Projects

SOYBEAN GENETIC MANAGEMENT AND UTILIZATION Appropriated (D)   Accession Number: 413196

SOYBEAN GENES RESISTANCE TO DISEASES Specific Cooperative Agreement (S)   Accession Number: 412081

SOYBEAN GENOME RESPONSE TO SCLEROTINIA AND OXALATE Specific Cooperative Agreement (S)   Accession Number: 408681

Publications

Genomic cross comparison of soybean pathogens and the symbiont Bradyrhizobium japonicum - (Abstract) - (20-Aug-08)

Preliminary analysis of soybean gene expression response to a Bradyrhizobium japonicum type III secretion system mutant - (Abstract) - (20-Aug-08)

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) - (10-Jun-08)

Gene expression responses in photosynthetic tissues to herbicides and pathogens - (Abstract)

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.

Microarray analysis of soybean treated with Fusarium virguliforme filtrate suggests a role of genes related to cell-wall modification and detoxification during resistance - (Abstract)

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.

Flux in the coding and small RNA transcriptomes during soybean seed and seedling development - (Abstract)

Vodkin, L., Jones, S., Gonzalez, D.O., Zabala, G., Hunt, M., Tuteja, J., 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)

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)

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)

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.

An update on soybean functional genomics and microarray resources for gene discovery and crop improvement - (Peer Reviewed Journal) - (17-Apr-07)

Development of a soybean gene expression database to cross compare microarray experiments - (Abstract)

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)

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.

Cross comparing gene expression profiles of nodulation and pathogen infection - (Abstract)

Clough, S.J. 2007. Cross comparing gene expression profiles of nodulation and pathogen infection. Plant and Animal Genome XV Conference. p. 91.

Development of soybean gene expression database (SGED) - (Abstract)

Li, M., Cai, Y., Clough, S.J. 2007. Development of soybean gene expression database (SGED). Plant and Animal Genome XV Conference. p. 313.

Genomic analysis of soybean resistance to Sclerotinia sclerotiorum - (Abstract)

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.

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)

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)

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)

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.46

GENOMIC RESPONSES IN SOYBEAN STEM TISSUE TO SCLEROTINIA - (Proceedings/Symposium)

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)

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.

IDENTIFICATION OF APHID RESISTANCE-RELATED DEFENSE RESPONSES IN SOYBEAN - (Abstract)

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.

SEARCHING FOR DEFENSE-RELATED GENE CANDIDATES FROM SOYBEAN THAT CONFER PARTIAL RESISTANCE TO SCLEROTINIA - (Abstract)

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)

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/Symposium)

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)

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/Symposium)

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.

COMPARING SOYBEAN GENOMIC RESPONSES TO PEST AND PATHOGENS - (Proceedings/Symposium)

Clough, S.J., Zou, J. Comparing soybean genomic responses to pest and pathogens. Cellular and Molecular Biology of Soybean Biennial Conference. p. 26

GLOBAL EXPRESSION ANALYSES USING MICROARRAYS OF A SOYBEAN CDNA UNIGENE SET - (Proceedings/Symposium)

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/Symposium)

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/Symposium)

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.

COMPARISON OF GENE EXPRESSION PROFILES AMONG SOYBEAN CULTIVARS WITH DIFFERENT DEGREES OF TOLERANCE TO FSG TOXIN - (Proceedings/Symposium)

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.

GLOBAL EXPRESSION ANALYSES USING MICROARRAYS OF A SOYBEAN CDNA UNIGENE SET - (Proceedings/Symposium)

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.

EXPRESSION PROFILING OF SOYBEAN RESPONSE TO PESTS AND PATHOGENS - (Abstract)

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/Symposium)

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)

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)

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/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.

MICROARRAY ANALYSIS OF SUDDEN DEATH SYNDROME IN SOYBEANS - (Abstract)

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.

GENE EXPRESSION PROFILING OF SOYBEAN RESPONSE DURING COMPATIBLE AND INCOMPATIBLE INTERACTIONS WITH THE BACTERIAL PATHOGEN PSEUDOMONAS SYRINGAE - (Abstract)

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.

GENOMIC ANALYSIS OF WHITE MOLD RESISTANCE IN SOYBEAN - (Abstract)

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)

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/Symposium)

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/Symposium) - (15-Jan-03)

GENE EXPRESSION PROFILING OF SOYBEAN IN RESPONSE TO NODULATION - (Proceedings/Symposium) - (15-Jan-03)

GENE EXPRESSION PROFILING OF SOYBEAN ROOT RESPONSE TO NODULATION - (Abstract) - (30-Jun-02)

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.