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United States Department of Agriculture

Agricultural Research Service

Research Project: CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES

Location: Corn Insects and Crop Genetics Research

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

Keeping an eye on the biology - (Peer Reviewed Journal)
Singer, S.R., Schwarz, J.A., Manduca, C.A., Fox, S.P., Iverson, E.R., Taylor, B., Cannon, S.B., May, G.D., et al. 2013. Keeping an eye on the biology. Science. 339(6118):408-409.
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement - (Peer Reviewed Journal)
Varshney, R.K., Song, C., Saxena, R.K., Azam, S., Yu, S., Sharpe, A.G., Cannon, S.B., Rosen, B., Tar'An, B., Millan, T., et al. 2013. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology. 31:240-246.
The model legume genomes - (Book / Chapter)
Cannon, S.B. 2013. The model legume genomes. In: Rose, R.J., editor. Legume Genomics: Methods and Protocols. Heidelberg, NY: Springer. p. 1-14.
Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean - (Peer Reviewed Journal)
Tian, Z., She, M., Zhao, M., Du, J., Cannon, S.B., Liu, X., Xu, X., Lam, H., Ma, J. 2012. Genome-Wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. The Plant Cell. 24(11): 4422-4436.
Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes - (Abstract Only)
Arnaud, E., Cooper, L., Shrestha, R., Menda, N., Nelson, R., Ramil, M., Matteis, L., Skofic, M., Bastow, R., Jaiswal, P., Mueller, L., Mclaren, G. 2012. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes. Meeting Abstract. Paper No. 67.
The impact of polyploidy on the evolution of a complex NB-LRR resistance gene cluster in soybean - (Peer Reviewed Journal)
Ashfield, T., Egan, A.N., Pfeil, B.E., Chen, N.W., Ratnaparkhe, M.B., Ameline-Torregrosa, C., Denny, R., Cannon, S.B., Doyle, J.J., Geffroy, V., Roe, B.A., Maroof, M.S., Young, N.D., Innes, R.W. 2012. The impact of polyploidy on the evolution of a complex NB-LRR resistance gene cluster in soybean. Plant Physiology. DOI:10.1104/CS.112.195040.
Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Paleopolyploid Soybean - (Peer Reviewed Journal)
Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P.B., Ma, J. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Paleopolyploid Soybean. The Plant Cell. 24(1):21-32.
A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms - (Peer Reviewed Journal)
Kudapa, H., Bharti, A.K., Cannon, S.B., Farmer, A.D., Deonovic, B., Kramer, R., Bohra, A., Weeks, N.T., Crow, J.A., Tuteja, R., Shah, T., Dutta, S., Gupta, D.K., Singh, A., Gaikwad, K., Sharma, T.R., May, G.D., Singh, N.K., Varshney, R.K. 2012. A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms. Molecular Plant. 5(5):1020-1028.
CViT: “Chromosome Visualization Tool” – A whole-genome viewer - (Peer Reviewed Journal)
Cannon, E.K., Cannon, S.B. 2011. CViT: “Chromosome Visualization Tool” – A whole-genome viewer. International Journal of Plant Genomics. DOI:10.1155/2011/373875.
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.
The medicago genome provides insight into evolution of rhizobial symbiosis - (Peer Reviewed Journal)
Young, N.D., Debelle, F., Oldroyd, G., Geurts, R., Cannon, S.B., Mayer, K.F., Gouzy, J., Van De Peer, Y., Schoof, H., Udvardi, M.K., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Proost, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Benedito, V.A., Murray, J.D., Naoumkina, M.A., Rosen, B., Silverstein, K.A., Tang, H., Rombauts, S., Zhao, P.X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Doyle, J.J., Dudez, A., Farmer, A.D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Gonzalez, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S., Jeong, D., Jing, Y., Jocker, A., Kenton, S.M., Kim, D., Klee, K., Lai, H., Lang, C., Lin, S., Macmill, S.L., Magdelenat, G., Matthews, L., Mccorrison, J., Monaghan, E.L., Mun, J., Najar, F.Z., Nicholson, C., Noirot, C., Paule, C.R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E.F., Riddle, C., Sallet, E., Samain, S., Samson, N., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Seigfried, M., Severin, A., Sherrier, J.D., Shi, R., Sims, S., Sinharoy, S., Sterck, L., Vasylenko, I., Viollet, A., Wang, K., Wang, B., Wang, X. 2011. The medicago genome provides insight into evolution of rhizobial symbiosis. Nature. 480(7378):520-524.
Evolutionary and comparative analyses of the soybean genome - (Peer Reviewed Journal)
Cannon, S.B., Shoemaker, R.C. 2012. Evolutionary and comparative analyses of the soybean genome. Journal of Breeding Science. 61(5):437-444.
Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa - (Peer Reviewed Journal)
Hiremath, P.J., Farmer, A., Woodward, J., Cannon, S.B., Kudapa, H., Tuteja, R., Kumar, A., Varshney, R.K. 2011. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnology Journal. 9:922-931.
Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.) - (Peer Reviewed Journal)
Dubey, A., Farmer, A., Schlueter, J., Cannon, S.B., Abernathy, B., Tuteja, R., Woodward, J., Varshney, R.K. 2011. Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Research. 18(3):153-164.
Legumes as a Model Plant Family - (Book / Chapter)
Cannon, S.B., Sato, S., Tabata, S., Young, N.D., May, G.D. 2011. Legumes as a Model Plant Family. In: Pratap, A., Kumar, J., editors. Biology and Breeding of Food Legumes. Cambridge, MA. CABI. p. 348-357.
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.
Polyploids did not Predate the Evolution of Nodulation in all Legumes     Reprint Icon - (Peer Reviewed Journal)
Cannon, S.B., Ilut, D., Farmer, A.D., Maki, S.L., May, G.D., Singer, S.R., Doyle, J.J. 2010. Nodule evolution did not depend on early polyploidy in the legumes. PLoS One. 5(7):e11630.
Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences     Reprint Icon - (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.
Evolutionary conservation, diversity and specificity of LTR retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison     Reprint Icon - (Peer Reviewed Journal)
Du, J., Tian, S., Hans, C., Jackson, S., Cannon, S.B., Shoemaker, R.C., Ma, J. 2010. Evolutionary conservation, diversity and specificity of LTR retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant Journal. 63(4):584-598.
A Fluorescence In Situ Hybridization System for Karyotyping Soybean - (Peer Reviewed Journal)
Findley, S.D., Cannon, S.B., Varala, K., Du, J., Ma, J., Hudson, M.E., Birchler, J., Stacey, G. 2010. A Fluorescence In Situ Hybridization System for Karyotyping Soybean. Genetics. 185:727-744.
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.
Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration - (Peer Reviewed Journal)
Nelson, R., Avraham, S., Shoemaker, R.C., May, G., Ware, D., Gessler, D.D. 2009. Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration. BioMed Central (BMC) BioData Mining. 10:309.
A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean - (Peer Reviewed Journal)
David, P., Chen, N., Pedrosa-Harand, A., Sevignac, M., Thareau, V., Cannon, S.B., Debouck, D., Langin, T., Geffroy, V. 2009. A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean. Plant Physiology. 151:1048-1065.
Sswap: a Simple Semantic Web Architecture and Protocol for Semantic Web Services     Reprint Icon - (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.
Update on Comparative Genomics of Legumes - (Review Article)
Cannon, S.B., May, G.D., Jackson, S.A. 2009. Update on Comparative Genomics of Legumes. Plant Physiology. 151:970-977.
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.
Beyond the Papilionoids – What can We Learn from Chamaecrista? - (Review Article)
Singer, S.R., Maki, S.L., Farmer, A.D., Ilut, D., May, G.D., Cannon, S.B., Doyle, J.J. 2009. Beyond the Papilionoids – What can We Learn from Chamaecrista? Plant Physiology. 151:1041-1047.
Evolutionary Genomics of LysM Genes in Land Plants - (Peer Reviewed Journal)
Zhang, X., Cannon, S.B., Stacey, G. 2009. Evolutionary Genomics of LysM Genes in Land Plants. BMC Evolutionary Biology. 9:183.
Genetics, Genomics and Breeding in Soybean - (Book / Chapter)
(03-Mar-09)
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.
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.
Replication of Nonautonomous Retroelements in Soybean Appears to be Both Recent and Common - (Peer Reviewed Journal)
Wawrzynski, A., Ashfield, T., Chen, N.W., Mammadov, J., Nguyen, A., Podicheti, R., Cannon, S.B., Thareau, V., Ameline-Torregrosa, C., Cannon, E., Chacko, B., Couloux, A., Dalwani, A., Denny, R., Deshpande, S., Egan, A., Glover, N., Howell, S., Ilut, D., Lai, H., Martin Del Campo, S., Metcalf, M., O'Bleness, M., Pfeil, B., Ratnaparkhe, M., Roe, B., Maroof, M., Samain, S., Sanders, I., Segurens, B., Sevignac, M., Sherman-Broyles, S., Tucker, D.M., Yi, J., Doyle, J.J., Geffroy, V., Roe, B., Maroof, M., Young, N., Innes, R.W. 2008. Replication of Nonautonomous Retroelements in Soybean Appears to be Both Recent and Common. Plant Physiology. 148:1760-1771.
The Soybean Breeder’s Toolbox: Updated Features and New Data - (Abstract Only)
(20-Jul-08)
Last Modified: 8/27/2014
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