cregan, P.B. 2005. Highly variable patterns of linkage disequilibrium in multiple soybean populations [abstract]. American Society of Agronomy Meetings. http://crops.confex.com/crops/2005am/techprogram/P5905.HTM.

Soybean Single Nucleotide Polymorphisms - from Genotypic Assay to Genetic Map Position. - (Abstract)

Specht, J.E., Lark, K.G., Chase, K., Choi, I., Song, Q., Hyten, D.L., Shoemaker, R.C., Cregan, P.B. 2005. Soybean single nucleotide polymorphisms - from genotypic assay to genetic map position [abstract]. American Society of Agronomy Meetings. November 9, 2005. (http://crops.confex.com/crops/2005am/techprogram/P6358.HTM).

Characterization of Flowering Time and Ssr Marker Analysis of Annual and Winter Type Brassica Napus Germplasm - (Abstract)

Cruz, V., Luhman, R., Rife, C.L., Shoemaker, R.C., Marek, L.F., Brummer, E.C., Gardner, C.A. 2006. Characterization of flowering time and ssr marker analysis of annual and winter type brassica napus germplasm [abstract]. Plant and Animal Genome VX Conference. Poster Presentation P144.

DNA Sequence Diversity in Modern Soybean and Its Asian Ancestors. - (Abstract)

Cregan, P.B., Hyten, D.L., Choi, I., Song, Q., Nelson, R.L., Zhu, Y., Costa, J., Specht, J., Shoemaker, R.C. 2005. Dna sequence diversity in modern soybean and its asian ancestors [abstract]. American Society of Agronomy Meetings. http://crops.confex.com/crops/2005am/techprogram/P5897.HTM.

Genomic Resources of Agronomic Crops - (Book/Chapter) - (30-Sep-05)

Evolution of Iron Acquisition in Higher Plants - (Peer Reviewed Journal)

Charlson, D.V., Shoemaker, R.C. 2006. Evolution of iron acquisition in higher plants. Journal of Plant Nutrition. 29:1109-1125.

Centric Regions of Soybean (Glycine Max L. MERR.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile - (Peer Reviewed Journal)

Lin, J., Jacobus, B., Sanmiguel, P., Walling, J., Yuan, Y., Shoemaker, R.C., Young, N., Jackson, S. 2005. Centric regions of soybean (Glycine max L. merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile. Genetics. 170:1221-1230.

Legumes As a Model Plant Family: Genomics for Food and Feed - (Peer Reviewed Journal)

Gepts, P., Beavis, W., Brummer, E.C., Shoemaker, R.C., Stalker, H.T., Weeden, N.F., Young, N.D. 2005. Legumes as a model plant family: genomics for food and feed. Plant Physiology. 137(4):1228-1235.

Bridging Model and Crop Legumes Through Comparative Genomics - (Peer Reviewed Journal)

Zhu, H., Choi, H., Cook, D., Shoemaker, R.C. 2005. Bridging model and crop legumes through comparative genomics. Plant Physiology. 137(4):1189-1196.

Identification of a Large Cluster of Coiled Coil-Nucleotide Binding Site-Leucine Rich Repeat-Type Genes from the Rps1 Region Containing Phytophthora Resistance Genes in Soybean - (Peer Reviewed Journal)

Bhattacharyya, M.K., Narayanan, N.N., Gao, H., Salimath, S.S., Santra, D.K., Kasuga, T., Liu, Y., Espinosa, B., Ellison, L., Marek, L., Shoemaker, R.C., Gijzen, M., Buzzell, R.I. 2005. Identification of a large cluster of coiled coil-nucleotide binding site-leucine rich repeat-type genes from the Rps1 region containing phytophthora resistance genes in soybean. Journal of Theoretical and Applied Genetics. 111:75-86.

Registration of 'ldx01-1-65' Soybean Germplasm - (Peer Reviewed Journal)

Diers, B.W., Arelli, P.R., Carlson, S.R., Fehr, W.R., Kabelka, E.A., Shoemaker, R.C., Wang, D. 2005. Registration of 'LDX01-1-65' soybean germplasm. Crop Science 45:1671-1672.

Different Patterns of Linkage Disequilibrium Around Three Disease Loci in Four Soybean Populations - (Abstract)

Hyten, D.L., Song, Q., Costa, J., Shoemaker, R.C., Cregan, P.B. 2005. Different patterns of linkage disequilibrium around three disease loci in four soybean populations. Meeting Abstract. Plant & Animal Genome XIII Abstract. P. 432.

Placing Palepolyploidy in Relation to Taxon Divergence: a Phylogenetic Analysis in Legumes Using 39 Gene Families - (Peer Reviewed Journal)

Pfeil, B., Schlueter, J., Shoemaker, R.C., Doyle, J. 2005. Placing palepolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Systematic Biology. 54(3):441-454.

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.

The Soybean Genome: Duplicative, Yet Unique - (Abstract)

Shoemaker, R.C., Schlueter, J., Scheffler, B.E. 2005. The soybean genome: duplicative, yet unique. Plant and Animal Genome Abstracts. W207:Legumes.

Preliminary Analysis of Single Nucleotide Polymorphisms in Soybean Detected B Estminer Analysis - (Abstract)

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)

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.

Microarrays for Global Expression Constructed with a Low Redundancy Set of 27,500 Sequenced Cdnas Representing An Array of Developmental Stages and Physiological Conditions of the Soybean Plant - (Peer Reviewed Journal)

Vodkin, L.O., Kahnna, A., Shealy, R.T., Clough, S.J., Gonzales, D.O., Philip, R., Zabala, G.C., Thibaud-Nissen, F., Sidarous, M., Stromvik, M.V., Shoop, E.G., Schmidt, C., Retzel, E., Erpelding, J., Shoemaker, R.C., Rodrizues-Huete, A.M., Polacco, J.C., Coryell, V., Keim, P., Gong, G., Lui, L., Pardinas, J.L., Schweitzer, P. 2004. Microarrays For Global Expression Constructed With A Low Redundancy Set of 27,500 Sequenced cDNAs Representing An Array of Developmental Stages and Physiological Conditions of The Soybean Plant. Biomed Central (BMC) Genomics. 5:73.

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.

Molecular Marker Satt481 Is Associated with Iron Deficiency Chlorosis Resistance in a Soybean Breeding Population - (Peer Reviewed Journal)

Charlson, D.V., Bailey, T.B., Cianzio, S.R., Shoemaker, R.C. 2005. Molecular marker satt481 is associated with iron deficiency chlorosis resistance in a soybean breeding population. Crop Science. 45:2394-2399.

Est Projects for the Study of Genome Evolution in Legumes - (Book/Chapter) - (01-Jul-04)

Genome Exploitation: Data Mining the Genome - (Other)

Gustafson, J.P., Shoemaker, R.C., Snape, J.W. 2005. Genome exploitation: data mining the genome. 23rd Stadler Genetics Symposium. Springer Publishing. 252 p.

Segmental Duplications Within the Glycine Max Genome Revealed by Fluorescence in Situ Hybridization of Bacterial Artificial Chromosomes - (Peer Reviewed Journal)

Pagel, J., Walling, J.G., Young, N.D., Shoemaker, R.C., Jackson, S.A. 2004. Segmental duplications within the glycine max genome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes. Genome. v. 47. p. 764-768.

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.

Features of a 103-Kb, Gene-Rich Region in Soybean Include An Inverted Perfect Repeat Cluster of Chs Genes Comprising the I Locus - (Peer Reviewed Journal)

Clough, S.J., Tuteja, J.H., Min, L., Marek, L.F., Shoemaker, R.C., Vodkin, L.O. 2004. Features of A 103-kb, Gene-rich Region In Soybean Include An Inverted Perfect Repeat Cluster of CHS Genes Comprising The i Locus. Genome. 47(5):819-831.

National Science Foundation-Sponsored Workshop Report: Draft Plan for Soybean Genomics - (Peer Reviewed Journal)

Stacey, G., Vodkin, L., Parrott, W.A., Shoemaker, R.C. 2004. National science foundation-sponsored workshop report: draft plan for soybean genomics. Plant Physiology. 135:59-70.

A New Integrated Genetic Linkage Map of the Soybean - (Peer Reviewed Journal)

Song, Q.J., Marek, L.F., Shoemaker, R.C., Lark, K.G., Consibido, V.C., Delannay, X., Specht, J.E., Cregan, P.B. 2003. A new integrated genetic linkage map of the soybean. Theoretical and Applied Genetics. v. 109. p. 122-128.

Sequence Annotation of Bac104j7 Containing the 10.71-KB Exact Invert Repeat Chs Cluster of the I Locus in Soybean - (Proceedings/Symposium)

Clough, S.J., Gregoire, R., Li, M., Marek, L., Shoemaker, R.C., Vodkin, L. 2004. Sequence annotation of bac104j7 containing the 10.71-kb exact invert repeat chs cluster of the i locus in soybean. Soybean Biotechnology Meeting. p. 80.

Soybean Bac Contigs Anchored with Rflps: Insights into Genome Duplication and Gene Clustering - (Peer Reviewed Journal)

Mudge, J., Huihuang, Y., Denny, R.L., Howe, D.K., Danesh, D., Marek, L.F., Retzel, E., Shoemaker, R.C., Young, N.D. 2004. Soybean bac contigs anchored with rflps: insights into genome duplication and gene clustering. Genome. v. 47. p. 361-372.

Characterization of Soybean Fgam Synthase Genes and Their Expression Within Nematode Feeding Sites - (Peer Reviewed Journal)

Vaghchhipawala, Z.E., Schlueter, J.A., Shoemaker, R.C., Mackenzie, S.A. 2004. Characterization of soybean fgam synthase genes and their expression within nematode feeding sites. Genome. v. 47. p. 404-413.

Comparative Physical Mapping Reveals Features of Microsynteny Between the Genomes of Glycine Max and Medicago Truncatula - (Peer Reviewed Journal)

Yan, H., Mudge, J., Kim, D., Shoemaker, R.C., Cook, D., Young, N.D. 2004. Comparative physical mapping reveals features of microsynteny between the genomes of glycine max and medicago truncatula. Genome. v. 47. p.141-155.

Genetic and Physical Mapping of the Soybean Rpg1-B Disease Resistance Gene Reveals a Complex Locus Containing Several Tightly Linked Families of Nbs-Lrr-Genes - (Peer Reviewed Journal)

Ashfield, T., Bocian, A., Held, D., Henk, A.D., Marek, L.F., Danesh, D., Lightfoot, D.A., Penuela, S., Meksem, K., Shoemaker, R.C. 2003. Genetic and physical mapping of the soybean rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of nbs-lrr-genes. Molecular Plant Microbe Interactions. v. 16. p. 817-826.

The Status of Soybean Genomics and Its Role in the Development of Soybean Biotechnologies - (Peer Reviewed Journal)

Shoemaker, R.C., Schlueter, J., Cregan, P.B., Vodkin, L. 2003. The status of soybean genomics and its role in the development of soybean biotechnologies. Agbioforum. v. 6. p. 1-10.

Soybean Genomics - (Monograph)

Shoemaker, R.C., Cregan, P.B., Vodkin, L. 2003. Soybean genomics. American Society of Agronomy Monograph Series. p. 235-255.

The Seed Protein, Oil, and Yield Qtl on Soybean Linkage Group I - (Peer Reviewed Journal)

CHUNG, J.I., OLSEN, H.L., GRAEF, G.L., STASWICH, P.E., LEE, D.J., CREGAN, P.B., SHOEMAKER, R.C., SPECHT, J.E. THE SEED PROTEIN, OIL, AND YIELD QTL ON SOYBEAN LINKAGE GROUP I. CROP SCIENCE. 2003. v. 43. p. 1053-1067.

Associating Ssr Markers with Soybean Resistance to Iron Chlorosis - (Peer Reviewed Journal)

CHARLSON, D.V., CIANZIO, S.R., SHOEMAKER, R.C. ASSOCIATING SSR MARKERS WITH SOYBEAN RESISTANCE TO IRON CHLOROSIS. JOURNAL OF PLANT NUTRITION. 2003. v. 26. p. 2267-2276.

Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean - (Peer Reviewed Journal)

GRAHAM, M.A., MAREK, L.F., SHOEMAKER, R.C. ORGANIZATION, EXPRESSION AND EVOLUTION OF A DISEASE RESISTANCE GENE CLUSTER IN SOYBEAN. GENETICS. 2002. v. 162. p. 1961-1977.

Sequence Analysis of the I Locus in Williams 82 - (Proceedings/Symposium)

Clough, S.J., Gregoire, R., Chan, W., Marek, L., Shoemaker, R.C., Vodkin, L. Sequence analysis of the i locus in williams 82. Cellular and Molecular Biology of Soybean Biennial Conference. p. 603.

Molecular Marker Analysis of Seed Size in Soybean - (Peer Reviewed Journal)

HOECK, J.A., FEHR, W.R., SHOEMAKER, R.C., WELKE, G.A., JOHNSON, S.L., CIANZIO, S.R. MOLECULAR MARKER ANALYSIS OF SEED SIZE IN SOYBEAN. CROP SCIENCE. 2003. V. 43. P. 68-74.