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ARS Home Midwest Area Ames, Iowa Corn Insects and Crop Genetics Research People







Jamie A O`Rourke    Research Geneticist (Plants) Corn Insect & Crop Genetics Research Unit  /ARSUserFiles/43345/Unit Photos/O'Rourke J 225x300.jpg

Jamie O’RourkeResearch Geneticist (Plants)716 Farmhouse Lane1567 Agronomy HallIowa State UniversityAmes, Iowa 50011-4014515-294-7824515-294-9359 (Fax) **Education**: B.S. Biology, University of Kansas
Ph.D. Genetics, Iowa State University  **Research Interests**: Improving crop yields and mitigating losses to biotic and abiotic stress is critical to food security. While crop production must support continued population growth, it must also become more sustainable, with fewer inputs and reduced environmental impact. My primary research interests are identifying and understanding gene expression changes induced by abiotic stress. My work focuses on iron and phosphorus deficiency in legumes. Iron (Fe) is an essential micronutrient for plants, involved in multiple physiological processes including photosynthesis and electron transport. Though Fe is abundant in soil, environmental conditions including high pH, calcareous soil composition, and aerobic conditions often render Fe insoluble and unavailable for plants. Of the worlds cultivated soils, roughly 30% are calcareous, including the upper Midwestern United States where over 90% of US soybeans are produced. Fe deficiency in soybean results in end of season yield loss. Conversely, excessive Fe is toxic, resulting in plant death. Thus, iron uptake is tightly regulated. Similarly, although phosphate is plentiful in soils, slow diffusion and high fixation within soils makes phosphorus one of the most rate-limiting nutrients in agricultural production. Thus, phosphorus is commonly applied as a fertilizer, but plants only utilize about 20% of the applied fertilizer with the rest lost through run-off and contributing to environmental problems such as water eutrophication. My lab focuses on understanding how plants alter gene expression patterns in response to iron and phosphorus deficiency to survive low nutrient growth conditions. To understand how these genes are involved in abiotic stress responses we use sequencing of RNA (RNA-seq) to identify all expressed and differentially expressed gene sequences. We also use a suite of associated tools to visualize expression patterns to identify biological pathways associated with stress tolerance. To understand the effect of a specific gene on abiotic stress tolerance, we knock down its expression in soybean using virus induced gene silencing (VIGS). These approaches have found high overlap in the genes affected by iron and phosphorus deficiency, indicating these nutrient deficiencies alter similar pathways. Interestingly, multiple stress exposure can alter gene expression patterns from those observed after a single stress event, suggesting plants can prime stress responses. These findings have important implications for plant breeding programs working on improved abiotic stress tolerance. Understanding the biological pathways associated with stress tolerance will facilitate the development of cultivars with enhanced stress tolerance and improved nutrient use efficiency. **Aims:** Improve understanding of how plants alter gene expression patterns and associated biological networks in response to iron and phosphorus deficiency to survive low nutrient growth conditions.**Background:**While crop production must support continued population growth, it must also become more sustainable, with fewer inputs and reduced environmental impact. My primary research interests are identifying and understanding gene expression changes induced by abiotic stress, specifically iron and phosphorus deficiency, in legumes. Iron (Fe) is an essential micronutrient, involved in multiple physiological processes.  Though abundant in soil, environmental conditions often render Fe insoluble and unavailable for plants. Of the worlds cultivated soils, roughly 30% are calcareous, including the upper Midwestern United States where over 90% of US soybeans are produced.  Fe deficiency in soybean results in end of season yield loss.  Conversely, excessive Fe is toxic, resulting in plant death.  Thus, iron uptake is tightly regulated.  Similarly, although phosphate is plentiful in soils, slow diffusion and high fixation within soils makes phosphorus (Pi) one of the most rate-limiting nutrients in agricultural production.  Thus, Pi is commonly applied as a fertilizer, but plants only utilize about 20% of the applied fertilizer with the rest lost through run-off and contributing to environmental problems such as water eutrophication.**Approach:** We utilize a suite of functional genomic tools including RNA sequencing (RNA-seq), to identify all expressed and differentially expressed gene sequences.  Virus induced gene silencing (VIGS) and VIGS coupled with RNA-seq is used to characterize gene function and identify associated gene networks.  Using bioinformatic tools we are able to visualize expression patterns and associate specific biological pathways with stress tolerance. **Outcomes:**  Our work has helped the hallmarks of the soybean iron deficiency stress response.  We have determined different nutrients affect the same biological pathways, though possibly in different ways and confirmed that early stress exposure may promote stress acclimation processes in soybean. Understanding the biological pathways associated with stress tolerance will facilitate the development of cultivars with enhanced stress tolerance and improved nutrient use efficiency.  Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean-(Peer Reviewed Journal) Chiteri, K.O., Rairdin, A., Sandu, K., Redsun, S., Farmer, A., O'Rourke, J.A., Cannon, S.B., Singh, A. 2024. Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean. BMC Genomics. 25. Article 270. https://doi.org/10.1186/s12864-024-10156-x.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.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.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.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.Soybean root system architecture trait study through genotypic, phenotypic, and shape-based clusters-(Peer Reviewed Journal) Falk, K.G., Juberi, T.Z., O'Rourke, J.A., Singh, A., Sarkar, S., Ganapathysubramanian, B., Singh, A.K. 2020. Soybean root system architecture trait study through genotypic, phenotypic and shape-based clusters. Plant Phenomics. https://doi.org/10.34133/2020/1925495.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.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.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.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.Fast neutron induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes-(Peer Reviewed Journal) Campbell, B.W., Hofstad, A., Sreekanta, S., Fu, F., Koono, T., O'Rourke, J.A., Vance, C.P., Muehlbauer, G.J., Stupar, R. 2016. Fast neutron induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. Theoretical and Applied Genetics. doi: 1007/S00122-016-2735-x.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.Transgene silencing of sucrose synthase in alfalfa (Medicago sativa L.) stem vascular tissue suggests a role for invertase in cell wall cellulose synthesis-(Peer Reviewed Journal) Samac, D.A., Bucciarelli, B., Miller, S.S., Yang, S.H., O'Rourke, J.A., Shin, S., Vance, C.P. 2015. Transgene silencing of sucrose synthase in alfalfa (Medicago sativa L.) stem vascular tissue suggests a role for invertase in cell wall cellulose synthesis. Biomed Central (BMC) Plant Biology. 15:283. doi:10.1186/s12870-015-0649-4.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.Genetic and physical map correlation-(Popular Publication) O'Rourke, J.A. 2014. Genetic and physical map correlation. Popular Publication. doi: 10.1002/9780470015902.a0000819.pub3.Transgene silencing of sucrose synthase in alfalfa stem vascular tissue by a truncated phosphoenolpyruvate carboxylase: sucrose synthase construct-(Abstract Only) Gronwald, J.W., Yang, S.H., Bucciarelli, B., Miller, S.S., O'Rourke, J.A., Shin, S., Samac, D.A., Vance, C.P. 2014. Transgene silencing of sucrose synthase in alfalfa stem vascular tissue by a truncated phosphoenolpyruvate carboxylase: sucrose synthase construct. Plant Biology. July 12-16, 2014. Portland, OR.Legume genomics: Understanding biology through DNA and RNA sequencing-(Peer Reviewed Journal) O'Rourke, J.A., Bolon, Y., Bucciarelli, B., Vance, C.P. 2014. Legume genomics: Understanding biology through DNA and RNA sequencing. Annals Of Botany. 113(7):1107-1120.The Medicago sativa Gene Index 1.2:  A web-accessible expression atlas of two Medicago sativa sub-species-(Abstract Only) Fu, F., O'Rourke, J.A., Bucciarelli, B., Yang, S.S., Samac, D.A., Lamb, J.F., Krom, N., Zhao, P.X., Gronwald, J.W., Vance, C.P. 2013. The Medicago sativa Gene Index 1.2:  A web-accessible expression atlas of two Medicago sativa sub-species. Cold Spring Harbor Meeting on Genome Informatics. October 30 - November 2, 2013. Cold Spring Harbor, NY.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.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.An RNA-seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants-(Peer Reviewed Journal) O'Rourke, J.A., Yang, S.H., Miller, S.S., Bucciarelli, B., Liu, J., Rydeen, A., Uhde-Stone, C., Tu, Z., Allan, D., Gronwald, J.W., Vance, C.P. 2012. An RNA-seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. Plant Physiology. 161(1):705-724.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.The transcriptome of common bean: nodules to beans-(Abstract Only) O'Rourke, J.A., Iniguez, L.P., Bucciarelli, B., Woody, J.L., McClean, P.E., Jackson, S.A., Shoemaker, R.C., Hernandez, G., Vance, C.P. 2011. The transcriptome of common bean: nodules to beans [abstract]. XIV National Congress of Biochemistry and Plant Molecular Biology and 7th Symposium Mexico - USA, November 29-December 2, 2011, Campeche, Mexico. p. 17.Transcriptome of common bean (Phaseolus vulgaris) through RNA-seq: nodulation, symbiotic nitrogen fixation, transcription factors-(Abstract Only) Hernandez, G., Iniguez, L.P., O'Rourke, J.A., McClean, P., Shoemaker, R.C., Jackson, S., Vance, C.P. 2012. Transcriptome of common bean (Phaseolus vulgaris) through RNA-seq: nodulation, symbiotic nitrogen fixation, transcription factors [abstract]. Plant and Animal Genome XX Conference, January 14-18, 2012, San Diego, California. Available: http://pag.confex.com/pag/xx/webprogram/Paper1559.html.The transcriptome of common bean: more than nodulation-(Abstract Only) O'Rourke, J.A., Iniguez, L.P., Bucciarelli, B., Woodey, J.L., McClean, P.E., Jackson, S.A., Shoemaker, R.C., Hernandez, G., Vance, C.P. 2011. The transcriptome of common bean: more than nodulation [abstract]. Plant Biology 2011, American Society of Plant Biologists Annual Meeting, August 6-10, 2011, Minneapolis, Minnesota. Available: http://abstracts.aspb.org/pb2011/public/M20/M2003.html.Identifying genes involved in nodulation and symbiotic nitrogen fixation (SNF) in Phaseolus vulgaris using RNAseq technology-(Abstract Only) Iniguez, L.P., O'Rourke, J.A., Bucciarelli, B., Woodey, J.L., Shoemaker, R.C., Hernandez, G., Vance, C.P. 2011. Identifying genes involved in nodulation and symbiotic nitrogen fixation (SNF) in Phaseolus vulgaris using RNAseq technology [abstract]. Plant Biology 2011, American Society of Plant Biologists Annual Meeting, August 6-10, 2011, Minneapolis, Minnesota. Available: http://abstracts.aspb.org/pb2011/public/P15/P15030.html.An integrative approach to genomic introgression mapping-(Peer Reviewed Journal) Severin, A.J., Peiffer, G., Xu, W.W., Hyten, D.L., Bucciarelli, B., O'Rourke, J.A., Bolon, Y.E., Grant, D.M., Farmer, A.D., May, G.D., Vance, C.P., Shoemaker, R.C., Stupar, R.M. 2010. An integrative approach to genomic introgression mapping. Plant Physiology. 154(1):3-12.Understanding the Regulation of Cell Wall Composition in Alfalfa-(Abstract Only) O'Rourke, J.A., Tesfaye, M., Yang, S.H., Lamb, J.F., Jung, H.G., Vance, C.P., Samac, D.A. 2010. Understanding the Regulation of Cell Wall Composition in Alfalfa [abstract]. Plant and Animal Genome XVIII Conference, January 9-13, 2010, San Diego, California. Available: http://www.intl-pag.org/18/abstracts/P07c_PAGXVIII_799.html. ProjectsLeveraging Crop Genetic Diversity and Genomics to Improve Biotic and Abiotic Stress Tolerance in SoybeanIn-House Appropriated (D)Accession Number:444061 ARS News ArticlesNo news articles listed for this employee.


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