Research Geneticist (Plants)
Corn Insect & Crop Genetics Research Unit
Research Geneticist (Plants) |
Research is focused on the high-throughput functional analysis of important agronomic genes in cereal crops. We use a variety of interdisciplinary approaches, including plant and microbial genetics, molecular biology, plant pathology, and bioinformatics & computational biology.
Additional Links
Velasquez-Zapata, V., Smith, S., Priyanka, S., Chapman, A.V., Jaiswal, N., Helm, M.D., Wise, R.P. 2024. Diverse epistatic effects in barley-powdery mildew interactions localize to host chromosome hotspots. iScience. https://doi.org/10.1016/j.isci.2024.111013.
Li, Z., Velásquez-Zapata, V., Elmore, J.M., Li, X., Xie, W., Deb, S., Tian, X., Banerjee, S., Jørgensen, H.J., Pederson, C., Wise, R.P., Thordal-Christensen, H. 2024. Powdery mildew effectors AVRA1 and BEC1016 target the ER J-domain protein HvERdj3B required for immunity in barley. Molecular Plant Pathology. 25(5). Article e13463. https://doi.org/10.1111/mpp.13463.
Boury, N., Van den Bogaard, M., Wlezien, E.B., Peters, N., Wise, R.P. 2024. The great petunia carnage of 2017: A clicker case study using petunias to describe effect of genetic modification on the biochemistry of flower color and phenotype in plants. CourseSource. https://doi.org/10.24918/cs.2024.15.
Velasquez-Zapata, V., Elmore, J.M., Patel, S., Smith, S., Fuerst, G.S., Wise, R.P. 2024. Protein-protein networks in an integrated barley-powdery mildew interactome. Fungal Genetics Conference Proceedings. Abstract no. 662A Protein-protein networks in an integrated barley-powdery mildew interactome. 32nd Fungal Genetics Conference March 12–17, 2024 | Asilomar Conference Grounds | Pacific Grove, CA |
Wise, R.P., Fuerst, G.S., Peters, N., Boury, N., McGhee, L., Greene, M., Michaelson, S., Gonzalez, J., Hayes, N., Schuck, R., Maffin, L., Hall, G., Hubbard, T., Whigham, E. 2024. iTAG: Interactive laboratory exercises to explore genotype and phenotype using Oregon Wolfe barley. The Plant Health Instructor. 24. https://doi.org/10.1094/PHI-E-2023-09-0009.
Velasquez-Zapata, V., Elmore, J.M., Patel, S., Smith, S., Fuerst, G.S., Wise, R.P. 2024. Host-pathogen networks in an integrated barley-powdery mildew interactome. Plant and Animal Genome Conference Proceedings. https://pag.confex.com/pag/31/work/papers/viewonly.cgi?password=860965&username=54280. International Plant & Animal Genome / PAG 31 • January 12-17, 2024 • San Diego, CA, USA
Velasquez-Zapata, V., Elmore, J.M., Patel, S., Smith, S., Fuerst, G.S., Wise, R.P. 2024. Network hubs in pathogen-host interactions: Targets for next-generation breeding. Barley Improvement Conference Proceedings, January 10-11, 2024, San Diego, California.
Velasquez-Zapata, V., Smith, S., Priyanka, S., Chapman, A.E., Wise, R.P. 2023. Transcriptome-based host epistasis and pathogen co-expression in barley-powdery mildew interactions. Genetics. https://doi.org/10.1101/2023.09.18.558274.
Velásquez-Zapata, V., Elmore, J.M., Wise, R.P. 2023. Bioinformatic analysis of yeast two-hybrid next-generation interaction screen data. In: Mukhtar, S., editor. Protein-Protein Interactions, Methods and Protocols. Methods in Molecular Biology. 2690:223-239. https://doi.org/10.1007/978-1-0716-3327-4_19.
Elmore, J.M., Velásquez-Zapata, V., Wise, R.P. 2023. Next-generation yeast two-hybrid screening to discover protein-protein interactions. In: Mukhtar, S.,editor. Protein-Protein Interactions, Methods and Protocols. Methods in Molecular Biology. 2690:205-222. https://doi.org/10.1007/978-1-0716-3327-4_19.
Velasquez-Zapata, V., Elmore, J., Fuerst, G.S., Wise, R.P. 2022. An interolog-based barley interactome as an integration framework for immune signaling. Genetics. 221(2). Article iyac056. https://doi.org/10.1093/genetics/iyac056.
Wlezien, E.B., Peters, N.T., Wise, R., Boury, N. 2022. Role of crop genetic diversity on pathogen impact: The tale of two pathogens. CourseSource. https://doi.org/10.24918/cs.2022.14.
Chapman, A.V., Elmore, J., McReynolds, M., Walley, J., Wise, R.P. 2021. SGT1-specific domain mutations impair interactions with the barley MLA6 immune receptor in association with loss of NLR protein. Molecular Plant-Microbe Interactions. 35(3):274-289. https://doi.org/10.1094/MPMI-08-21-0217-R.
Velasquez-Zapata, V., Elmore, M.J., Fuerst, G.S., Wise, R.P. 2021. Multi-layered characterization of the barley interactome links MLA immune receptor signaling with defense gene expression. International Congress on Molecular Plant-Microbe Interactions. 34. https://doi.org/10.1094/MPMI-34-9-S2.1.
Chapman, A.E., Hunt, M., Surana, P., Velasquez-Zapata, V., Xu, W., Fuerst, G.S., Wise, R.P. 2021. Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1. Meeting Proceedings. 34. https://doi.org/10.1094/MPMI-34-7-S1.1.
Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. BMC Bioinformatics. 22. Article 205. https://doi.org/10.1186/s12859-021-04120-9.
Velasquez-Zapata, V., Elmore, M.J., Banerjee, S., Dorman, K., Wise, R.P. 2021. Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor. PLoS Computational Biology. 17(4). Article e1008890. https://doi.org/10.1371/journal.pcbi.1008890.
Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. Constructing Zea mays genes from RNA-Seq expression data using FINDER - a fully automated gene annotator. Maize Annual Meetings. 41.
Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. bioRxiv. https://doi.org/10.1101/2021.02.04.429837.
Chapman, A.V., Hunt, M., Surana, P., Velasquez-Zapata, V., Xu, W., Fuerst, G.S., Wise, R.P. 2020. Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1. Genetics. 217(2). https://doi.org/10.1093/genetics/iyaa026.
Banerjee, S., Velasquez-Zapata, V., Fuerst, G.S., Elmore, J.M., Wise, R.P. 2020. NGPINT: a next-generation protein-protein interaction software. Briefings in Bioinformatics. 22(4). https://doi.org/10.1093/bib/bbaa351.
Hunt, M., Banerjee, S., Surana, P., Liu, M., Fuerst, G.S., Mathioni, S., Meyers, B.C., Nettleton, D., Wise, R.P. 2019. Small RNA discovery in the interaction between barley and the powdery mildew pathogen. Biomed Central(BMC)Genomics. 20. https://doi.org/10.1186/s12864-019-5947-z.
Carter, M., Helm, M., Chapman, A., Wan, E., Restrepo Sierra, A., Innes, R., Bogdanove, A., Wise, R.P. 2019. Convergent evolution of effector protease recognition by Arabidopsis and barley. Molecular Plant-Microbe Interactions. 32(5):550-565. https://doi.org/10.1094/MPMI-07-18-0202-FI.
Carter, M., Bogdanove, A., Innes, R., Wise, R.P. 2018. A confounding effect of bacterial titer in a type III delivery-based assay of eukaryotic effector function. Molecular Plant-Microbe Interactions. 31(11):1115-1116. https://doi.org/10.1094/MPMI-05-18-0128-LE.
Mistry, D., Wise, R.P., Dickerson, J. 2017. DiffSLc: A graph centrality method to detect essential proteins of a protein-protein interaction network. PLoS One. https://doi.org/10.1371/journal.pone.0187091.
Elmore, J.M., Perovic, D., Ordon, F., Schweizer, P., Wise, R.P. 2018. A genomic view of biotic stress resistance. In: Stein, N., Muehlbauer, G., editors. The Barley Genome. Cham, Switzerland: Springer International. p. 233-257. https://doi.org/10.1007/978-3-319-92528-8_14.
Surana, P., Xu, R., Fuerst, G.S., Chapman, A., Nettleton, D., Wise, R.P. 2017. Inter-chromosomal transfer of immune regulation during infection of barley with the powdery mildew pathogen. Genes, Genomes, and Genomics. https://doi.org/10.1534/g3.117.300125.
Lu, X., Kracher, B., Saur, I., Bauer, S., Ellwood, S.R., Wise, R.P., Yaeno, T., Maekawa, T., Schulze-Lefert, P. 2016. Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen. Proceedings of the National Academy of Sciences. 113(42):e6486-6495. doi:10.1073/pnas.1612947113.
McGhee, L., Hayes, N., Schuck, R., Maffin, L., Hall, G., Hubband, T., Whigham, E., Fuerst, G.S., Wise, R.P. 2016. iTAG Barley: A grade 7-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe Barley. iTunes. Available: https://itunes.apple.com/us/book/itag-barley-grade-7-12-curriculum/id1110510488?mt=11 & https://itunes.apple.com/us/book/itag-barley-grade-7-12-curriculum/id1108586855?mt=11.
Zuo, T., Zhang, J., Lithio, A., Dash, S., Weber, D., Wise, R.P., Nettleton, D., Peterson, T. 2016. Genes and small RNA transcripts exhibit dosage-dependent expression pattern in maize copy-number alterations. Genetics. 203(1):1177-1190. doi: 10.1534/genetics.116.188235.
Munoz-Amatriain, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J., Moscou, M., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G., Wise, R.P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bartos, J., Bhat, P., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J., Dolezel, J., Grimwood, J., Schmutz, J., Duma, D., Altschmied, L., Blake, T., Bregitzer, P.P., Cooper, L., Dilbirligi, M., Falk, A., Feiz, L., Graner, A., Gustafson, P., Hayes, P., Lemaux, P., Mammadov, J., Close, T. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal. 84(1):216-227. doi: 10.1111/tpj.12959.
Xu, W., Meng, Y., Surana, P., Fuerst, G.S., Nettleton, D., Wise, R.P. 2015. The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions. Frontiers in Plant Science. 6:409. DOI:10.3389/fpls.2015.00409.
Whigham, E., Qi, S., Mistry, D., Surana, P., Xu, R., Fuerst, G.S., Pliego, C., Bindschedler, L., Spanu, P., Dickerson, J., Innes, R.W., Nettleton, D., Bogdanove, A.J., Wise, R.P. 2015. Broadly conserved fungal effector BEC1019 suppresses host cell death and enhances pathogen virulence in powdery mildew of barley (Hordeum vulgare L.). Molecular Plant-Microbe Interactions. 28(9): 968-983. DOI: http://dx.doi.org/10.1094/MPMI-02-15-0027-FI.
Liu, J., Cheng, X., Liu, D., Xu, W., Wise, R.P., Shen, Q. 2014. The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling. PLoS Genetics. 10(12):e1004755. DOI:10.1371/journal.pgen.1004755.
Cernadas, R.A., Doyle, E.L., Nino-Liu, D., Wilkins, K.E., Bancroft, T., Wang, L., Schmidt, C., Caldo, R., Yang, B., White, F.F., Nettleton, D., Wise, R.P., Bogdanove, A. 2014. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. PLoS Pathogens. DOI: 10.1371/journal.ppat.1003972.
Xu, W., Meng, Y., Wise, R.P. 2014. Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. New Phytologist. 201(4):1396-1412.
Hayes, N., Maffin, L., McGhee, L., Hall, G., Hubbard, T., Whigham, E., Wise, R.P. 2013. iTAG Barley: A 9-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe barley. iTunes. Available: https://itunes.apple.com/us/book/itag-barley/id715260619?mt=11.
Mascher, M., Muehlbauer, G.J., Rokhsar, D.S., Chapman, J., Schmutz, J., Barry, K., Munoz-Amatriain, M., Close, T.J., Wise, R.P., Schulman, A.H., Himmelbach, A., Mayer, K.F., Scholz, U., Poland, J.A., Stein, N., Waugh, R. 2013. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant Journal. DOI: 10.1111/tpj.12319.
Ballini, E., Lauter, N.C., Wise, R.P. 2013. Prospects for advancing defense to cereal rusts through genetical genomics. Frontiers in Plant Science. 4:117.
Pliego, C., Nowara, D., Bonciani, G., Gheorghe, D., Xu, R., Surana, P., Whigham, E., Nettleton, D., Bogdanove, A., Wise, R.P., Schweizer, P., Bindschedler, L., Spanu, P. 2013. Host-Induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors. Molecular Plant-Microbe Interactions. 26(6):633-642.
Mayer, K., Waugh, R., Langridge, P., Close, T.J., Wise, R.P., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbaueer, G.J., Stein, N., Ariyadasa, R., Schulte, D., Poursarebani, N., Zhou, R., Steuernagel, B., Mascher, M., Scholz, U., Shi, B., Madishetty, K., Svensson, J.T., Bhat, P., Moscou, M., Resnik, J., Hedley, P., Liu, H., Morris, J., Frenkel, Z., Korol, A., Berges, H., Taudien, S., Felder, M., Groth, M., Platzer, M., Himmelbach, A., Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Ciardo, G., Ma, Y., Wanamaker, S., Cattonaro, F., Vendramin, V., Scalabrin, S., Radovic, S., Wing, R., Morgante, M., Nussbaumer, T., Gundlach, H., Martis, M., Poland, J.A., Spannagl, M., Pfeifer, M., Moisy, C., Tanskanen, J., Zuccolo, A., Russell, J., Druka, A., Marshall, D., Bayer, M., Sampath, D., Febrer, M., Caccamo, M., Tanaka, T., Platzer, M., Fincher, G., Schmutzer, T. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-716.
Wise, R.P., Surana, P., Fuerst, G.S., Xu, R., Mistry, D., Dickerson, J., Nettleton, D. 2014. Flor revisited (again): eQTL and mutational analysis of NB-LRR mediated immunity to powdery mildew in barley. Journal of Integrative Agriculture. 13(2):237-243.
Kronmiller, B.A., Wise, R.P. 2013. TEnest 2.0: Computational annotation and visualization of nested transposable elements. In: Peterson, T., editor. Methods in Molecular Biology. New York, NY: Springer. p. 305-320.
Meng, Y., Wise, R.P. 2012. HvWRKY10, HvWRKY19, and HvWRKY28 positively regulate Mla-triggered immunity and basal defense to barley powdery mildew. Molecular Plant-Microbe Interactions. DOI:10.1094/MPMI-04-12-0082-R.
Blake, V.C., Kling, J.G., Hayes, P.M., Jannink, J., Jillella, S.R., Lee, J., Matthews, D.E., Chao, S., Close, T.J., Muehlbauer, G.J., Smith, K.P., Wise, R.P., Dickerson, J.A. 2012. The hordeum toolbox - the barley CAP genotype and phenotype resource. The Plant Genome. DOI: 10.385/plantgenome2012.03.0002.
Moeller, J.R., Moscou, M.J., Bancroft, T., Skadsen, R.W., Wise, R.P., Whitham, S.A. 2012. Differential regulation of host mRNA translation during obligate pathogen-plant interactions. Molecular Biosystems. 8:2153-2165.
Maffin, L., Hall, G., Hubbard, T., Whigham, E., Wise, R.P. 2012. iTAG Barley: A 9-12 classroom module to explore gene expression and segregation using Oregon Wolfe Barley. American Society of Plant Biologists. http://c.ymcdn.com/sites/my.aspb.org/resource/group/a9372bf4-9ae4-4d0b-ad0c-595c9dfc3543/itag_v20_march_2013.pdf.
Dash, S., Van Hemert, J., Hong, L., Wise, R.P., Dickerson, J.A. 2011. PLEXdb: Gene expression resources for plants and plant pathogens. Nucleic Acids Research. 40(D1):D1194-D1201.
Meyer, J.M., Pei, D., Wise, R.P. 2011. Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L. The Plant Genome. 4(3):283-299.
Moscou, M.J., Lauter, N.C., Steffenson, B., Wise, R.P. 2011. Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genetics. 7(7):DOI: 10.1371/journal.pgen.1002208.
Moscou, M.J., Lauter, N.C., Caldo, R.A., Nettleton, D., Wise, R.P. 2011. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions. Molecular Plant-Microbe Interactions. 24(6):694-705.
Wise, R.P., Meng, Y., Moscou, M.J., Xu, W. 2010. Regulators of Innate Immunity in Cereal-fungal Interactions. In: Antoun, H., Avis, T., Brisson, L., Prevost, D., Trepanier, M., editors. Biology of Plant-Microbe Interactions. St. Paul, MN: International Society for Molecular Plant-Microbe Interactions. p. 1-7.
Nino-Liu, D.O., Bancroft, T., Rajaram, M.L., Moscou, M., Caldo, R., Schmidt, C., Dorman, K., Yang, B., Patil, P., Szurek, B., Koebnik, R., Van Sluys, M., Leach, J.E., Salzberg, S.L., White, F.F., Nettleton, D., Wise, R.P., Bogdanove, A.J. 2017. Targeting of the rice transcriptome by TAL effectors of Xanthomonas oryzae. In: Wolpert, T., Shiraishi T., Collmer A., Akimitsu K., and Glazebrook J., editors. Genome-Enabled Analysis of Plant-Pathogen Interactions. St. Paul, Minnesota: American Phytopathological Society Press. p.193-206. https://doi.org/10.1094/9780890544983.021.
Abebe, T., Wise, R.P., Skadsen, R.W. 2009. Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike while the Lemma and the Palea Primarily Protect the Seed. The Plant Genome. 2(3):247-259.
Abebe, T., Melmaiee, K., Berg, V., Wise, R.P. 2009. Drought Response in the Spikes of Barley: Gene Expression in the Lemma, Palea, Awn, and Seed. Functional and Integrative Genomics. 10(2):191-205.
Wang, K., Frame, B., Xu, X., Moeller, L., Lamkey, K., Wise, R.P. 2009. Strategies for the Production of Maize-derived Pharmaceuticals using Cytoplasmic Male Sterile Lines: in vitro Tissue Culture/Transformation and Field Breeding Approaches. Maydica. 54(1):199-210.
Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M.R., Churas, C., Pasternak, S., Forrest, D.K., Wise, R.P., Ware, D., Wing, R., Waterman, M., Livny, M., Schwartz, D.C. 2009. A Single Molecule Scaffold for the Maize Genome. PLoS Genetics. 5(11):1-14.
Xi, L., Moscou, M.J., Meng, Y., Xu, W., Caldo, R.A., Shaver, M., Nettleton, D., Wise, R.P. 2009. Transcript-based Cloning of RRP46, a Regulator of rRNA Processing and R-Gene-Independent Cell Death in Barley–Powdery Mildew Interactions. The Plant Cell. 21(10):3280-3295.
Kronmiller, B.A., Wise, R.P. 2009. Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-associated Region of Maize. Plant Physiology. doi: 10.1104. p. 109.143370. 151(2):483-495.
Schreiber, A.W., Sutton, T., Caldo, R.A., Kalashyan, E., Lovell, B., Mayo, G., Muehlbauer, G.J., Druka, A., Waugh, R., Wise, R.P., Langridge, P., Baumann, U. 2009. Comparative Transcriptomics in the Triticeae. BioMed Central (BMC) Genetics. 10:285.
Wise, R.P., Lauter, N.C., Szabo, L.J., Schweizer, P. 2009. Genomics of Biotic Interactions in the Triticeae. In: Feuillet, C., Muehlbauer, G., editors. Genetics and Genomics of the Triticeae. New York, NY: Springer. p. 559-589.
Druka, A., Druka, I., Centeno, A.G., Li, H., Sun, Z., Thomas, W.T., Bonar, N., Steffenson, B.J., Ullrich, S.E., Kleinhofs, A., Wise, R.P., Close, T.J., Potokina, E., Luo, Z., Wagner, C., Schweizer, G.F., Marshall, D.F., Kearsey, M.J., Williams, R.W., Waugh, R. 2008. Towards Systems Genetic Analyses in Barley: Integration of Phenotypic, Expression and Genotype Data into GeneNetwork. BioMed Central (BMC) Genetics. 9:73.
Meng, Y., Moscou, M., Wise, R.P. 2008. Blufensin1 Negatively Impacts Basal Defense in Response to Barley Powdery Mildew. Plant Physiology. 149(1):271-285.
Hu, P., Meng, Y., Wise, R.P. 2009. Functional Contribution of Chorismate Synthase, Anthranilate Synthase, and Chorismate Mutase to Penetration Resistance in Barley-Powdery Mildew Interactions. Molecular Plant-Microbe Interactions. 22(3):311-320.
Schulte, D., Close, T.J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G., Sato, K., Schulman, A.H., Waugh, R., Wise, R.P., Stein, N. 2009. The International Barley Sequencing Consortium — At the Threshold of Efficient Access to the Barley Genome. Plant Physiology. 149(1):142-147.
Potokina, E., Druka, A., Luo, Z., Moscou, M., Wise, R.P., Waugh, R., Kearsey, M. 2008. Tissue Dependent Limited Pleiotropy Affects Gene Expression in Barley. Plant Journal. 56(2):287-296. DOI: 10.1111/j.1365-313X.2008.03601.x. Available: http://www3.interscience.wiley.com/cgi-bin/fulltext/120696653/HTMLSTART.
Druka, A., Potokina, E., Luo, Z., Bonar, N., Druka, I., Zhang, L., Marshall, D.F., Steffenson, B.J., Close, T.J., Wise, R.P., Kleinhofs, A., Williams, R.W., Kearsey, M.J., Waugh, R. 2008. Exploiting Regulatory Variation to Identify Genes Underlying Quantitative Resistance to the Wheat Stem Rust Pathogen Puccinia graminis f. sp. tritici in Barley. Theoretical and Applied Genetics. 117(2):261-272. Available: http://www.springerlink.com/content/x16mlth1489u8161/fulltext.html.
Moscou, M.J., Caldo, R.A., Lauter, N.C., Wise, R.P. 2008. Construction of Coexpression Networks to Explore Barley-Powdery Mildew Interactions. In: Lorito, M., Woo, S.L., Scala, F., editors. Biology of Plant Microbe Interactions: The Impact of "omics." Volume 6. St. Paul, MN: APS Press. p. 113-117.
Hu, P., Wise, R.P. 2008. Diversification of Lrk/Tak Kinase Gene Clusters is Associated with Subfunctionalization and Cultivar-specific Transcript Accumulation in Barley. Functional and Integrative Genomics. 8:199-209. Available: http://www.springerlink.com/content/cn67678u46506857/fulltext.html.
Moscou, M.J., Lauter, N.C., Caldo, R.A., Wise, R.P. 2007. Gene-For-Gene-Mediated Transcriptome Reprogramming in Barley-Powdery Mildew Interactions [abstract]. Annual International Plant & Animal Genome Conference. Abstract Book. p. 88.
Cannon, E.K., Dash, S., Lu, H., Nadkarni, D., Thomas, A., Lauter, N.C., Brendel, V., Wise, R.P., Dickerson, J.A. 2007. PLEXdb: Plant and Pathogen Expression Database and Tools for Comparative and Functional Genomics Analysis [abstract]. Annual International Plant & Animal Genome Conference. Abstract Book. p. 351.
Lauter, N.C., Moscou, M.J., Rodriguez, J.E., Fuerst, G.S., Steffenson, B.J., Jin, Y., Szabo, L.J., Wise, R.P. 2007. Genetical Genomic Dissection of Stem Rust Infection in Barley [abstract]. Annual International Plant & Animal Genome Conference. Book of Abstracts. p. 17.
Kronmiller, B.A., Wise, R.P. 2007. TEnest: Automated Chronological Annotation and Visualization of Nested Plant Transposable Elements. Plant Physiology. 146(1):45-59.
Potokina, E., Druka, A., Luo, Z.W., Wise, R.P., Waugh, R., Kearsey, M.J. 2008. Gene Expression Quantitative Trait Locus Analysis of 16,000 Barley Genes Reveals a Complex Pattern of Genome-wide Transcriptional Regulation. Plant Journal. 53(1):90-101.
Wise, R.P., Moscou, M.M., Whitham, S.A., Bogdanove, A.J. 2007. Transcript Profiling in Host-pathogen Interactions. Annual Review of Phytopathology. 45:329-369.
Luo, Z.W., Potokina, E., Druka, A., Wise, R.P., Waugh, R., Kearsey, M.J. 2007. SFP genotyping from Affymetrix arrays is robust but largely detects cis-acting expression regulators. Genetics. 176:789-800.
Wise, R.P., Muehlbauer, G. 2006. High-throughput gene expression studies provide clues for how cereal crops grow. USDA-NRI Research Highlight. 3:1-2.
Rossi, C., Cuesta-Marcos, A., Vales, I., Gomez-Pando, L., Orjeda, G., Wise, R.P., Sato, K., Hori, K., Capettini, F., Vivar, H., Chen, X., Hayes, P. 2006. Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA. Molecular Breeding. 18(4):355-366.
Rossi, C., Cuesta-Marcos, A., Vales, I., Gomez-Pando, L., Orjeda, G., Wise, R.P., Sato, K., Hori, K., Capettini, F., Vivar, H., Chen, X., Hayes, P. 2006. Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA. Molecular Breeding 18:355-366.
Kirst, M., Caldo, R., Casati, P., Tanimoto, G., Walbot, V., Wise, R.P., Buckler Iv, E.S. 2006. Contribution of genetic diversity to type 1 errors in short-oligonucleotide microarray analysis. Plant Biotechnology Journal. 4:489-498.
Caldo, R.A., Nettleton, D., Peng, J., Wise, R.P. 2006. Stage-specific Suppression of Basal Defense Discriminates Barley Plants Containing Fast- and Delayed-acting Mla Powdery Mildew Resistance Alleles. Molecular Plant-Microbe Interactions. 19(9):939-947.
Nettleton, D., Hwang, G., Caldo, R.A., Wise, R.P. 2006. Estimating the number of true null hypotheses from a histogram of p-values. Journal of Agricultural, Biological, and Environmental Statistics. 11:337-356.
Wise, R.P., Caldo, R.A., Hong, L., Shen, L., Dickerson, J.A. 2007. BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens. In: David Edwards editor. Plant Bioinformatics: Methods and Protocols. Secaucus, N.J. Springer. p. 347-363.
Halterman, D.A., Wise, R.P. 2006. Upstream open reading frames of the barley Mla13 powdery mildew resistance gene function cooperatively to down-regulate translation. Molecular Plant Pathology. 7:167-176.
Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R.P., Close, T., Kleinhofs, A. 2006. An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics. 6(3):202-211.
Caldo, R.A., Nettleton, D., Wise, R.P. 2006. Interplay of gene-specific disease resistance, basal defense, and the suppression of host responses to barley powdery mildew. In: Sanchez, F., Quinto, C., Lopez-Lara, I., Geiger, O., editors. Biology of Plant Microbe Interactions. St. Paul, MN: International Society of Molecular Plant-Microbe Interactions. Vol. 5, p. 620-624.
Wise, R.P., Shen, L., Gong, J., Xin, J., Caldo, R., Nettleton, D., Dickerson, J. 2005. BarleyBase/WheatPLEX: The triticeae hub of PLEXdb plant expression database. International Triticeae Mapping Initiative Workshop. Available: http://wheat.pw.usda.gov/ITMI/ITMI2005/Wise_BarleyBase/.
Caldo, R.A., Nettleton, D., Wise, R.P. 2005. Interplay of gene-specific disease resistance, basal defense, and the suppression of host-responses. 2005 Society for In Vitro Biology Proceedings. PS1.
Williams, A., Caldo, R., Hanna, D., McLean, L., Tanimoto, G., Wise, R.P. 2005. Affymetrix maize pilot expression array. Plant and Animal Genome XIII Conference Proceedings. P897.
Shen, L., Gong, J., Caldo, R.A., Nettleton, D., Cook, D., Wise, R.P., Dickerson, J.A. 2005. BarleyBase - Putting large-scale plant expression profiling data into a functional genomics context. Plant and Animal Genome XIII Conference Proceedings. P878.
Caldo, R.A., Nettleton, D., Wise, R.P. 2005. Induction of basal defense differentiates rapid and delayed host-specific barley resistance to powdery mildew. Plant and Animal Genome XIII Conference Proceedings. P665.
Halterman, D.A., Wise, R.P. 2005. Multiple Upstream Open Reading Frames Of The Barley Mla13 Powdery Mildew Resistance Gene Collectively Down-Regulate Translation. XIII Plant and Animal Genome Conference Proceedings. p. P729.
Kronmiller, B., Gobelman Werner, K.S., Wise, R.P. 2005. Sequencing a 1.3 Mb contig spanning the rf1 fertility restorer locus as a prototype to assess complex-genome coverage strategies. 47th Annual Maize Genetics Conference Abstracts. P184.
Shen, L., Gong, J., Caldo, R.A., Nettleton, D., Cook, D., Wise, R.P., Dickerson, J.A. 2005. Barleybase - an expression profiling database for plant genomics. Nucleic Acids Research. 33:D614-D618.
Wise, R.P., Caldo, R.A., Halterman, D.A., Nettleton, D.A. 2004. Flor revisited: Systems biology in barley-powdery mildew interactions. Cereal Rusts and Mildews Conference European and Mediterranean Proceedings. Abstract 1.14, Cereal Rusts and Powdery Mildews Bulletin.
Caldo, R.A., Nettleton, D.A., Wise, R.P. 2004. Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. The Plant Cell. 16:2514-2528.
Tang, X., Gong, J., Xin, J., Lishuang, S., Turner, S., Caldo, R., Nettleton, D., Wise, R.P., Dickerson, J. 2004. BarleyBase - An expression profiling database for cereal genomics. Plant and Animal Genome XII Conference. p. 944.
Kronmiller, B., Gobelman Werner, K.S., Wise, R.P. 2004. Comparative analysis of a one-megabase sequence spanning the maize Rf1 fertility restorer with the rice genome. 46th Maize Genetics Conference. p. 112.
Kronmiller, B., Gobelman Werner, K.S., Wise, R.P. 2004. Comparative analysis of a one-megabase sequence spanning the maize rf1 fertility restorer with the rice genome. Proceedings of Keystone Symposia "Comparative Genomics of Plants." p. 117.
Halterman, D.A., Wise, R.P. 2004. A single amino acid substitution in the sixth leucine-rich repeat of barley Mla6 and Mla13 alleviates dependence on Rar1 for disease resistance signaling. Plant and Animal Genome Conference Proceedings. XII Conference. p. 858.
Caldo, R.A., Nettleton, D., Wise, R.P. 2004. Interplay of non-specific and specific modulation patterns of barley transcriptional responses during powdery mildew infection. Plant and Animal Genome Conference Proceedings. XII Conference. p. 793.
Druka, A., Muehlbauer, G., Caldo, R., Wise, R.P., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., Marshall, D., Waugh, R. 2004. Parallel gene expression analysis in cereal development. Plant and Animal Genome XII Conference. p. 783.
Halterman, D.A., Wise, R.P. 2004. Deciphering Rar1 signaling specificity in barley/powdery mildew interactions. Plant and Animal Genome Conference Proceedings. XII Conference. p. W199.
Wise, R.P., Caldo, R.A., Nettleton, D.S., Dickerson, J.A. 2004. Probe-level analysis of gene-for-gene-specified responses in barley-powdery mildew interactions. Plant and Animal Genome Conference Proceedings. XII Conference. p. W264.
Hu, P., Wise, R.P. 2004. Physical mapping of new Lrk and Tak receptor-like kinase gene clusters in barley. Plant and Animal Genome Conference Proceedings. XII Conference. p. 857.
Wise, R.P., Caldo, R.A., Nettleton, D.A. 2004. Parallel expression profiling of gene-for-gene-specified responses in barley-powdery mildew interactions.Plant and Animal Genome XII Conference. p. W33.
Halterman, D.A., Wise, R.P. 2004. A single amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling. Plant Journal. 38:215-226.
Close, T., Wanamaker, S., Caldo, R., Turner, S., Ashlock, D., Dickerson, J., Wing, R., Muehlbauer, G., Kleinhofs, A., Wise, R.P. 2004. A new resource for cereal genomics: 22k barley genechip comes of age. Plant Physiology. 134:960-968.
HALTERMAN, D.A., WISE, R.P. A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING. AVAILABLE FROM: http://www.apsnet.org/meetings/2003/abstracts/a03ma232.htm. AMERICAN PHYTOPATHOLOGICAL SOCIETY ANNUAL MEETING. 2003. Phytopathology 93:S32 Publication no. P-2003-0232-AMA.
HALTERMAN, D.A., WISE, R.P. A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING. AVAILABLE FROM: http://abstracts.aspb.org/pb2003/public/P49/1386.html. AMERICAN SOCIETY OF PLANT BIOLOGISTS ANNUAL MEETING. 2003. Poster 821 Session 49; Plant Pathogen/Symbiont Interactions.
CALDO, R., NETTLETON, D., TURNER, S., DICKERSON, J., WISE, R.P. PARALLEL EXPRESSION PROFILING OF GENE-FOR-GENE-SPECIFIED RESPONSES IN BARLEY-POWDERY MILDEW INTERACTIONS. AVAILABLE FROM: http://www.ispmb2003.com/. PLANT MOLECULAR BIOLOGY INTERNATIONAL CONFERENCE PROCEEDINGS. 2003. Poster S21-51.
CALDO, R., NETTLETON, D., TURNER, S., ASHLOCK, D., DICKERSON, J., WISE, R.P. COMPREHENSIVE TRANSCRIPTIONAL PROFILING OF BARLEY-POWDERY MILDEW INTERACTIONS USING AFFYMETRIX GENECHIPS. AVAILABLE FROM: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=658. KEYSTONE SYMPOSIA. 2003.
HALTERMAN, D.A., WISE, R.P. POWDERY MILDEW INDUCED MLA MRNAS ARE ALTERNATIVELY SPLICED AND CONTAIN UPSTREAM OPEN READING FRAMES THAT CUMULATIVELY DOWN-REGULATE TRANSLATION. AVAILABLE FROM: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=658. KEYSTONE SYMPOSIA. 2003.
HALTERMAN, D.A., WEI, F., WISE, R.P. POWDERY MILDEW INDUCED MLA MRNAS ARE ALTERNATIVELY SPLICED AND CONTAIN UPSTREAM OPEN READING FRAMES THAT CUMULATIVELY DOWN REGULATE TRANSLATION. AVAILABLE FROM: http://www.intl-pag.org/11/abstracts/P7b_P827_XI.html. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. 2003. ABSTRACT NO. P827.
HALTERMAN, D.A., WISE, R.P. MLA RESISTANCE SPECIFICITIES ARE NOT LINEAR DESCENDANTS OF A COMMON ANCESTOR, BUT EVOLVED SEPARATELY SUBSEQUENT TO GENE DUPLICATION. AVAILABLE FROM: http://www.intl-pag.org/11/abstracts/P7b_P828_XI.html. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. 2003. ABSTRACT NO. P828.
Wise, R.P., Caldo, R.A., Turner, S., Ashlock, D., Dickerson, J. 2003. Parallel expression analysis using barley microarrays. Plant and Animal Genome Conference Proceedings. XI Conference. p. W50.
Turner, S., Wise, R.P. 2003. Evolutionary organization of the Mla locus in the poaceae. Plant and Animal Genome Conference Proceedings. XI Conference. p. 351.
Hu, P., Wise, R.P. 2003. Genome-wide physical mapping of pathogen-response genes in barley. Plant and Animal Genome Conference Proceedings. XI Conference. p. 403.
Caldo, R.A., Wise, R.P. 2003. Elucidation of the incompatible and compatible barley-powdery mildew interactions using affymetrix genechips: a microarray representation of the quadratic check. Plant and Animal Genome Conference Proceedings. XI Conference. p. 758.
Halterman, D.A., Wei, F., Wise, R.P. 2003. Powdery mildew induced Mla mRNAs are alternatively spliced and contain upstream open reading frames. Plant Physiology. 131(2):558-567.
Cui, X., Hsia, A., Liu, F., Ashlock, D.A., Wise, R.P., Schnable, P.S. 2003. Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize. Genetics. 163:685-698.
Wise, R.P., Pring, D.R. 2002. Nuclear-mediated mitochondrial gene regulation and male fertility in higher plants: light at the end of the tunnel? Proceedings of the National Academy of Sciences. 99:10240-10242.
Wise, R.P., Schulze-Lefert, P., Zhou, F., Kurth, J., Halterman, D.A., Wei, F., Elliot, C. 2002. Resistance gene. Patent Application. U.S. Patent 10/148,351.
Temporal Control of Immunity to Powdery Mildew in Barley Cooperative Agreement (A) Accession Number:438180 Regulatory Networks in Cereal Host-Fungal Pathogen Interactions In-House Appropriated (D) Accession Number:443549 Temporal Control of Immunity to Powdery Mildew in Barley Interagency Reimbursable Agreement (I) Accession Number:438250