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                    U.S. DEPARTMENT OF AGRICULTURE
 Soybean/maize Germplasm, Pathology, and Genetics Research: Urbana, IL
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ARS Home Midwest Area Urbana, Illinois Soybean/maize Germplasm, Pathology, and Genetics Research People & Locations







Steven J Clough
                        Soybean/maize Germplasm, Pathology, and Genetics Research

                        




                        
                        Research Geneticist (Plants)
                        Phone: (217) 265-6452
                        
                        
                        Fax: (217) 244-7703(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsIdentify and Characterize Resistance to Soybean Pathogens and Pests
                                                    In-House Appropriated
                                                                    (D)Accession Number: 442114Institutional Biological Safety Committee (IBC) Agreement - University of Illinois
                                                    Non-Funded Cooperative Agreement
                                                                    (N)Accession Number: 441587The Continued Development and Dissemination of a Comprehensive and Sustainable Management Program for the Main Foliar Diseases of Soybean
                                                    Reimbursable Cooperative Agreement
                                                                    (R)Accession Number: 445619**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Reduction in productivity of soybean plants infested with Neohyadatothrips variabilis (Thysanoptera: Thripidae) with and without soybean vein necrosis virus
                                                        

- (Peer Reviewed Journal)Lagos-Kutz, D.M., Pawlowski, M.L., Han, J., Clough, S.J., Hartman, G.L. 2023. Reduction in productivity of soybean plants infested with Neohyadatothrips variabilis (Thysanoptera: Thripidae) with and without soybean vein necrosis virus. Phytoparasitica. 51:437-445. https://doi.org/10.1007/s12600-023-01070-1.An NBS-LRR protein in the Rpp1 locus negates the dominance of Rpp1-mediated resistance against Phakopsora pachyrhizi in soybean
                                                        

- (Peer Reviewed Journal)Wei, W., Wu, X., Garcia, A., McCoppin, N.K., Gomes Viana, J.P., Murad, P.S., Walker, D.R., Hartman, G.L., Domier, L.L., Hudson, M.E., Clough, S.J. 2022. An NBS-LRR protein in the Rpp1 locus negates the dominance of Rpp1-mediated resistance against Phakopsora pachyrhizi in soybean. The Plant Journal. 113(5):915-933. https://doi.org/10.1111/tpj.16038.The role of a soybean 14-3-3 gene (Glyma05g29080) on white mold resistance and nodulation investigations using CRISPR-Cas9 editing and RNA silencing
                                                        

- (Peer Reviewed Journal)Zhang, Y., Blahut-Beatty, L., Zheng, S., Clough, S.J., Simmonds, D.H. 2022. The role of a soybean 14-3-3 gene (Glyma05g29080) on white mold resistance and nodulation investigations using CRISPR-Cas9 editing and RNA silencing. Molecular Plant-Microbe Interactions. 36(3):159-164. https://doi.org/10.1094/MPMI-07-22-0157-R.Characterization and analysis of the promoter region of Monodehydroascorbate reductase 4 (CpMDAR4) in papaya
                                                        

- (Peer Reviewed Journal)Zerpa-Catanho, D.P., Clough, S.J., Ming, R. 2022. Characterization and analysis of the promoter region of Monodehydroascorbate reductase 4 (CpMDAR4) in papaya. Plant Reproduction. 35:233-264. https://doi.org/10.1007/s00497-022-00447-2.Transcriptome profiling reveals molecular players in early soybean - Sclerotinia sclerotiorum interaction
                                                        

- (Peer Reviewed Journal)Wei, W., Wu, X., Blahut-Beatty, L., Simmonds, D.H., Clough, S.J. 2022. Transcriptome profiling reveals molecular players in early soybean - Sclerotinia sclerotiorum interaction. Phytopathology. 112(8):1739-1752. https://doi.org/10.1094/PHYTO-08-21-0329-R.Characterization and comparison of intestinal bacterial microbiomes of Euschistus heros and Piezodorus guildinii collected in Brazil and the United States
                                                        

- (Peer Reviewed Journal)Moro, M.S., Wu, X., Wei, W., Mendes, L.W., Allen, K.C., Pinheiro, J.B., Clough, S.J., Zucchi, M.I. 2021. Characterization and comparison of intestinal bacterial microbiomes of Euschistus heros and Piezodorus guildinii collected in Brazil and the United States. Frontiers in Microbiology. 12:769965. https://doi.org/10.3389/fmicb.2021.769965.A first draft genome of the Sugarcane borer, Diatraea saccharalis
                                                        

- (Peer Reviewed Journal)Borges Dos Santos, L., Viana, J., Francischini, F., Fogliata, S.V., Joyce, A.L., De Souza, A.P., Murua, M.G., Clough, S.J., Zucchi, M.I. 2020. A first draft genome of the Sugarcane borer, Diatraea saccharalis. F1000Research. 9:1269. https://doi.org/10.12688/f1000research.26614.1.Genome-wide expression of low temperature response genes in Rosa hybrida L.
                                                        

- (Peer Reviewed Journal)Valquíria Dos Reis, M., Vaughn Rouhana, L., Sadeque, A., Koga, L., Clough, S.J., Calla, B., Duarte de Oliveira Paiva, P., Korban, S.S. 2019. Genome-wide expression of low temperature response genes in Rosa hybrida L.. Plant Physiology and Biochemistry. 146:238-248. https://doi.org/10.1016/j.plaphy.2019.11.021.Population genomics of the neotropical stink bug, Euschistus heros: The most important emerging insect pest to soybean in Brazil
                                                        

- (Peer Reviewed Journal)Zucchi, M.I., Cordeiro, E., Wu, X., Marise Lamana, L., Brown, P.J., Manjunatha, S., Gomes Viana, J., Omoto, C., Pinheiro, J., Clough, S.J. 2019. Population genomics of the neotropical stink bug, Euschistus heros: The most important emerging insect pest to soybean in Brazil. Frontiers in Genetics. 10:1035. https://doi.org/10.3389/fgene.2019.01035.Patterns of genome-wide variation, population differentiation and SNP discovery of the red banded stink bug (Piezodorus guildinii)
                                                        

- (Peer Reviewed Journal)Zucchi, M.I., Cordeiro, E., Allen, K.C., Lamana, L.M., Viana, J., Brown, P.J., Omoto, C., Pinheiro, J., Clough, S.J. 2019. Patterns of genome-wide variation, population differentiation and SNP discovery of the red banded stink bug (Piezodorus guildinii). Scientific Reports. 9:14480. https://doi.org/10.1038/s41598-019-50999-z.Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal
                                                        

- (Peer Reviewed Journal)Francischini, F., Cordeiro, E.M., De Campos, J.B., Pereira, A.S., Viana, J., Wu, X., Wei, W., Brown, P.J., Joyce, A., Murua, G., Fogliata, S., Clough, S.J., Zucchi, M.I. 2019. Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal. PLoS ONE. https://doi.org/10.1371/journal.pone.0220031.Two colors, one species: The case of Melissodes nigroaenea (Apidae: Eucerini), an important pollinator of cotton fields in Brazil
                                                        

- (Peer Reviewed Journal)Grando, C., Amon, N.D., Clough, S.J., Guo, N., Wei, W., Azevedo, P., Lopez-Uribe, M.M., Zucchi, M.I. 2018. Two colors, one species: The case of Melissodes nigroaenea (Apidae: Eucerini), an important pollinator of cotton fields in Brazil. Sociobiology. 64:645-653. https://doi.org/10.13102/sociobiology.v65i4.3464.Morphological and molecular characterization of Brazilian populations of Diatraea saccharalis (Lepidoptera: Crambidae) and the evolutionary relationship among Diatraea spp.

- (Peer Reviewed Journal)Francischini, F.J., De Campos, J.B., Pereira, A.A., Viana, J.G., Grinter, C.C., Clough, S.J., Zucchi, M.I. 2017. Morphological and molecular characterization of Brazilian populations of Diatraea saccharalis (Lepidoptera: Crambidae) and the evolutionary relationship among Diatraea spp. PLoS One. 12(11):e0186266.Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil
                                                        

- (Peer Reviewed Journal)Wei, W., Mesquita, A., Figueiro, A., Wu, X., Manjunatha, S., Wickland, D.P., Hudson, M.E., Juliatta, F.C., Clough, S.J. 2017. Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil. BMC Genomics. 18:849. https://doi.org/10.1186/s12864-017-4160-1.Heritability of agronomic traits correlated with reduced stink bug damage in an F2:3 soybean population derived from IAC-100
                                                        

- (Peer Reviewed Journal)Da Fonseca Santos, M., Moller, M., Clough, S.J., Baldin Pinheiro, J. 2017. Heritability of agronomic traits correlated with reduced stink bug damage in an F2:3 soybean population derived from IAC-100. Journal of Crop Improvement. doi.org/10.1080/15427528.2017.1370404.A novel receptor-like kinase involved in fungal pathogen defense in Arabidopsis thaliana
                                                        

- (Peer Reviewed Journal)Ray, J., Yang, X., Kong, F., Guo, T., Deng, F., Clough, S.J., Ramonell, K. 2018. A novel receptor-like kinase involved in fungal pathogen defense in Arabidopsis thaliana. Journal of Phytopathology. 166:506-515. https://doi.org/10.1111/jph.12711.Resistance of soybean genotypes to Sclerotinia sclerotiorum isolates in different incubation environments

- (Peer Reviewed Journal)Castro, L., Figueiro, A., Nogueira, A., Clough, S.J., Juliatti, F. 2016. Resistance of soybean genotypes to Sclerotinia sclerotiorum isolates in different incubation environments. Genetics and Molecular Research. 15(4):gmr15049061. doi: http://dx.doi.org/10.4238/gmr15049061.Investigating the control of chlorophyll degradation by genomic correlation mining

- (Peer Reviewed Journal)Ghandchi, F.P., Caetano-Anolles, G., Clough, S.J., Ort, D.R. 2016. Investigating the control of chlorophyll degradation by genomic correlation mining. PLoS One. 11(9):eo162327.Similarities and differences in global gene expression profiles between herbicide- and pathogen-induced PSII inhibition

- (Peer Reviewed Journal)Zhu, J., Li, M., Clough, S.J. 2015. Similarities and differences in global gene expression profiles between herbicide- and pathogen-induced PSII inhibition. Journal of Plant Biochemistry & Physiology. 3:157. doi:10.4172/2329-9029.1000157.The role of invertases in plant compensatory responses to simulated herbivory
                                                        

- (Peer Reviewed Journal)Siddappaji, M.H., Krishnankutty, S.M., Calla Zalles, B., Clough, S.J., Paige, K.N. 2015. The role of invertases in plant compensatory responses to simulated herbivory. Biomed Central (BMC) Plant Biology. 15:278.If photoinhibition of soybean photosystem II enhances the hypersensitive response, it is not solely due to blockage of electron transfer flow at D1

- (Peer Reviewed Journal)Zhu, J., Neece, D.J., Calla Zalles, B., Clough, S.J. 2015. If photoinhibition of soybean photosystem II enhances the hypersensitive response, it is not solely due to blockage of electron transfer flow at D1. Journal of Plant Biochemistry & Physiology. 3:156. doi:10.4172/2329-9029.1000156.Transcriptome analyses suggest a disturbance of iron homeostasis in soybean leaves during white mould disease establishment
                                                        

- (Peer Reviewed Journal)Calla Zalles, B., Blahut-Beatty, L., Koziol, L., Simmonds, D.H., Clough, S.J. 2014. Transcriptome analyses suggest a disturbance of iron homeostasis in soybean leaves during white mould disease establishment. Molecular Plant Pathology. 15(6):576-588. DOI:10.1111/mpp.12113.Genomic evaluation of oxalate-degrading transgenic soybean in response to Sclerotinia sclerotiorum infection
                                                        

- (Peer Reviewed Journal)Calla Zalles, B., Blahut-Beatty, L., Koziol, L., Zhang, Y., Neece, D.J., Carbajulca, D., Garcia, A., Simmonds, D.H., Clough, S.J. 2014. Genomic evaluation of oxalate-degrading transgenic soybean in response to Sclerotinia sclerotiorum infection. Molecular Plant Pathology. 15(6):563-575. DOI:10.1111/mpp.12115.EF-2DE Analysis and Protein Identification

- (Peer Reviewed Journal)Wu, X., Clough, S.J., Huber, S.C., Oh, M. 2013. EF-2DE Analysis and Protein Identification. Bio-protocol. 3(19):1-8.14-3-3 Proteins SGF14c and SGF14l play critical roles during soybean nodulation

- (Peer Reviewed Journal)Radwan, O., Wu, X., Govindarajulu, M., Libault, M., Neece, D.J., Berg, H.R., Stacey, G., Taylor, C.G., Huber, S.C., Clough, S.J. 2012. 14-3-3 Proteins SGF14c and SGF14l play critical roles during soybean nodulation. Plant Physiology. 160:2125-2136.Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max

- (Peer Reviewed Journal)Zabala, G., Campos, E., Varala, K.K., Bloomfield, S., Jones, S.I., Win, H., Tuteja, J.H., Calla, B., Clough, S.J., Hudson, M., Vodkin, L.O. 2012. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. Biomed Central (BMC) Plant Biology. 12:177.Effects of Fusarium virguliforme phytotoxin on soybean gene expression suggests a multi-dimensional defense approach

- (Peer Reviewed Journal)Radwan, O., Li, M., Calla, B., Li, S., Hartman, G.L., Clough, S.J. 2013. Effects of Fusarium virguliforme phytotoxin on soybean gene expression suggests a multi-dimensional defense approach. Molecular Plant Pathology. 14 (3):293-307.Genome-wide identification of genes regulated by the Rcs Phosphorelay system in Erwinia amylovora

- (Peer Reviewed Journal)Wang, D., Qi, M., Calla, B., Korban, S., Clough, S.J., Sudin, G.W., Toth, I., Cock, P.J., Zhao, Y. 2011. Genome-wide identification of genes regulated by the Rcs Phosphorelay system in Erwinia amylovora. Molecular Plant-Microbe Interactions. 25(1):6-17.The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli

- (Peer Reviewed Journal)Wang, D., Calla, B., Vimolmangkang, S., Korban, S.S., Wu, X., Huber, S.C., Clough, S.J., Zhao, Y. 2011. The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli. PLoS One. 6(9):e25293.Transcriptional analysis of soybean roots response to Fusarium virguliforme, the causal agent of sudden death syndrome

- (Peer Reviewed Journal)Radwan, O., Liu, Y., Clough, S.J. 2011. Transcriptional analysis of soybean roots response to Fusarium virguliforme, the causal agent of sudden death syndrome. Molecular Plant-Microbe Interactions. 24:958-972.Regulatory genes and environmental regulation of amylovoran biosynthesis in Erwinia amylovora

- (Proceedings)Wang, D., Korban, S.S., Sundin, G.W., Clough, S.J., Toth, I., Zhao, Y. 2011. Regulatory genes and environmental regulation of amylovoran biosynthesis in Erwinia amylovora. Acta Horticulture Proceedings. 896:195-202 http://www.actahort.org/books/896/896_25.htm.Biotic Stress Globally Down-Regulates Photosynthesis Genes

- (Peer Reviewed Journal)Bilgin, D.D., Zavala, J.A., Zhu, J., Clough, S.J., Ort, D.R., Delucia, E.H. 2010. Biotic Stress Globally Down-Regulates Photosynthesis Genes. Plant Cell and Environment. doi: 10.1111/j.1365-3040.2010.02167.x.Complete Transcriptome of the Soybean Root Hair Cell, a Single Cell Model, and its Alteration in Response to Bradyrhizobium japonicum Infection

- (Peer Reviewed Journal)Libault, M., Farmer, A., Brechenmacher, L., Franck, W.L., Drnevich, J., Langley, R.J., Bilgin, D.D., Radwan, O., Neece, D.J., Clough, S.J., May, G., Stacey, G. 2009. Complete Transcriptome of the Soybean Root Hair Cell, a Single Cell Model, and its Alteration in Response to Bradyrhizobium japonicum Infection. Plant Physiology. 152: 541-552.Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and In Silico Mapping in Relation to Resistance Markers

- (Peer Reviewed Journal)Calla, B., Vuong, T., Radwan, O., Hartman, G.L., Clough, S.J. 2009. Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and In Silico Mapping in Relation to Resistance Markers. The Plant Genome. 2:149-166.Soybean root defense responses to Fusarium virguliforme infection reveals a role of defense related genes during resistance

- (Abstract Only)Radwan, O., Clough, S.J. 2009. Soybean root defense responses to Fusarium virguliforme infection reveals a role of defense related genes during resistance [abstract]. American Phytopathology Society. 99:S106.Preliminary Analysis of High-Throughput Expression Data and Small RNA in Soybean Stem Tissue Infected with Sclerotinia sclerotiorum

- (Abstract Only)Calla, B., Varala, K.K., Win, H., Hudson, M.E., Vodkin, L.O., Clough, S.J. 2009. Preliminary Analysis of High-Throughput Expression Data and Small RNA in Soybean Stem Tissue Infected with Sclerotinia sclerotiorum [abstract]. Proceedings of the International Sclerotinia Workshop. May 31-June 4, 2009, Wilmington, NC. P. 6.Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome

- (Peer Reviewed Journal)Zhu, J., Patzoldt, W.L., Radwan, O., Tranel, P.J., Clough, S.J. 2009. Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome. The Plant Genome. 2:191-205.Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and in Silico Mapping in Relation to Resistance Markers

- (Peer Reviewed Journal)Calla, B., Vuong, T., Radwan, O., Hartman, G.L., Clough, S.J. 2009. Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and in Silico Mapping in Relation to Resistance Markers. The Plant Genome. 2:149-166.A Robust Plant RNA Isolation Method for Affymetrix Genechip® Analysis and Quantitative Real-Time RT-PCR

- (Peer Reviewed Journal)Bilgin, D.D., Delucia, E.H., Clough, S.J. 2009. A Robust Plant RNA Isolation Method for Affymetrix Genechip® Analysis and Quantitative Real-Time RT-PCR. Nature Protocols. 4:333-340.Differences and Similarities of Soybean Defense-Related Genes Suppressed by Pathogenic and Symbiotic Bacteria

- (Abstract Only)Osman, R., Clough, S.J. 2009. Differences and Similarities of Soybean Defense-Related Genes Suppressed by Pathogenic and Symbiotic Bacteria [abstract]. Annual International Plant and Animal Genome Conference. January 10-14, 2009, San Diego, CA. Available: http://www.intl-pag.org/pag/17/abstracts/W52_PAGXVII_364.htmlGenomic Cross Comparison of Soybean Pathogens and the Symbiont Bradyrhizobium japonicum

- (Abstract Only)Radwan, O., Calla, B., Clough, S.J. 2008. Genomic Cross Comparison of Soybean Pathogens and the Symbiont Bradyrhizobium japonicum [abstract]. 4th International Conference on Legume Genomics and Genetics, December 7-12, 2008, Puerto Vallarta, Mexico. 2008 CDROM.Preliminary Analysis of Soybean Gene Expression Response to a Bradyrhizobium japonicum Type III Secretion System Mutant

- (Abstract Only)Radwan, O., Carbajulca, D., Libault, M., Brechenmacher, L., Clough, S.J. 2008. Preliminary Analysis of Soybean Gene Expression Response to a Bradyrhizobium japonicum Type III Secretion System Mutant [abstract]. 4th International Conference on Legume Genomics and Genetics, December 7-12, 2008, Puerto Vallarta, Mexico. 2008 CDROM.Transcriptome response to glyphosate in sensitive and resistant soybean

- (Peer Reviewed Journal)Zhu, J., Patzoldt, W.L., Shealy, R.T., Vodkin, L.O., Clough, S.J., Tranel, P.J. 2008. Transcriptome response to glyphosate in sensitive and resistant soybean. Journal of Agricultural and Food Chemistry. 56:6355-6363.Elevated Ozone Alters Soybean-Virus Interaction

- (Peer Reviewed Journal)Bilgin, D.D., Aldea, M., O'Neill, B.F., Benitez, M., Li, M., Clough, S.J., Delucia, E.H. 2008. Elevated Ozone Alters Soybean-Virus Interaction. Molecular Plant-Microbe Interactions. 21(10):1297-1308.Microarray analysis of soybean treated with Fusarium virguliforme filtrate suggests a role of genes related to cell-wall modification and detoxification during resistance

- (Abstract Only)Radwan, O., Li, M., Clough, S.J. 2008. Microarray analysis of soybean treated with Fusarium virguliforme filtrate suggests a role of genes related to cell-wall modification and detoxification during resistance [abstract]. In: Proceedings of the 12th Biennial Conference on Molecular and Cellular Biology of the Soybean. July 20-23, 2008. Indianapolis, Indiana. p. 91.Gene expression responses in photosynthetic tissues to herbicides and pathogens

- (Abstract Only)Clough, S.J., Zhu, J., Tranel, P., Patzholdt, W.L., Radwan, O., Li, M., Calla, B. 2008. Gene expression responses in photosynthetic tissues to herbicides and pathogens [abstract]. In: Proceedings of the 12th Biennial Conference on Molecular and Cellular Biology of the Soybean. July 20-23, 2008. Indianapolis, Indiana. p. 25.Flux in the coding and small RNA transcriptomes during soybean seed and seedling development

- (Abstract Only)Vodkin, L., Jones, S., Gonzalez, D.O., Zabala, G., Hunt, M., Tuteja, J., Radwan, O., Calla, B., Clough, S.J., Varala, K., Win, H., Hudson, M. 2008. Flux in the coding and small RNA transcriptomes during soybean seed and seedling development [abstract]. In: Proceedings of the 12th Biennial Conference on Molecular and Cellular Biology of the Soybean. July 20-23, 2008. Indianapolis, Indiana. p. 27.Identification of four soybean reference genes for gene expression normalization

- (Peer Reviewed Journal)Libault, M., Thibivilliers, S., Radwan, O., Clough, S.J., Stacey, G. 2008. Identification of four soybean reference genes for gene expression normalization. The Plant Genome. 1:44-54.Genomic analysis of soybean defense response to Sclerotinia sclerotiorum

- (Abstract Only)Calla, B., Simmonds, D., Clough, S.J. 2008. Genomic analysis of soybean defense response to Sclerotinia sclerotiorum [abstract]. American Phytopathological Society Annual Meeting. 98:S30.Cross comparison of soybean gene expression upon infection by pathogens and the symbiont Bradyrhizobium japonicum

- (Abstract Only)Radwan, O., Zernova, O., Lozovaya, V., Clough, S.J. 2008. Cross comparison of soybean gene expression upon infection by pathogens and the symbiont Bradyrhizobium japonicum [abstract]. American Phytopathological Society Annual Meeting. 98:S129.Soybean defense responses to the soybean aphid

- (Peer Reviewed Journal)Li, Y., Zou, J., Li, M., Bilgin, D., Vodkin, L.O., Hartman, G.L., Clough, S.J. 2008. Soybean defense responses to the soybean aphid. New Phytologist. 179(1):185-195.A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis

- (Peer Reviewed Journal)Wan, J., Zhang, X., Neece, D.J., Ramonell, K.M., Clough, S.J., Kim, S., Stackey, M.G., Stacey, G. 2008.  A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. The Plant Cell. 20(2):471-481.Transcription profiling of soybean nodulation by Bradyrhizobium japonicum

- (Peer Reviewed Journal)Brechenmacher, L., Moon-Young, K., Zou, J., Benitez, M., Li, M., Joshi, T., Calla, B., Lee, M., Philip, R., Libault, M., Vodkin, L.O., Xu, D., Lee, S., Clough, S.J., Stacey, G. 2008. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions. 21(5):631-645.Identification and functional analysis of candidate Sclerotinia defense genes in soybean

- (Abstract Only)Calla, B., Simmonds, D., Clough, S.J. 2008. Identification and functional analysis of candidate Sclerotinia defense genes in soybean [abstract]. ARS Sclerotinia Initiative Annual Meeting. p. 12.A LysM Receptor-like Kinase Plays a Critical Role in Chitin Signaling and Fungal Resistance in Arabidopsis

- (Peer Reviewed Journal)Wan, J., Zhang, X., Neece, D.J., Ramonell, K.M., Clough, S.J., Kim, S., Stacey, M.G., Stacey, G. 2008. A LysM Receptor-like Kinase Plays a Critical Role in Chitin Signaling and Fungal Resistance in Arabidopsis. The Plant Cell. 20:471-481.An Update on Soybean Functional Genomics and Microarray Resources for Gene Discovery and Crop Improvement

- (Peer Reviewed Journal)Vodkin, L.O., Thibaud-Nissen, F., Gonzales, D.O., Zabala, G., Clough, S.J., Shealy, R. 2007. An Update on Soybean Functional Genomics and Microarray Resources for Gene Discovery and Crop Improvement. Petria. 17(1):43-53.Development of a soybean gene expression database to cross compare microarray experiments

- (Abstract Only)Li, M., Calla, B., Zhu, J., Cai, D., Clough, S.J. 2007. Development of a soybean gene expression database to cross compare microarray experiments. International Congress on Molecular Plant-Microbe Interactions. July 21-27, 2007. Sorrento, Italy. p. 324.Genomic analysis of soybean resistance to Sclerotinia sclerotiorm

- (Abstract Only)Calla, B., Zhang, Y., Simmonds, D., Clough, S.J. 2007. Genomic analysis of soybean resistance to Sclerotinia sclerotiorm [abstract]. ARS Sclerotinia Initiative Annual Meeting. p. 22.Genomic analysis of soybean resistance to Sclerotinia sclerotiorum

- (Abstract Only)Calla, B., Zhang, Y., Simmonds, D., Clough, S.J. 2007. Genomic analysis of soybean resistance to Sclerotinia sclerotiorum. Plant and Animal Genome XV Conference. January 13-17, 2007. San Diego, CA. p. 284.Development of soybean gene expression database (SGED)

- (Abstract Only)Li, M., Cai, Y., Clough, S.J. 2007. Development of soybean gene expression database (SGED). Plant and Animal Genome XV Conference. p. 313.Cross comparing gene expression profiles of nodulation and pathogen infection

- (Abstract Only)Clough, S.J. 2007. Cross comparing gene expression profiles of nodulation and pathogen infection. Plant and Animal Genome XV Conference. p. 91.Transcription changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection

- (Peer Reviewed Journal)Zabala, G., Zou, J., Tuteja, J., Gonzalez, D.O., Clough, S.J., Vodkin, L.O. 2006. Transcription changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. Biomed Central (BMC) Genomics. 6:26.DEVELOPMENT OF PCR-BASED MARKERS FOR RESISTANCE TO SCLEROTINIA STEM ROT IN SOYBEAN

- (Abstract Only)Vuong, T.D., Calla, B., Diers, B.W., Clough, S.J., Hartman, G.L. 2006. Development of PCR-based markers for resistance to sclerotinia stem rot in soybean. ARS Sclerotinia Initiative Annual Meeting. January 18-20, 2006. Bloomington, MN. p. 18.DNA MICROARRAY ANALYSIS OF SOYBEAN-MICROBE INTERACTIONS

- (Abstract Only)Clough, S.J. 2005. DNA microarray analysis of soybean-microbe interactions [abstract]. Korean-Japan Joint Seminar Collaborative Researches on Biological Science.  p. 2.EXPRESSION PROFILING SOYBEAN RESPONSE TO PSEUDOMONAS SYRINGAE REVEALS NEW DEFENSE-RELATED GENES AND RAPID HR-SPECIFIC DOWN REGULATION OF PHOTOSYNTHESIS

- (Peer Reviewed Journal)Zou, J., Rodriguez-Zas, S., Aldea, M., Zhu, Min Li, Gonzalez, D., Vodkin, L., Delucia, E., Clough, S.J. 2005. Expression profiling soybean response to pseudomonas syringae reveals new defense-related genes and rapid HR-specific down regulation of photosynthesis. Molecular Plant-Microbe Interactions. 18:1161-1174.GENE EXPRESSION PROFILING OF OXALATE OXIDASE TRANSGENIC SOYBEAN CHALLENGED WITH SCLEROTINIA SCLEROTIORUM

- (Abstract Only)Calla, B., Zhang, Y., Hubbard, S., Davidson, A., Rioux, S., Simmonds, D., Clough, S.J. 2005. Gene expression profiling of oxalate oxidase transgenic soybean challenged with sclerotinia sclerotiorum. Proceedings of the International Sclerotinia Workshop. June 12-16, 2005 pg.46IDENTIFICATION OF APHID RESISTANCE-RELATED DEFENSE RESPONSES IN SOYBEAN

- (Abstract Only)Li, Y., Zou, J., Hartman, G.L., Clough, S.J. 2005. Identification of aphid resistance-related defense responses in soybean [abstract]. Plant and Animal Genome Conference Proceedings.GENOMIC RESPONSES IN SOYBEAN STEM TISSUE TO SCLEROTINIA

- (Proceedings)Clough, S.J., Vuong, T., Diers, B., Hartman, G.L. 2006. Genomic responses in soybean stem tissue to sclerotinia. Proceedings of the International Sclerotinia Workshop. p. 22.MICROARRAY ANALYSIS OF OXALATE OXIDASE TRANSGENIC SOYBEAN CHALLENGED WITH SCLEROTINIA SCLEROTIORUM

- (Abstract Only)Clough, S.J., Hubbard, S., Zhang, Y., Davidson, A., Rioux, S., Calla, B., Simmonds, D. 2005. Microarray analysis of oxalate oxidase transgenic soybean challenged with Sclerotinia sclerotiorum [abstract]. ARS Sclerotinia Initiative Annual Meeting. Available: http://www.whitemoldresearch.com/posters2004/Clough.pdf.SEARCHING FOR DEFENSE-RELATED GENE CANDIDATES FROM SOYBEAN THAT CONFER PARTIAL RESISTANCE TO SCLEROTINIA

- (Abstract Only)Vuong, T., Hartman, G.L., Clough, S.J. 2005. Searching for defense-related gene candidates from soybean that confer partial resistance to sclerotinia [abstract]. Proceedings of the International Sclerotinia Workshop. p. 53.MICROARRAY ANALYSIS OF DIFFERENTIAL GENE EXPRESSION BETWEEN RESISTANCE AND SUSCEPTIBLE SOYBEAN CULTIVARS IN RESPONSE TO APHIS GLYCINES

- (Abstract Only)Li, Y., Zou, J., Li, M., Hartman, G.L., Clough, S.J. 2004. Microarray Analysis of Differential Gene Expression Between Resistance and Susceptible Soybean Cultivars in Response to Aphis Glycines [abstract]. Cellular and Molecular Biology of Soybean Biennial Conference.  p.121.IDENTIFICATION OF APHID RESISTANCE-RELATED DEFENSE RESPONSES IN SOYBEAN

- (Proceedings)Li, Y., Zou, J., Hartman, G.L., Clough, S.J. 2005. Identification of aphid resistance-related defense responses in soybean. Plant and Animal Genome Conference. p. 239.DOWN REGULATION OF CHLOROPLAST GENES SPECIFIC TO HR

- (Abstract Only)Zhu, J., Zou, J., Aldea, M., Delucia, E., Clough, S.J. 2005. Down regulation of chloroplast genes specific to hr. [abstract]. Proceedings of the Plant and Animal Genome XIII Conference; San Diego, California Jan. p. 242.GENE FUNCTIONAL ANALYSIS IN SOYBEAN BY MICROARRAY

- (Proceedings)Vodkin, L., Shealy, R., Khanna, A., Thibaud-Nissen, F., Clough, S.J., Philip, R., Shoop, E., Schmidt, C., Retzel, E. 2005. Gene functional analysis in soybean by microarray. Plant and Animal Genome. p. 54.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.GLOBAL EXPRESSION ANALYSES USING MICROARRAYS OF A SOYBEAN CDNA UNIGENE SET

- (Proceedings)Gonzales, D., Thibaud-Nissen, F., Clough, S.J., Stromvik, M., Retzel, E., Vodkin, L. 2004. Global expression analyses using microarrays of a soybean cdna unigene set. Plant and Animal Genome Conference Proceedings. p. 115.EXPRESSION PROFILING OF SOYBEAN RESPONSES TO BACTERIAL PATHOGEN PSEUDOMONAS SYRINGAE

- (Proceedings)Zou, J., Rodriguez-Zas, S., Gonzales, D., Vodkin, L., Clough, S.J. 2004. Expression profiling of soybean responses to bacterial pathogen pseudomonas syringae. Soybean Biotechnology Meeting. p. 114.ASSIGNMENT OF MOLECULAR LINKAGE GROUPS TO SOYBEAN CHROMOSOMES

- (Proceedings)Zou, J., Lee, J., Xu, S.S., Cregan, P.B., Clough, S.J., Hymowitz, T. 2004. Assignment of molecular linkage groups to soybean chromosomes. Soybean Biotechnology Meeting. p.12.GLOBAL EXPRESSION ANALYSES USING MICROARRAYS OF A SOYBEAN CDNA UNIGENE SET

- (Proceedings)Gonzales, D., Zabala, G., Jones, S., Boone, A., Sidarous, M., Khanna, A., Thibaud-Nissen, F., Clough, S.J., Shealy, R., Stromvik, M. 2004. Global expression analyses using microarrays of a soybean cdna unigene set. Soybean Biotechnology Meeting. p.272.COMPARING SOYBEAN GENOMIC RESPONSES TO PEST AND PATHOGENS

- (Proceedings)Clough, S.J., Zou, J. Comparing soybean genomic responses to pest and pathogens. Cellular and Molecular Biology of Soybean Biennial Conference.  p. 26COMPARISON OF GENE EXPRESSION PROFILES AMONG SOYBEAN CULTIVARS WITH DIFFERENT DEGREES OF TOLERANCE TO FSG TOXIN

- (Proceedings)Li, M., Zou, J., Li, S., Vodkin, L., Clough, S.J. 2004. Comparison of gene expression profiles among soybean cultivars with different degrees of tolerance to fsg toxin. Plant and Animal Genome Conference. p. 12.EXPRESSION PROFILING OF SOYBEAN RESPONSE TO PESTS AND PATHOGENS

- (Abstract Only)Clough, S.J., Zou, J., Vuong, T., Li, M., Li, Y., Hartman, G.L., Rodriguez-Zas, S., Vodkin, L.O. 2004. Expression profiling of soybean response to pests and pathogens [abstract]. International Conference on Legume Genomics and Genetics. p. 246.DNA MICROARRAY AND PROTEOMIC ANALYSIS OF ROOT HAIR INFECTION

- (Proceedings)Stacey, G., Huang, S., Wan, J., Zou, J., Clough, S.J., Scheffler, B.E., Kim, S., Nguyen, H. 2004. DNA microarray and proteomic analysis of root hair infection. International Conference on Legume Genomics and Genetics. p. 183-184.GENE EXPRESSION PROFILING OF SOYBEAN RESPONSE DURING COMPATIBLE AND INCOMPATIBLE INTERACTIONS WITH THE BACTERIAL PATHOGEN PSEUDOMONAS SYRINGAE

- (Abstract Only)Zou, J., Rodriguez-Zas, S., Gonzales, D.O., Vodkin, L.O., Clough, S.J. 2004. Gene expression profiling of soybean response during compatible and incompatible interactions with the bacterial pathogen pseudomonas syringae [abstract]. International Conference on Legume Genomics and Genetics. p. 245.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.MICROARRAY ANALYSIS OF DEFENSE AGAINST SCLEROTINIA STEM ROT IN SOYBEAN

- (Abstract Only)Vuong, T., Zou, J., Hartman, G.L., Clough, S.J. 2004. Microarray analysis of defense against sclerotinia stem rot in soybean [abstract]. Plant and Animal Genome Conference.FLORAL DIP:  AGROBACTERIUM-MEDIATED GERM-LINE TRANSFORMATION

- (Book / Chapter)Clough, S.J. 2003. Transgenic plants:  Methods and protocols. In: Pena, L., editors. Methods in Molecular Biology. Totowa, N.J.: The Humana Press, Inc.  p: 91-101.SEQUENCE ANNOTATION OF BAC104J7 CONTAINING THE 10.71-KB EXACT INVERT REPEAT CHS CLUSTER OF THE I LOCUS IN SOYBEAN

- (Proceedings)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.GENE EXPRESSION PROFILING OF SOYBEAN RESPONSE DURING COMPATIBLE AND INCOMPATIBLE INTERACTIONS WITH THE BACTERIAL PATHOGEN PSEUDOMONAS SYRINGAE

- (Abstract Only)Zou, J., Rodriguez-Zas, S., Tuteja, J., Gonzales, D.O., Vodkin, L.O., Clough, S.J. 2004. Gene expression profiling of soybean response during compatible and incompatible interactions with the bacterial pathogen pseudomonas syringae [abstract]. Plant and Animal Genome Conference. p.273.MICROARRAY ANALYSIS OF SUDDEN DEATH SYNDROME IN SOYBEANS

- (Abstract Only)Li, M., Zou, J., Li, S., Vodkin, L.O., Clough, S.J. 2004. Microarray analysis of sudden death syndrome in soybeans [abstract]. Plant and Animal Genome Conference. p. 273.GENOMIC ANALYSIS OF WHITE MOLD RESISTANCE IN SOYBEAN

- (Abstract Only)Clough, S.J., Vuong, T.D., Hartman, G.L. 2002. Genomic Analyis of white mold resistence in soybean. APS Annual Meeting. v. 93. p. S17.PROGRESS AND CHALLENGES IN MANAGEMENT OF SCLEROTINIA SCLEROTIORUM ON SOYBEAN

- (Abstract Only)Kull, L.S., Hartman, G.L., Vuong, T.D., Clough, S.J., Graef, G., Powers, K., Steadman, J.R. 2004. Progress and challenges in management of sclerotinia sclerotiorum on soybean [abstract]. Soybean Research World Conference Proceedings.GENETIC ANALYSIS OF WHITE MOLD RESISTANCE USING MICROARRAYS

- (Proceedings)Vuong, T.D., Hartman, G.L., Clough, S.J. 2003. Genetic analysis of white mold resistance using microarrays. Proceedings of the International Sclerotinia Workshop. v. January. p.18.SEQUENCE ANALYSIS OF BAC104J7 AND THE I LOCUS IN WILLIAMS 82

- (Proceedings)GENE EXPRESSION PROFILING OF SOYBEAN IN RESPONSE TO NODULATION

- (Proceedings)SEQUENCE ANALYSIS OF THE I LOCUS IN WILLIAMS 82

- (Proceedings)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.GENE EXPRESSION PROFILING OF SOYBEAN ROOT RESPONSE TO NODULATION

- (Abstract Only)


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