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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL AND STRUCTURAL GENETIC ANALYSIS OF SOYBEAN AND OTHER LEGUMES

Location: Corn Insects and Crop Genetics Research

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

Visual mining methods for RNA-Seq data: data structure, dispersion estimation and significance testing - (Peer Reviewed Journal)
Yin, T., Majumder, M., Chowdhury, N., Cook, D., Shoemaker, R.C., Graham, M.A. 2013. Visual mining methods for RNA-Seq data: data structure, dispersion estimation and significance testing. Journal of Data Mining in Genomics & Proteomics. 4:139.
Replication protein A subunit 3 and the iron efficiency response in soybean - (Peer Reviewed Journal)
Atwood, S., O'Rourke, J., Peiffer, G., Yin, T., Majumder, M., Zhang, C., Cianzio, S., Hill, J., Cook, D., Whitham, S., Shoemaker, R.C., Graham, M.A. 2013. Replication protein A subunit 3 and the iron efficiency response in soybean. Plant Cell and Environment. DOI: 10.1111/pce.12147.
Genomic heterogeneity and structural variation in soybean near-isogenic lines - (Peer Reviewed Journal)
Stec, A., Bhaskar, P., Bolon, Y., Nolan, R., Shoemaker, R.C., Vance, C.P., Stupar, R. 2013. Genomic heterogeneity and structural variation in soybean near-isogenic lines. Frontiers in Plant Science. 4:104.
Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway - (Peer Reviewed Journal)
Morales, A., O'Rourke, J.A., Van De Mortel, M., Schneider, K., Bancroft, T., Borem, A., Nelson, R., Nettleton, D., Baum, T., Shoemaker, R.C., Frederick, R.D., Abdelnoor, R.V., Pedley, K.F., Whitham, S.A., Graham, M.A. 2013. Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway. Functional Plant Biology. DOI:10.1071/FP12296.
Evaluation and QTL mapping of phosphorous concentration in soybean seed - (Peer Reviewed Journal)
King, K.E., Lauter, N.C., Lin, S., Scott, M.P., Shoemaker, R.C. 2013. Evaluation and QTL mapping of phosphorous concentration in soybean seed. Euphytica. 189(2):261-269.
Molecular mapping of the mutant fap4(A24) allele for elevated palmitate concentration in soybean - (Peer Reviewed Journal)
Oltmans-Deardorff, S.E., Fehr, W.R., Welke, G.A., Shoemaker, R.C., Graham, M.A. 2012. Molecular mapping of the mutant fap4(A24) allele for elevated palmitate concentration in soybean. Crop Science. 53(1):106-111.
Marker-assisted selection for elevated concentrations of the a' subunit of B-conglycinin and its influence on agronomic and seed traits of soybean - (Peer Reviewed Journal)
Oltmans-Deardorff, S.E., Fehr, W.R., Shoemaker, R.C. 2012. Marker-assisted selection for elevated concentrations of the a' subunit of B-conglycinin and its influence on agronomic and seed traits of soybean. Crop Science. 53:1-8.
Inheritance and molecular mapping of an allele providing resistance to Cowpea mild mottle virus-like symptoms in soybean - (Peer Reviewed Journal)
Brace, R.C., Fehr, W.R., Graham, M.A. 2012. Inheritance and molecular mapping of an allele providing resistance to Cowpea mild mottle virus-like symptoms in soybean. Crop Science. 52(5):2109-2114.
The future of soybean genomics is here - (Review Article)
Shoemaker, R.C., Severin, A., Woody, J.L., Cannon, S.B., Graham, M.A. 2013. The future of soybean genomics is here. Grain Legumes. 1:16-18.
Large homogeneous genome regions (Isochores) in soybean (Glycine max (L.) Merr.) - (Peer Reviewed Journal)
Woody, J.L., Beavis, W., Shoemaker, R.C. 2012. Large homogeneous genome regions (Isochores) in soybean (Glycine max (L.) Merr.). Frontiers in Plant Genetics and Genomics. 3:98 DOI:10.3389/fgene.2012.00098.
Advances on molecular studies of the interaction soybean - Asian rust - (Peer Reviewed Journal)
Morales, A., Borem, A., Graham, M.A., Abelnoor, R. 2012. Advances on molecular studies of the interaction soybean - Asian rust. Crop Breeding and Applied Biotechnology. 12:1-7.
Identification of candidate genes underlying an iron efficiency QTL in soybean - (Peer Reviewed Journal)
Peiffer, G.A., King, K.E., Severin, A.J., May, G.D., Cianzio, S.R., Lin, S., Lauter, N.C., Shoemaker, R.C. 2012. Identification of candidate genes underlying an iron efficiency QTL in soybean. Plant Physiology. 158(4):1745-1754.
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.
Mapping of iron and zinc quantitative trait loci in soybean for association to iron deficiency chlorosis resistance - (Peer Reviewed Journal)
King, K., Peiffer, G., Lauter, N.C., Lin, S., Cianzio, S., Shoemaker, R.C. 2013. Mapping of iron and zinc quantitative trait loci in soybean (glycine max (L.) Merr.) for association to iron deficiency chlorosis resistance. Journal of Plant Nutrition. 36(14):2132-2153.
Gene Expression: Sizing it all up - (Peer Reviewed Journal)
Woody, J.L., Shoemaker, R.C. 2011. Gene Expression: Sizing it all up. Frontiers in Plant Genetics and Genomics. 2:70.
Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development - (Peer Reviewed Journal)
Liu, J., Horstman, H.D., Braun, E., Graham, M.A., Zhang, C., Navarre, D., Lee, Y., Nettleton, D., Hill, J.H., Whitham, S.A. 2011. Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. Journal of Plant Physiology. 157(3):2363-1378.
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.
Sequencing crop genomes: approaches and applications - (Peer Reviewed Journal)
Jackson, S.A., Lee, S., Schmutz, J., Shoemaker, R.C. 2011. Sequencing crop genomes: approaches and applications. New Phytologist. 191:915-925.
Identification of genes that mediate protection against soybean pathogens - (Book / Chapter)
(26-Nov-10)
Functional analysis of the Asian soybean rust resistance pathway mediated by Rpp2 - (Peer Reviewed Journal)
Pandey, A.K., Yang, C., Zhang, C., Graham, M.A., Horstman, H.D., Lee, Y., Zabotina, O.A., Hill, J.H., Pedley, K.F., Whitham, S.A. 2011. Functional analysis of the Asian soybean rust resistance pathway mediated by Rpp2. Molecular Plant-Microbe Interactions. Molecular Plant-Microbe Interactions. 24:194-206.
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.
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.
Bifurcation and Enhancement of Autonomous-Non-Autonomous Retrotransposon Partnership through LTR Swapping in Soybean - (Peer Reviewed Journal)
Du, J., Tian, Z., Bowen, N., Schmutz, J., Shoemaker, R.C., Ma, J. 2010. Bifurcation and Enhancement of Autonomous-Non-Autonomous Retrotransposon Partnership through LTR Swapping in Soybean. The Plant Cell. 22:48-61.
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 Within Syntenic Regions Between Soybean and Medicago Truncatula and Their Contribution to Local Genome Evolution - (Peer Reviewed Journal)
Joseph, B., Schlueter, J., Du, J., Graham, M.A., Ma, J., Shoemaker, R.C. 2009. Retrotransposons Within Syntenic Regions Between Soybean and Medicago Truncatula and Their Contribution to Local Genome Evolution. The Plant Genome. 2(3):211-223.
Soybean Comparative Genomics - (Book / Chapter)
Ma, J., Cannon, S.B., Jackson, S.A., Shoemaker, R.C. 2010. Soybean Comparative Genomics. In: Bilyeu, K., Ratnaparkhe, M.B., and Kole, C., editors. Genetics, Genomics, and Breeding of Soybean. Routledge, New York. p. 245-262.
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.
Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions Following Polyploidy in the Ancestor of Soybean - (Peer Reviewed Journal)
Innes, R.W., Ameline-Torregrosa, C., Ashfield, T., Cannon, E., Cannon, S.B., Chacko, B., Chen, N.W., Couloux, A., Dalvani, A., Denny, R., Deshpade, S., Doyle, J.J., Egan, A., Geffroy, V., Glover, N., Hans, C.S., Howell, S., Ilut, D., Jackson, S., Lai, H., Mammadov, J., Martin Del Campo, S., Metcalf, M., Nguyen, A., O'Bleness, M., Pfeil, B., Podicheti, R., Ratnaparkhe, M., Roe, B., Saghai, M.A., Samain, S., Sanders, I., Segurens, B., Sevigna, M., Sherman-Broyles, S., Thareau, V., Tucker, D., Walling, J., Wawrzynski, A., Yi, J., Young, N.D. 2008. Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions Following Polyploidy in the Ancestor of Soybean. Plant Physiology. 148:1740-1759.
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 Candidate Genes for the Rpp4 Asian Soybean Rust Resistance Locus in Soybean - (Abstract Only)
(20-Jul-08)
Targeted Sequencing and Analyses of the Rpp4 Asian Soybean Rust Resistance Locus in Soybean - (Abstract Only)
(20-Jul-08)
Targeted Sequencing of the Rpp2 Asian Soybean Rust Resistance Locus - (Abstract Only)
(20-Jul-08)
Last Modified: 8/27/2014
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