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                    U.S. DEPARTMENT OF AGRICULTURE
 Corn Insects and Crop Genetics Research: Ames, IA
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ARS Home Midwest Area Ames, Iowa Corn Insects and Crop Genetics Research People & Locations







Michelle A Graham
                        Corn Insects and Crop Genetics Research

                        




                        
                        Research Leader
                        Phone: (515) 294-3626
                        
                        
                        Fax: (515) 294-9359(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsLeveraging Crop Genetic Diversity and Genomics to Improve Biotic and Abiotic Stress Tolerance in Soybean
                                                    In-House Appropriated
                                                                    (D)Accession Number: 444061Government Owned Vehicle and Equipment Use by Non-federal Employees for Collaborative Research
                                                    Non-Funded Cooperative Agreement
                                                                    (N)Accession Number: 443594Developing the Perfect Molecular Markers and New Germplasm for Rapid Incorporation of Resistance to Soil Borne Pathogens in Soybean
                                                    Reimbursable Cooperative Agreement
                                                                    (R)Accession Number: 445901**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi
                                                        

- (Peer Reviewed Journal)Kendrick, M.D., Ramachandran, S.R., Wright, A.L., Lincoln, L.M., Whitham, S.A., Graham, M.A., Pedley, K.F. 2024. The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi. Molecular Plant-Microbe Interactions. https://doi.org/10.1094/MPMI-01-24-0007-R.GmGLU1 and GmRR4 contribute to iron deficiency tolerance in soybean
                                                        

- (Peer Reviewed Journal)Kohlhase, D.R., O'Rourke, J.A., Graham, M.A. 2024. GmGLU1 and GmRR4 contribute to iron deficiency tolerance in soybean. Frontiers in Plant Science. 15. https://doi.org/10.3389/fpls.2024.1295952.Virus induced gene silencing confirms oligogenic inheritance of brown stem rot resistance in soybean
                                                        

- (Peer Reviewed Journal)McCabe, C.E., Lincoln, L.M., O'Rourke, J.A., Graham, M.A. 2024. Virus induced gene silencing confirms oligogenic inheritance of brown stem rot resistance in soybean. Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1292605.Coupling VIGS with short and long-term stress exposure to understand the Fiskeby III iron deficiency stress response
                                                        

- (Peer Reviewed Journal)O'Rourke, J.A., Graham, M.A. 2022. Coupling VIGS with short and long-term stress exposure to understand the Fiskeby III iron deficiency stress response. International Journal of Molecular Sciences. 24(1).Article 647. https://doi.org/10.3390/ijms24010647.Identification of candidate genes for a major quantitative disease resistance locus from soybean PI 427105B for resistance to phytophthora sojae
                                                        

- (Peer Reviewed Journal)Karhoff, S., Vargas-Garcia, C., Lee, S., Mian, R.M., Graham, M.A., Dorrance, A., McHale, L. 2022. Identification of candidate genes for a major quantitative disease resistance locus from soybean PI 427105B for resistance to phytophthora sojae. Frontiers in Plant Science. 13. Article 893652.Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing
                                                        

- (Peer Reviewed Journal)Natukunda, M.I., Mantilla-Perez, M.B., Graham, M.A., Liu, P., Salas-Fernandez, M.G. 2022. Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing. BMC Genomics. 23. Article 95. https://doi.org/10.1186/s12864-021-08251-4.Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids
                                                        

- (Peer Reviewed Journal)Natukunda, M.I., Hohenstein, J.D., McCabe, C.E., Graham, M.A., Qi, Y., Singh, A.K., MacIntosh, G.C. 2021. Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids. BMC Genomics. 22. Article 887. https://doi.org/10.1186/s12864-021-08147-3.Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.)
                                                        

- (Peer Reviewed Journal)Otyama, P.I., Chamberlin, K., Ozias-Akins, P., Graham, M.A., Cannon, E.K.S., Cannon, S.B., MacDonald, G.E., Anglin, N.L. 2022. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). Genes, Genomes, Genetics. 12(1). Article jkab382. https://doi.org/10.1093/g3journal/jkab382.Comparing early transcriptomic responses of 18 soybean (Glycine max) genotypes to iron stress
                                                        

- (Peer Reviewed Journal)Kohlhase, D.R., Mccabe, C.E., Singh, A.K., O'Rourke, J.A., Graham, M.A. 2021. Comparing early transcriptomic responses of 18 soybean (Glycine max) genotypes to iron stress. International Journal of Molecular Sciences. 22(21). Article 11643. https://doi.org/10.3390/ijms222111643.Mining Fiskeby III and Mandarin (Ottawa) expression profiles to understand iron stress tolerant responses in soybean
                                                        

- (Peer Reviewed Journal)O'Rourke, J.A., Morrisey, M.J., Merry, R., Espina, M.J., Lorenz, A.J., Stupar, R.M., Graham, M.A. 2021. Mining Fiskeby III and Mandarin (Ottawa) expression profiles to understand iron stress tolerant responses in soybean. International Journal of Molecular Sciences. 22(20). Article 11032. https://doi.org/10.3390/ijms222011032.Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.)
                                                        

- (Pre-print Publication)Otyama, P.I., Chamberlin, K., Ozias-Akins, P., Graham, M.A., Cannon, E.K.S., Cannon, S.B., MacDonald, G.E., Anglin, N.L. 2021. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in Arachis hypogaea. bioRxiv. https://doi.org/10.1101/2021.06.03.446924.Characterizing short and long term iron stress responses in iron deficiency tolerant and susceptible soybean (Glycine max L. Merr.)
                                                        

- (Peer Reviewed Journal)Atencio, L., Salazar, J., Moran Lauter, A., Gonzales, M.D., O'Rourke, J.A., Graham, M.A. 2021. Characterizing short and long term iron stress responses in iron deficiency tolerant and susceptible soybean (Glycine max L. Merr.). Plant Stress. 2.Article 100012. https://doi.org/10.1016/j.stress.2021.100012.Gene expression responses to sequential nutrient deficiency stresses in soybean.
                                                        

- (Peer Reviewed Journal)O'Rourke, J.A., Graham, M.A. 2021. Gene expression responses to sequential nutrient deficiency stresses in soybean. International Journal of Molecular Sciences. 22(3). Article 1252. https://doi.org/10.3390/ijms22031252.A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database
                                                        

- (Peer Reviewed Journal)Brown, A.V., Connors, S., Huang, W., Wilkey, A., Grant, D.M., Weeks, N.T., Cannon, S.B., Graham, M.A., Nelson, R. 2020. A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research. 49(D1):D1496-D1501. https://doi.org/10.1093/nar/gkaa1107.Genotypic characterization of the U.S. peanut core collection
                                                        

- (Peer Reviewed Journal)Otyama, P.I., Kulkarni, R., Chamberlin, K., Ozias-Akins, P., Chu, Y., Lincoln, L.M., MacDonald, G.E., Anglin, N.L., Dash, S., Bertioli, D.J., Fernandez-Baca, D., Graham, M.A., Cannon, S.B., Cannon, E.K.S. 2020. Genotypic characterization of the U.S. peanut core collection. G3, Genes/Genomes/Genetics. 10(11):4013-4026. https://doi.org/10.1534/g3.120.401306.New tools for characterizing early brown stem rot disease resistance signaling in soybean
                                                        

- (Peer Reviewed Journal)McCabe, C.E., Graham, M.A. 2020. New tools for characterizing early brown stem rot disease resistance signaling in soybean. The Plant Genome. 13(3). Article e20037. https://doi.org/10.1002/tpg2.20037.Examining short-term responses to a long-term problem: RNA-seq analyses of iron deficiency chlorosis tolerant soybean
                                                        

- (Peer Reviewed Journal)Moran Lauter, A., Rutter, L., Cook, D., O'Rourke, J.A., Graham, M.A. 2020. Examining short-term responses to a long-term problem: RNA-seq analyses of iron deficiency chlorosis tolerant soybean. International Journal of Molecular Sciences. 21:3591. https://doi.org/10.3390/ijms21103591.Genotypic characterization of the U.S. peanut core collection

- (Abstract Only)Otyama, P.I., Kulkarni, R., Chamberlin, K.D., Ozias-Akins, P., Chu, Y., Lincoln, L.M., Macdonald, G.E., Anglin, N.L., Dash, S., Bertoli, D., Fernandez-Baca, D., Graham, M.A., Cannon, S.B., Cannon, E.K. 2020. Genotypic characterization of the U.S. peanut core collection [abstract]. In proceedings: American Peanut Research and Education Society, July 2020. Available: https://apresinc.com/wp-content/uploads/2020/06/OtyamaPI-Abstract-2020.pdf.Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches
                                                        

- (Peer Reviewed Journal)Assefa, T., Zhang, J., Chowda-Reddy, R.V., Moran Lauter, A.N., Singh, A., O'Rourke, J.A., Graham, M.A., Singh, A.K. 2020. Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches. Biomed Central (BMC) Plant Biology. 20:42. https://doi.org/10.1186/s12870-020-2237-5.Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean
                                                        

- (Peer Reviewed Journal)O'Rourke, J.A., Mccabe, C.E., Graham, M.A. 2020. Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean. Functional and Integrative Genomics. 20:321-341. https://doi.org/10.1007/s10142-019-00709-9.Visualization methods for differential expression analysis
                                                        

- (Peer Reviewed Journal)Rutter, L., Moran Lauter, A.N., Graham, M.A., Cook, D. 2019. Visualization methods for differential expression analysis. BMC Bioinformatics. 20:458. https://doi.org/10.1186/s12859-019-2968-1.Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)
                                                        

- (Peer Reviewed Journal)Kohlhase, D.R., O'Rourke, J.A., Owen, M.D.K., Graham, M.A. 2019. Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus). Biomed Central (BMC) Plant Biology. 19:182. https://doi.org/10.1186/s12870-019-1795-x.Rpp1 encodes a ULP1-NBS-LRR protein that controls immunity to Phakopsora pachyrhizi in soybean
                                                        

- (Peer Reviewed Journal)Pedley, K.F., Pandey, A.K., Ruck, A.L., Lincoln, L.M., Whitham, S.A., Graham, M.A. 2018. Rpp1 encodes a ULP1-NBS-LRR protein that controls immunity to Phakopsora pachyrhizi in soybean. Molecular Plant-Microbe Interactions. 32:120-133.The MAPK kinase kinase GmMEKK1 regulates cell death and defense responses
                                                        

- (Peer Reviewed Journal)Xu, H., Zhang, C., Li, Z., Wang, Z., Jiang, X., Shi, Y., Braun, E., Mei, Y., Qiu, W., Li, S., Wang, B., Xu, J., Navarre, D.A., Ren, D., Cheng, N., Nakata, P.A., Graham, M.A., Whitman, S., Liu, J. 2018. The MAPK kinase kinase GmMEKK1 regulates cell death and defense responses. Plant Physiology. doi:10.1104/pp.18.00903.Leveraging RNA-Seq to characterize resistance to brown stem rot and the Rbs3 locus in soybean
                                                        

- (Peer Reviewed Journal)McCabe, C.E., Cianzio, S.R., O'Rourke, J.A., Graham, M.A. 2018. Leveraging RNA-Seq to characterize resistance to brown stem rot and the Rbs3 locus in soybean. Molecular Plant-Microbe Interactions. 31(10):1083-1094. https://doi.org/10.1094/MPMI-01-18-0009-R.ggenealogy: An R package for visualizing genealogical data
                                                        

- (Peer Reviewed Journal)Rutter, L., Vanderplas, S., Cook, D., Graham, M.A. 2019. ggenealogy: An R package for visualizing genealogical data. Journal of Statistical Software. 89(13)1-31. https://doi.org/10.18637/jss.v089.i13.Soybean functional genomics: Bridging the genotype to phenotype gap
                                                        

- (Book / Chapter)O'Rourke, J.A., Graham, M.A., Whitham, S. 2017. Soybean functional genomics: Bridging the genotype to phenotype gap. In: Nguyen H., Bhattacharyya M., editors. The Soybean Genome. Cham, Switzerland: Springer International. p.151-170.Transcriptome response of Lolium arundinaceum to the fungal endophyte Epichloe coenophiala

- (Peer Reviewed Journal)Dinkins, R.D., Nagabhyru, P., Graham, M.A., Boykin, D.L., Schardl, C.L. 2016. Transcriptome response of Lolium arundinaceum to the fungal endophyte Epichloe coenophiala. New Phytologist. doi: 10.1111/nph.14103.Identifying new sources of resistance to Brown Stem Rot in Soybean

- (Peer Reviewed Journal)McCabe, C.E., Singh, A., Leandro, L., Cianzio, S., Graham, M.A. 2016. Identifying new sources of resistance to Brown Stem Rot in Soybean. Crop Science. doi: 10.2135/cropsci2015.08.0492.Virus-induced gene silencing and transient gene expression in soybean using Bean pod mottle virus infectious clones

- (Peer Reviewed Journal)Whitham, S.A., Lincoln, L.M., Chowda-Reddy, R., Dittman, J.D., O'Rourke, J.A., Graham, M.A. 2016. Virus-induced gene silencing and transient gene expression in soybean using Bean pod mottle virus infectious clones. Current Protocols in Plant Biology. doi:10.1002/cppb.20012.The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies

- (Peer Reviewed Journal)O'Rourke, J.A., Fu, F., Bucciarelli, B., Yang, S.S., Samac, D.A., Lamb, J.F., Monteros, M., Graham, M.A., Gronwald, J.W., Krom, N., Li, J., Dai, X., Zhao, P.X., Vance, C.P. 2015. The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. BioMed Central (BMC) Genetics. 16:502. DOI: 10.1186/s12864-015-1718-7.Gaining insight into soybean defense responses using functional genomics approaches

- (Review Article)Liu, J., Graham, M.A., Pedley, K.F., Whitham, S.A. 2015. Gaining insight into soybean defense responses using functional genomics approaches. Briefings in Functional Genomics. DOI:10.1093/bfgp/elv009.Transcriptome response in different tissues of Lolium arundinaceum to the fungal endophyte Epichloe coenophiala

- (Abstract Only)Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

- (Peer Reviewed Journal)Belamkar, V., Weeks, N.T., Bharti, A.K., Farmer, A.D., Graham, M.A., Cannon, S.B. 2014. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. Biomed Central (BMC) Genomics. 15:950. DOI:10.1186/1471-2164-15-950.Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves

- (Peer Reviewed Journal)Moran Lauter, A., Peiffer, G.A., Yin, T., Cook, D., Shoemaker, R.C., Graham, M.A. 2014. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. Biomed Central (BMC) Genomics. 15:702 DOI: 10.1186/1471-2164-15-702.The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families

- (Peer Reviewed Journal)Link, T.I., Lang, P., Scheffler, B.E., Duke, M.V., Graham, M.A., Cooper, B., Tucker, M.L., Van De Mortel, M., Voegele, R.T., Mendgen, K., Baum, T.J., Whitham, S.A. 2014. The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families. Molecular Plant Pathology. 15(4):379-393. DOI:10.1111/mpp.12099.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. DOI 10.4172/2153-0602.1000139.A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar
                                                        

- (Peer Reviewed Journal)O'Rourke, J.A., Iniguez, L.P., Bucciarelli, B., Roessler, J., Schumtz, J., McClean, P., Jackson, S.A., Hernandez, G., Graham, M.A., Stupar, R.M., Vance, C.P. 2013. A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar. Frontiers in Plant Genetics and Genomics. DOI:10.3389/fpls.2013.00210.Replication protein A subunit 3 and the iron efficiency response in soybean

- (Peer Reviewed Journal)Atwood, S., O'Rourke, J.A., 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.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.Investigating nitrogen deficiency in common beans

- (Abstract Only)O'Rourke, J.A., Iniguez, L.P., Bucciarelli, B., Woodey, J.L., Shoemaker, R.C., Graham, M.A., Cannon, S.B., Mcclean, P.E., Jackson, S.A., Hernandez, G., Vance, C.P. 2012. Investigating nitrogen deficiency in common beans [abstract]. Molecular & Cellular Biology of the Soybean Conference, August 12-15, 2012, Des Moines, Iowa. Available: http://www.extension.iastate.edu/registration/events/soybean/speakeranchor.htm#speaker16.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.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.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.Day temperature influences the male-sterile locus in soybean

- (Peer Reviewed Journal)Wiebbecke, C.E., Graham, M.A., Cianzio, S.R., Palmer, R.G. 2012. Day temperature influences the male-sterile locus in soybean. Crop Science. 52(4):1503-1510.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.Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlates with fungal penetration and haustoria formation

- (Peer Reviewed Journal)Schneider, K.T., Van De Mortel, M., Bancroft, T.J., Nelson, R., Nettleton, D., Braun, E., Frederick, R.D., Baum, T.J., Graham, M.A., Whitham, S.A. 2011. Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlates with fungal penetration and haustoria formation. Plant Physiology. 157:355-371.Identification of genes that mediate protection against soybean pathogens

- (Book / Chapter)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.Gene expression patterns are correlated with genomic and genic structure in soybean

- (Peer Reviewed Journal)Woody, J.L., Severin, A., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.T., Weeks, N.T., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2011. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 54(1):10-18.RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome

- (Peer Reviewed Journal)Severin, A.J., Woody, J.L., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2010. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. Biomed Central (BMC) Plant Biology. 10:610.Complementary Genetic and Genomic Approaches Help Characterize the Linkage Group I Seed Protein QTL in Soybean

- (Peer Reviewed Journal)Bolon, Y.E., Joseph, B., Cannon, S.B., Graham, M.A., Diers, B.W., Farmer, A.D., May, G.D., Muehlbauer, G.J., Specht, J.E., Tu, Z., Weeks, N.T., Xu, W.W., Shoemaker, R.C., Vance, C.P. 2010. Complementary Genetic and Genomic Approaches Help Characterize the Linkage Group I Seed Protein QTL in Soybean. Biomed Central (BMC) Plant Biology. 10:41. Available: http://www.biomedcentral.com/1471-2229/10/41.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.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.Genomic Studies in Soybean: Toward Understanding Seed Oil and Protein Production

- (Abstract Only)Bolon, Y.E., Joseph, B., Cannon, S.B., Diers, B., Farmer, A., Graham, M.A., May, G., Muehlbauer, G., Specht, J., Tu, Z., Weeks, N., Xu, W., Shoemaker, R.C., Vance, C.P. 2008. Genomic Studies in Soybean: Toward Understanding Seed Oil and Protein Production [abstract]. IV International Conference on Legume Genomics and Genetics, December 7-12, 2008, Puerto Vallarta, Mexico. Abstract No. W28. p. 101 and Abstract No. P57, p. 63.IDENTIFICATION OF CANDIDATE GENES FOR THE RPP4 ASIAN SOYBEAN RUST RESISTANCE LOCUS IN SOYBEAN

- (Abstract Only)Targeted Sequencing and Analyses of the Rpp4 Asian Soybean Rust Resistance Locus in Soybean

- (Abstract Only)Targeted Sequencing of the Rpp2 Asian Soybean Rust Resistance Locus

- (Abstract Only)Molecular genetic analysis of seed protein control at Linkage Group I in soybean near-isogenic lines

- (Abstract Only)Bolon, Y.E., Joseph, B., Cannon, S.B., Diers, B., Farmer, A., Graham, M.A., May, G., Muehlbauer, G., Specht, J., Weeks, N., Shoemaker, R.C., Vance, C.P. 2008. Molecular Genetic Analysis of Seed Protein Control at Linkage Group I in Soybean Near-Isogenic Lines [abstract]. 12th Biennial Conference on Molecular and Cellular Biology of the Soybean, July 20-23, 2008, Indianapolis, Indiana.Dissecting the molecular response of soybean to Asian soybean rust

- (Abstract Only)Sequence Level Analysis of Recently Duplicated Regions in the Soybean [Glycine max (L.) Merr.] Genome

- (Peer Reviewed Journal)Van, K., Kim, D., Mei Cai, C., Young Kim, M., Shin, J., Graham, M.A., Shoemaker, R.C., Choi, B., Yang, T., Lee, S. 2008. Sequence Level Analysis of Recently Duplicated Regions in the Soybean [Glycine max (L.) Merr.] Genome. DNA Research. 15:93-102.Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines

- (Peer Reviewed Journal)O'Rourke, J.A., Charlson, D.V., Gonzalez, D.O., Vodkin, L.O., Graham, M.A., Cianzio, S.R., Grusak, M.A., Shoemaker, R.C. 2007. Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. Biomed Central (BMC) Genomics. 8:476.DEFENSIN-LIKE GENES:  GENOMIC PERSPECTIVES ON A DIVERSE SUPERFAMILY IN PLANTS

- (Peer Reviewed Journal)Graham, M.A., Silverstein, K.A., Vandenbosch, K.A. 2008. Defensin-like genes:  genomic perspectives on a diverse superfamily in plants. The Plant Genome/Crop Science. 48:S3-S11.Gene expression profiling of soybean near-isogenic lines contrasting in seed protein and oil

- (Abstract Only)Bolon, Y.E., Diers, B., Graham, M.A., Muehlbauer, G., Shoemaker, R.C., Specht, J., Vance, C.P. 2008. Gene expression profiling of soybean near-isogenic lines contrasting in seed protein and oil [abstract]. XVI Plant and Animal Genome Conference Proceedings, January 12-16, 2008, San Diego, California. Abstract W481.BIOINFORMATIC RESOURCES FOR SOYBEAN GENETIC AND GENOMIC RESEARCH

- (Book / Chapter)Grant, D.M., Nelson, R., Graham, M.A., Shoemaker, R.C. 2008. Bioinformatic resources for soybean genetic and genomic research. In: Stacey, Gary, editor. Genetics and Genomics of Soybean. New York, New York. Springer. p. 141-162.BIPHASIC RESPONSES OF RESISTANT AND SUSCEPTIBLE SOYBEAN PLANTS TO SOYBEAN RUST, PHAKOPSORA PACHYRHIZI

- (Peer Reviewed Journal)Van De Mortel, M., Recknor, J.C., Graham, M.A., Nettleton, D., Dittman, J., Nelson, R., Godoy, C.V., Abdelnoor, R.V., Almeida, A.M., Baum, T.J., Whitham, S.A. 2007. Biphasic responses of resistant and susceptible soybean plants to soybean rust, Phakopsora pachyrhizi. Molecular Plant-Microbe Interactions. 20:887-899.Phosphorus stress in common bean: root transcript and metabolic responses

- (Peer Reviewed Journal)Hernandez, G., Ramirez, M., Valdes-Lopez, O., Gebeyaw, M.T., Graham, M.A., Czechowski, T., Schlereth, A., Wandrey, M., Erban, A., Cheung, F., Wu, H., Lara, M., Town, C.D., Kopka, J., Udvardi, M.K., Vance, C.P. 2007. Phosphorus stress in common bean: root transcript and metabolic responses. Plant Physiology. 144:752-767.SMALL CYSTEINE-RICH PEPTIDES RESEMBLING ANTIMICROBIAL PEPTIDES HAVE BEEN UNDER-PREDICTED IN PLANTS

- (Peer Reviewed Journal)Silverstein, K.A., Moskal, Jr, W.A., Wu, H.C., Underwood, B.A., Graham, M.A., Town, C.D., Vandenbosch, K.A. 2007. Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant Journal. 51:262-280.Recent advances in legume-microbe interactions: recognition, defense response and symbiosis from a genomic perspective

- (Peer Reviewed Journal)Samac, D.A., Graham, M.A. 2007. Recent advances in legume-microbe interactions: recognition, defense response, and symbiosis from a genomic perspective. Plant Physiology. 144:582-587.RECOVERING FROM IRON DEFICIENCY CHLOROSIS IN NEAR ISOGENIC SOYBEANS:  A MICROARRAY STUDY

- (Peer Reviewed Journal)O'Rourke, J., Graham, M.A., Vodkin, L., Gonzalez, D., Cianzio, S., Shoemaker, R.C. 2007. Recovering from iron deficiency chlorosis in near isogenic soybeans:  a microarray study. Plant Physiology and Biochemistry. 45:287-292.RECOVERING FROM IRON DEFICIENCY CHLOROSIS IN NEAR ISOGENIC SOYBEANS:  A MICROARRAY STUDY

- (Abstract Only)O'Rourke, J.A., Graham, M.A., Cianzio, S.R., Shoemaker, R.C. 2007. Recovering from iron deficiency chlorosis in near isogenic soybeans: a microarray study [abstract]. Iron Nutrition and Interactions in Plants Symposium. Paper No. S6-P-21.IDENTIFICATION OF CANDIDATE PHOSPHORUS STRESS INDUCED GENES IN PHASEOLUS VULGARIS L. THROUGH CLUSTERING ANALYSIS ACROSS SEVERAL PLANT SPECIES

- (Peer Reviewed Journal)Graham, M.A., Ramirez, M., Valdes-Lopez, O., Lara, M., Tesfaye, M., Vance, C.P., Hernandez, G. 2006. Identification of candidate phosphorus stress induced genes in Phaseolus vulgaris L. through clustering analysis across several plant species. Functional Plant Biology. 33(8):789-797.
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                                                Scientists Identify Rust Resistance Genes in Soybeans


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