Steven J. Clough


Dr. Clough is known internationally for his work on Arabidopsis transformation. His main research focus is on the use of genomics and molecular biology to explore plant-microbe and plant-pest interactions, mainly in soybean. His work improves our understanding of plant defense biology and identifies soybean genes affecting defense.

Primary Disciplines


  • Ph.D.: Plant Pathology, University of Georgia — 1996
  • M.S.: Plant Pathology, University of Georgia — 1991
  • B.A.: Biochemistry, University of California, Berkeley — 1986

Academic Positions

  • Research Geneticist, USDA-ARS, Urbana, Illinois (2001 - present)
  • Assistant Professor, Dept. of Crop Science, University of Illinois at Urbana-Champaign (2001 - present)
  • Postdoctoral Research Associate, Dept. of Crop Science, University of Illinois at Urbana-Champaign (1996 - 2001)

Honors, Recognition, and Outstanding Achievements - Other

  • The Clough and Bent 1998 publication (Plant Journal 16:735-743) on the floral dip transformation of Arabidopsis was rated as the #1 citation in the biological sciences (plants and animal journals) for the 10-year period of 1996-2005 and has been cited in 9,569 scientific publications (ISI Web of Knowledge, Thomson Reuters), or 12,887 publications (Google Scholar) as of June 30, 2017.

Chapters in Books

  • Clough, S.J. (2004). Floral dip: Agrobacterium-mediated germ-line transformation. pp 91-101 In: Transgenic plants: methods and protocols. Methods in Molecular Biology. L. Pena, ed. The Humana Press, Inc., Totowa, NJ.
  • Clough, S.J. and L.O. Vodkin (2004). Soybean microarrays: a genomic tool for crop improvement. pp 267-282 In: Genomics for Legume Crops. R.F. Wilson, C. Brummer, eds. American Oil Chemists Society Press, Urbana, IL.
  • Wan, J., K. Ramonell, X. Zhang, S. Clough, R. Zhang, M. Libault, G.H. Son, M.G. Stacey, J.C. Hong and G. Stacey (2008). Chitin signaling in Arabidopsis. pp 1-4 In: Biology of Plant Microbe Interactions, Vol. 6. M. Lorito, S.L. Woo, and F. Scala, eds. The American Phytopathological Society, St. Paul, MN.
  • Wei Wei and Steven J. Clough. (2016) Sclerotinia sclerotiorum: Molecular Aspects in Plant-Pathogenic Interactions. Revisão Anual de Patologia de Plantas 24:174-189.

Selected Articles in Journals

  • Clough, S.J., M.A. Schell, and T.P. Denny (1994). Evidence for the involvement of a volatile extracellular factor in Pseudomonas solanacearum virulence gene expression. Mol. Plant Microbe Interact. 7:621-630.
  • Clough, S.J., A.B. Flavier, M.A. Schell, and T.P. Denny (1997). Differential expression of virulence genes and motility in Ralstonia (Pseudomonas) solanacearum during exponential growth. Appl. Environ. Microbiol. 63:844-850.
  • Flavier, A.B., S.J. Clough, M.A. Schell, and T.P. Denny (1997). Identification of 3-hydroxypalmitic acid methyl ester as a novel autoregulator controlling virulence in Ralstonia solanacearum. Mol. Microbiol. 26:251-259.
  • Clough, S.J., K.-E. Lee, M.A. Schell, and T.P. Denny (1997). A two-component system in Ralstonia (Pseudomonas) solanacearum modulates production of PhcA-regulated virulence factors in response to 3-hydroxypalmitic acid methyl ester. J. Bacteriol. 179:3639-3648
  • Clough, S.J. and A.F. Bent (1998). Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16:735-743.
  • Yu, I-c., K.A. Fengler, S.J. Clough, and A.F. Bent (2000). Identification of Arabidopsis mutants exhibiting an altered hypersensitive response in gene-for-gene disease resistance. Mol. Plant Microbe Interact. 13:277-286.
  • Palanichelvam, K., P. Oger, S.J. Clough, C.E. Cha, A.F. Bent, and S. K. Farrand (2000). A second T-region of the soybean-supervirulent chrysopine-type Ti plasmid pTIChry5, and construction of a fully disarmed vir helper plasmid. Mol. Plant Microbe Interact. 13:1081-1091.
  • Clough, S.J., K.A. Fengler, B. Lippok, R.K. Smith, I-c Yu, and A.F. Bent (2000). The Arabidopsis dnd1 “defense, no death” gene encodes a mutated cyclic nucleotide gated ion channel. Proc. Nat. Acad. Sci. USA. 97:9323-9328.
  • Desfeux, C., S.J. Clough, and A.F. Bent (2000). Female reproductive tissues are the primary target of Agrobacterium-mediated transformation in the Arabidopsis floral-dip method. Plant Physiol. 123:895-904.
  • Clough, S.J., J. Tuteja, M. Li, L. F. Marek, R.C. Shoemaker, and L.O. Vodkin (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 47:819-831.
  • Tuteja, J.H., S.J. Clough, W.-C. Chan, and L.O. Vodkin (2004). Tissue specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max. Plant Cell 16: 819-835.
  • Vodkin, L.O., A. Khanna, R.T. Shealy, S.J. Clough, D.O. Gonzales, R. Philip, G.C. Zabala, F. Thibaud-Nissen, M. Sidarous, M.V. Stromvik, E.G. Shoop, C. Schmidt, E. Retzel, J. Erpelding, R.C. Shoemaker, A.M. Rodrizues-Huete, J.C. Polacco, V. Coryell, P. Keim, G. Gong, L. Lui, J.L. Pardinas, and P. Schweitzer (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. BMC Genomics 5:73.
  • Zou, J., S. Rodriguez-Zas, M. Aldea, M. Li, J. Zhu, D.O. Gonzales, L.O. Vodkin, E. DeLucia and S.J. Clough (2005). Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid HR-specific down regulation of photosynthesis. Mol. Plant-Microbe Interact. 18:1161-1174.
  • Zabala, G., J. Zou, J. Tuteja, D.O. Gonzales, S.J. Clough, and L.O. Vodkin (2006). Transcription changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. BMC Plant Biol. 6:26.
  • Vodkin, L.O., F. Thibaud-Nissen, D.O. Gonzales, G. Zabala, S.J. Clough, and R.T. Shealy, (2007). An update on soybean functional genomics and microarray resources for gene discovery and crop improvement. Petria 17:43-53.
  • Brechenmacher,L., M.-Y. Kim, M. Benitez, M. Li, T. Joshi, B. Calla, M.P. Lee, M. Libault, L.O. Vodkin, D. Xu, S.-H. Lee, S.J. Clough, and G. Stacey (2008). Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Mol. Plant-Microbe Interact. 21:631-645.
  • Wan, J., X. Zhang, D. Neece, K.M. Ramonell, S.J. Clough, S-Y. Kim, M.G. Stacey, and G. Stacey (2008). A LysM receptor-like kinase mediates chitin perception and fungal resistance in Arabidopsis. The Plant Cell 20:471-481.
  • Libault, M., S. Thibivilliers, O. Radwan, S.J. Clough, and G. Stacey (2008). Identification of four soybean reference genes for gene expression normalization. The Plant Genome 1:44-54.
  • Zhu, J., W.L. Patzoldt, R.T. Shealy, L.O. Vodkin, S.J. Clough, and P.J. Tranel (2008). Transcriptional profiling in response to glyphosate in sensitive and resistant soybean. J. Agricul. Food Chem. 56:6355-6363.
  • Bilgin, D.D., Bilgin, D.D., M. Aldea, B.F. O'Neill, M. Benitez, M. Li, S.J. Clough, and E.H. DeLucia (2008). Elevated ozone alters soybean-virus interaction. Mol. Plant-Microbe Interact 21:1297-1308.
  • Li, Y., J. Zou, M. Li, D.D. Bilgin, L.O. Vodkin, G.L. Hartman, and S.J. Clough (2008). Soybean defense responses to the soybean aphid. New Phytologist 179:185-195.
  • Bilgin, D.D., E.H. DeLucia, and S.J. Clough (2009). A robust plant RNA isolation method suitable for Affymetrix Genechip analysis and quantitative real-time RT-PCR. Nature Protocols 4:333-340.
  • Calla, B., T. Vuong, O. Radwan, G.L. Hartman, and S.J. Clough (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.
  • Zhu, J., W.L. Patzoldt, O. Radwan, P.J. Tranel, and S.J. Clough (2009). Effects of photosystem II interfering herbicides atrazone and bentazon on the soybean transcriptome. The Plant Genome 2:191-205.
  • Libault, M., A. Farmer, L. Brechenmacher, J. Drnevich, R.J. Langley, D.D. Bilgin, O. Radwan, D. Neece, S.J. Clough, G.D. May, and G. Stacey (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.
  • Bilgin, D.D., J.A. Zavala, J. Zhu, S.J. Clough, D.R. Ort, and E.H. DeLucia (2010). Biotic stress globally down-regulates photosynthesis genes. Plant Cell Environ. 33:1597-1613.
  • Radwan, O., Y. Liu, and S.J. Clough (2011). Transcriptional analysis of soybean roots response to Fusarium virguliforme, the causal agent of sudden death syndrome. Mol. Plant-Microbe Interact. 24:958-972.
  • Wang, D., B. Calla, S. Vimolmangkang, X. Wu, S.S. Korban, S.C. Huber, S.J. Clough, and Youfu Zhao (2011). Orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli. PLoS ONE. 6(9): e25293.
  • Wang, D., M. Qi, B. Calla, S.S. Korban, S.J. Clough, G.W. Sundin, I. Toth, P.J.A. Cock, and Youfu Zhao (2011). Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora. Mol. Plant-Microbe Interact. 25:6-17.
  • Zabala, G., E. Campos, K.K. Varala, S. Bloomfield, S.I. Jones, H. Win, J.H. Tuteja, B. Calla, S.J. Clough, M. Hudson, and L.O. Vodkin (2012). Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. BMC Plant Biol. 12:177.
  • Radwan, O., X. Wu, M. Govindarajulu, M. Libault, D.J. Neece, M.-H. Oh, R.H. Berg, G. Stacey, C.G. Taylor, S.C. Huber, and S.J. Clough (2012). 14-3-3 proteins SGF14c and SGF14l play critical roles during soybean nodulation. Plant Physiol. 160:2125-2136.
  • Radwan, O., M. Li, B. Calla, S. Li, G.L. Hartman, and S.J. Clough (2013). Effect of Fusarium virguliforme phytotoxin on soybean gene expression suggests a role in multidimensional defence. Mol. Plant Pathol. 14:293-307.
  • Zabala, G., Campos. E.,Varala, K.K., Bloomfield. S., Jones, S.I., Win, H., Tuteja, J.H., Calla, B., Clough, S.J., Hudson, M. and Vodkin, L.O. (2012). Divergent Patterns of Endogenous Small RNA Populations from Seed and Vegetative Tissues of Glycine max. BMC Plant Biol. 12:177.
  • Radwan, O., Li, M., Calla, B., Li, S., Hartman, G.L. and S.J. Clough, S.J. (2012). Effect of Fusarium virguliforme phytotoxin on soybean gene expression suggests a multi-dimensional defense approach. Mol. Plant Pathol. 14:293-307.
  • Radwan, O., Wu, X., Govindarajulu, M., Libault, M., Neece, D.J., Oh, M.-H, Berg, R.H., Stacey, G., Taylor, C.G., Huber, S.C., and Clough, S.J. (2012). 14-3-3 proteins SGF14c and SGF14l play critical roles during soybean nodulation. Plant Physiol.160:2125-2136.
  • Calla, B., Blahut-Beatty, L., Koziol, L., Simmonds, D., Clough, S.J. (2014). Transcriptome analyses suggest a disturbance of iron homeostasis in soybean leaves during white mold disease establishment. Mol. Plant Pathol.15:576-588.
  • Calla, B., Blahut-Beatty, L., Koziol, L., Zhang, Y., Neece, D.J., Carbajulca, D., Garcia, A., Simmonds, D.H., and Clough, S.J. (2014). Genomic evaluation of oxalate-degrading transgenic soybean in response to Sclerotinia sclerotiorum infection. Mol. Plant Pathol.15:563-575.
  • Siddappaji, M.H., Scholes, D.R., Krishnankutty, S.M., Calla, B., Clough, S.J., Zielinski, R.E., and Paige, K.N. (2015). The role of invertases in plant compensatory responses to simulated herbivory. BMC Plant Biol. 15:278.
  • Zhu, J., Neece, D.J., Calla, B., and 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. J. Plant Biochem. Physiol. 3:157. doi:10.4172/2329
  • Zhu, J., Li, M., and Clough, S.J. (2015). Similarities and differences in global gene expression profiles between herbicide- and pathogen-induced PSII inhibition. J. Plant Biochem. Physiol. 3:157. doi:10.4172/2329-9029.1000157.
  • Castro L.H.S., Figueiro A.A., Nogueira A.P.O., Clough S.J., Fernando C. J. (2016). Resistance of soybean genotypes to Sclerotinia sclerotiorum isolates in different incubation environments. Genetics and Molecular Research 15(4):gmr15049061.
  • 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):e0162327.
  • Wei Wei and Steven J. Clough (2016). Sclerotinia sclerotiorum: Molecular Aspects in Plant-Pathogenic Interactions. Revisão Anual de Patologia de Plantas 24:174-189.
  • Wei W., Oliveira Mesquita, A., Figueiró, A., Wu, X., Manjunatha, S., Wickland, D.P., Hudson, M., Juliatti, F.C., and 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.
  • Francischini, F.J.B., de Campos, J.B., Pereira, A.A., Viana, J.P.G., Galvan, T.L., Grinter, C.C., Clough, S.J., and Zucchi, M.I. (2017). Morphological and Molecular Characterization of Brazilian Populations of Diatraea saccharalis (Lepidoptera: Crambidae) and the Evolutionary Relationship among Diatraea spp. PLosONE: Submitted June 12, 2017
  • Francischini, F.J.B., Cordeiro, E.M.G., de Campos, J.B., Alves-Pereira, A., Viana, J.P.G., Wu, X., Wei, W., Brown, P., Joyce, A., Murua, G., Fogliata, S., Clough, S.J., and Zucchi, M.I. Diatraea saccharalis history of colonization in the Americas: the case for human-mediated dispersal. PLosONE. Revision submitted March 11, 2019