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ARS Home Pacific West Area Albany, California Western Regional Research Center Crop Improvement and Genetics Research People & Locations







Roger  Thilmony
                        Crop Improvement and Genetics Research

                        




                        
                        Research Molecular Biologist
                        Phone: (510) 559-5761
                        
                        
                        Fax: (510) 559-5818(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsMolecular Resources for Enhanced Crop Biotechnology
                                                    In-House Appropriated
                                                                    (D)Accession Number: 444561Genomics and Biotechnological Approaches to Reduce the Impact of Wildfire Smoke on Grape Composition
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 442592Developing New Methodologies to Obtain High- Throughput, Transgene- Free Gene Edited Microvine
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 442597Smoke Exposure Effects on Grape Berry Development and Metabolism
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 443120**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum
                                                        

- (Peer Reviewed Journal)Lei, L., Gordon, S.P., Liu, L., Sade, N., Lovell, J., Rubio-Wilhelmi, M., Singan, V., Sreedasyam, A., Hestrin, R., Philipps, J., Hernandez, B.T., Barry, K., Shu, S., Jenkins, J., Schmutz, J., Goodstein, D., Thilmony, R.L., Blumwald, E., Vogel, J. 2023. The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkad245.CRISPR-Cas9 gene editing of the Sal1 gene family in wheat
                                                        

- (Peer Reviewed Journal)Mohr, T.J., Horstman, J.D., Gu, Y.Q., Elarabi, N.I., Abdallah, N.A., Thilmony, R.L. 2022. CRISPR-Cas9 gene editing of the Sal1 gene family in wheat. Plants. 11(17). Article 2259. https://doi.org/10.3390/plants11172259.Tissue-specific expression of Ruby in Mexican lime (C. aurantifolia) confers anthocyanin accumulation in fruit
                                                        

- (Peer Reviewed Journal)Thilmony, R.L., Dasgupta, K., Shao, M., Harris, D., Hartman, J., Harden, L.A., Chan, R., Thomson, J.G. 2022. Tissue-specific expression of Ruby in Mexican lime (C. aurantifolia) confers anthocyanin accumulation in fruit. Frontiers in Plant Science. 13. Article 945738. https://doi.org/10.3389/fpls.2022.945738.Lilac limes: more than just a pretty fruit

- (Trade Journal)Thomson, J.G., Thilmony, R.L. 2022. Lilac limes: more than just a pretty fruit. Citrograph. 13(3):48-51. Available: https://citrus-research-board-static.sfo2.digitaloceanspaces.com/citrograph/pdf/CRB-Citrograph-Mag-Q3-Summer-2022-Web.pdfEfficient gene stacking in rice using the GAANTRY system
                                                        

- (Peer Reviewed Journal)Hathwaik, L.T., Horstman, J.D., Thomson, J.G., Thilmony, R.L. 2021. Efficient gene stacking in rice using the GAANTRY system. Rice. 14. Article 17 (2021). https://doi.org/10.1186/s12284-021-00460-5.Gene assembly in agrobacterium via nucleic acid transfer using recombinase technology (GAANTRY)
                                                        

- (Book / Chapter)Hathwaik, L.T., Thomson, J.G., Thilmony, R.L. 2021. Gene assembly in agrobacterium via nucleic acid transfer using recombinase technology (GAANTRY). In: Bandyopadhyay, A., Thilmony, R.L, editors. Rice Genome Engineering and Gene Editing. Methods in Molecular Biology. New York, NY: Humana. p. 3-17.Isolation of novel citrus and plum fruit promoters and their functional characterization for fruit biotechnology
                                                        

- (Peer Reviewed Journal)Dasgupta, K., Hotton, S., Belknap, W., Syed, Y., Dardick, C.D., Thilmony, R.L., Thomson, J.G. 2020. Isolation of novel citrus and plum fruit promoters and their functional characterization for fruit biotechnology. BioMed Central (BMC)Biotechnology. 20. https://doi.org/10.1186/s12896-020-00635-w.Transgene stacking in potato using the GAANTRY system
                                                        

- (Peer Reviewed Journal)McCue, K.F., Gardner, E.B., Chan, R., Thilmony, R.L., Thomson, J.G. 2019. Transgene stacking in potato using the GAANTRY system. BMC Research Notes. 12:457. https://doi.org/10.1186/s13104-019-4493-8.Transgenic Lilium longiglorum plants containing the bar-uidA gene controlled by the rice RPC1, Agrobacterium rolD, mas2, and CaMV 355 promotors

- (Peer Reviewed Journal)Kamo, K.K., Thilmony, R.L., Bauchan, G.R. 2019. Transgenic Lilium longiglorum plants containing the bar-uidA gene controlled by the rice RPC1, Agrobacterium rolD, mas2, and CaMV 355 promotors. Plant Cell Tissue and Organ Culture. 13(2):303-312.A versatile and robust Agrobacterium-based gene stacking system generates high quality transgenic Arabidopsis plants
                                                        

- (Peer Reviewed Journal)Collier, R., Thomson, J.G., Thilmony, R.L. 2018. A versatile and robust Agrobacterium-based gene stacking system generates high quality transgenic Arabidopsis plants. Plant Journal. 95(4):573-583. https://doi.org/10.1111/tpj.13992.Salt tolerance of two perennial grass Brachypodium sylvaticum accessions
                                                        

- (Peer Reviewed Journal)Sade, N., del Mar Rubio-Wilhelmi, M., Ke, X., Brotman, Y., Wright, M., Khan, I., De Souza, W., Bassil, E., Tobias, C.M., Thilmony, R.L., Vogel, J.P., Blumwald, E. 2018. Salt tolerance of two perennial grass Brachypodium sylvaticum accessions. Plant Molecular Biology. 96(3):305-314. https://doi.org/10.1007/s11103-017-0696-3.Escherichia coli O157:H7 converts plant-derived choline to glycine betaine for osmoprotection during pre- and post-harvest colonization of injured lettuce leaves
                                                        

- (Peer Reviewed Journal)Scott, R.A., Thilmony, R.L., Harden, L.A., Zhou, Y., Brandl, M. 2017. Escherichia coli O157:H7 converts plant-derived choline to glycine betaine for osmoprotection during pre- and post-harvest colonization of injured lettuce leaves. Frontiers in Microbiology. 8:2436. https://doi.org/10.3389/fmicb.2017.02436.Measurement of Transgene Copy Number in Potatoes Using Droplet Digital PCR
                                                        

- (Abstract Only)Mc Cue, K.F., Collier, R.A., Gardner, E.B., Thilmony, R.L. 2018. Measurement of Transgene Copy Number in Potatoes Using Droplet Digital PCR. Meeting Abstract. 95(3):208-229. https://doi.org/10.1007/s12230-018-9650-4.Accurate measurement of transgene copy number in crop plants using droplet digital PCR
                                                        

- (Peer Reviewed Journal)Collier, R.A., Dasgupta, K., Xing, Y., Hernandez, B., Shao, M., Rohozinski, D., Kovak, E., Lin, J.W., De Oliveira, M., Stover, E.W., Mc Cue, K.F., Harmon, F.G., Blechl, A.E., Thomson, J.G., Thilmony, R.L. 2017. Accurate measurement of transgene copy number in crop plants using droplet digital PCR. Plant Journal. 90:1014-1025. https://doi.org/10.1111/tpj.13517.Novel R2R3-MYB transcription factors from Prunus americana regulate differential patterns of anthocyanin accumulation in tobacco and citrus
                                                        

- (Peer Reviewed Journal)Dasgupta, K., Thilmony, R.L., Stover, E.W., Oliveira, M.L., Thomson, J.G. 2017. Novel R2R3-MYB transcription factors from Prunus americana regulate differential patterns of anthocyanin accumulation in tobacco and citrus. GM Crops & Food. 8:85-105. https://doi.org/10.1080/21645698.2016.1267897.Novel R2R3-MYB transcription factors from Prunus Americana regulate differential patterns of anthocyanin accumulation in tobacco and citrus

- (Peer Reviewed Journal)Dasgupta, K., Thilmony, R.L., Stover, E.W., Oliveira, M.L., Thomson, J.G. 2017. Novel R2R3-MYB transcription factors from Prunus Americana regulate differential patterns of anthocyanin accumulation in tobacco and citrus . GM Crops & Food. 8:85-105. doi: 10.1080/21645698.2016.1267897PIECE 2.0: an update for the plant gene structure comparison and evolution database
                                                        

- (Peer Reviewed Journal)Wang, Y., Xu, L., Thilmony, R.L., You, F., Gu, Y.Q., Coleman-Derr, D.A. 2016. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Research. 45(D1):1015-1020. https://doi.org/10.1093/nar/gkw935.Draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659

- (Peer Reviewed Journal)Valdes, J., Collier, R.A., Wang, Y., Huo, N., Gu, Y.Q., Thilmony, R.L., Thomson, J.G. 2002. Draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659. Genome Announcements. 4:1-2.Use of Agrobacterium rhizogenes strain 18r12v and paromomycin selection for transformation of Brachypodium distachyon and Brachypodium sylvaticum

- (Peer Reviewed Journal)Collier, R.A., Bragg, J., Hernandez, B., Vogel, J., Thilmony, R.L. 2016. Use of Agrobacterium rhizogenes strain 18r12v and paromomycin selection for transformation of Brachypodium distachyon and Brachypodium sylvaticum. Frontiers in Plant Science. doi: 10.3389/fpls.2016.00716.Small cyclic amphipathic peptides (SCAmpPs) genes in citrus provide promising tools for more effective tissue specific transgenic expression
                                                        

- (Peer Reviewed Journal)Belknap, W.R., Thomson, J.G., Thilmony, R.L., McCue, K.F., Hao, G., Stover, E.W. 2017. Small cyclic amphipathic peptides (SCAmpPs) genes in citrus provide promising tools for more effective tissue specific transgenic expression. Acta Horticulturae. 1172:85-90. https://doi.org/10.17660/ActaHortic.2017.1172.15.Brachypodium seed - a potential model for studying grain development of cereal crops

- (Book / Chapter)Wu, J., Thilmony, R.L., Gu, Y.Q. 2016. Brachypodium seed - a potential model for studying grain development of cereal crops. In:Vogel, J., editor. Genetics and Genomics of Brachypodium. Cham, Switzerland:Springer International Publishing. p. 219-243. doi: 10.1007/7397.2015.12.The development of novel Blood and Cara cara like citrus varieties

- (Trade Journal)Thomson, J.G., Dasgupta, K., Thilmony, R.L. 2015. The development of novel Blood and Cara cara like citrus varieties. Citrograph. 6:3/65-69.AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants

- (Peer Reviewed Journal)Wang, Y., Thilmony, R.L., Zhao, Y., Chen, G., Gu, Y.Q. 2014. AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bau117.Transgene autoexcision in switchgrass pollen mediated by the Bxb1 recombinase

- (Peer Reviewed Journal)Somleva, M.N., Chang, A.X., Ryan, K.P., Thilmony, R.L., Peoples, O., Snell, K.D., Thomson, J.G. 2014. Transgene autoexcision in switchgrass pollen mediated by the Bxb1 recombinase. BioMed Central (BMC)Biotechnology. 14:79. doi: 10.1186/1472-6750-14-79.Net Venn - An integrated network analysis web platform for gene lists

- (Peer Reviewed Journal)Wang, Y., Thilmony, R.L., Gu, Y.Q. 2014. Net Venn - An integrated network analysis web platform for gene lists. Nucleic Acids Research. DOI: 10.1093/narlgku331.The wheat HMW-glutenin 1Dy10 gene promoter controls endosperm expression in Brachypodium distachyon
                                                        

- (Peer Reviewed Journal)Thilmony, R.L., Guttman, M.E., Lin, J.W., Blechl, A.E. 2014. The wheat HMW-glutenin 1Dy10 gene promoter controls endosperm expression in Brachypodium distachyon. GM Crops. 5:36-43.Novel gene expression tools for rice biotechnology

- (Abstract Only)Comparative proteomic analysis of the effect of temperature and fertilizer on gliadin and glutenin accumulation in the developing endosperm and flour from Triticum aestivum L. cv. Butte 86

- (Peer Reviewed Journal)Hurkman II, W.J., Tanaka, C.K., Vensel, W.H., Thilmony, R.L., Altenbach, S.B. 2013. Comparative proteomic analysis of the effect of temperature and fertilizer on gliadin and glutenin accumulation in the developing endosperm and flour from Triticum aestivum L. cv. Butte 86. Proteome Science. doi:10.1186/1477-5956-11-8.Screening promoters for Anthurium transformation using transient expression

- (Peer Reviewed Journal)Matsumoto Brower, T.K., Keith, L.M., Cabos, R.Y.M., Suzuki, J.Y., Gonsalves, D., Thilmony, R.L. 2013. Screening promoters for Anthurium transformation using transient expression. Plant Cell Reports. 32:443-451.PIECE: A database for plant gene structure comparison and evolution

- (Peer Reviewed Journal)Wang, Y., You, F., Lazo, G.R., Luo, M., Thilmony, R.L., Gordon, S.P., Gu, Y.Q., Kianian, S. 2012. PIECE: A database for plant gene structure comparison and evolution. Nucleic Acids Research. D1159-D1166.Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection

- (Peer Reviewed Journal)Bragg, J., Wu, J., Gordon, S.P., Guttman, M.E., Thilmony, R.L., Lazo, G.R., Gu, Y.Q., Vogel, J.P. 2012. Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection. PLoS One. 7(9):e41916. doi:10.1371/journal.pone.0041916.Bxb1 recombinase mediates site-specific deletions in transgenic wheat

- (Peer Reviewed Journal)Blechl, A.E., Lin, J.W., Shao, M., Thilmony, R.L., Thomson, J.G. 2012. Bxb1 recombinase mediates site-specific deletions in transgenic wheat. Plant Molecular Biology Reporter. doi:10.1007/s11105-012-0454-2.The Bxb1 recombination system demonstrates heritable transmission of site-specific excision in Arabidopsis

- (Peer Reviewed Journal)Thomson, J.G., Chan, R., Smith, J.D., Thilmony, R.L., Yau, Y., Wang, Y., Ow, D.W. 2012. The Bxb1 recombination system demonstrates heritable transmission of site-specific excision in Arabidopsis. BioMed Central (BMC)Biotechnology. 12:9 doi:10.1186/1472-6750-12-9.The OsGEX2 gene promoter confers pollen sperm cell-specific expression in transgenic rice

- (Peer Reviewed Journal)Cook, M.A., Thilmony, R.L. 2012. The OsGEX2 gene promoter confers pollen sperm cell-specific expression in transgenic rice. Planta. DOI: 10.1007/s11105-012-0429-3.Transformation of Lesquerella fendleri with the new binary vector pGPro4-35S

- (Peer Reviewed Journal)Chen, G.Q., Thilmony, R.L., Lin, J.T. 2012. Transformation of Lesquerella fendleri with the new binary vector pGPro4-35S. Online Journal of Biological Sciences. 11(3)90-95. DOI: 10.3844/ojbsci.2011.90.95.Novel sull binary vectors enable an inexpensive foliar selection method in Arabidopsis

- (Peer Reviewed Journal)Thomson, J.G., Cook, M.A., Guttman, M.E., Smith, J.D., Thilmony, R.L. 2011. Novel sull binary vectors enable an inexpensive foliar selection method in Arabidopsis. BMC Research Notes. 4(44) Available: http://www.biomedcentral.com/1756-0500/4/44.Development of site-specific recombinase technology for precise crop plant genome modification

- (Abstract Only)Thomson, J.G., Yau, Y., Chan, R., Thilmony, R.L. 2010. Development of site-specific recombinase technology for precise crop plant genome modification. International Association of Plant Biotechnology Congress (IAPB), June 6-11, 2010, St. Louis, MO.The phiC31 Recombinase Demonstrates Heritable Passage of Site-specific Genomic Excision in Arabidopsis

- (Peer Reviewed Journal)Thomson, J.G., Chan, R., Thilmony, R.L., Ow, D.W. 2010. The phiC31 Recombinase Demonstrates Heritable Passage of Site-specific Genomic Excision in Arabidopsis. BioMed Central (BMC)Biotechnology. Available: doi:10.1186/1472-6750-10-17.The effect of high temperature on cell structure and gluten protein accumulation in the endosperm of the developing wheat (Triticum aestivum L.) grain

- (Proceedings)Hurkman Ii, W.J., Tanaka, C.K., Thilmony, R.L., Williams, T.G., Wood, D.F., Vensel, W.H., Dupont, F.M., Altenbach, S.B. 2010. The effect of high temperature on cell structure and gluten protein accumulation in the endosperm of the developing wheat (Triticum aestivum L.) grain. International Gluten Workshop. pp. 50-54.The LP2 leucine-rich repeat receptor kinase promoter directs  organ-specific, light-responsive expression in transgenic rice

- (Peer Reviewed Journal)Thilmony, R.L., Guttman, M.E., Thomson, J.G., Blechl, A.E. 2009. The LP2 leucine-rich repeat receptor kinase promoter directs organ-specific, light-responsive expression in transgenic rice. Plant Biotechnology Journal. 7:867-882.Intragenic Tools for Improved Rice Biotechnology and Biosafety

- (Abstract Only)Thilmony, R.L., Cook, M.A. 2009. Intragenic Tools for Improved Rice Biotechnology and Biosafety(abstract). Crop Improvement and Utilization Intragenics Workshop. p. 2.ParA resolvase catalyzes site-specific excision of DNA from the Arabidopsis genome

- (Peer Reviewed Journal)Thomson, J.G., Yuan-Yeu, Y., Blanvillain, R., Chiniquy, D., Thilmony, R.L., Ow, D.W. 2009. ParA resolvase catalyzes site-specific excision of DNA from the Arabidopsis genome. Transgenic Research. 18:237-248.A Simple and Inexpensive Method for Sending Binary Vector Plasmid DNA by Mail

- (Peer Reviewed Journal)Thilmony, R.L., Thomson, J.G. 2008. A simple and inexpensive method for sending binary vector plasmid dna by mail. Plant Biotechnology.  25:403-406.A Novel Rice LRR-Receptor Kinase Promoter with Organ-Specific Expression

- (Abstract Only)RAR1, a Central Player in Plant Immunity, is Targeted by Pseudomonas syringae Effector AvrB

- (Peer Reviewed Journal)Shang, Y., Li, X., Cui, H., He, P., Thilmony, R.L., Chintamanani, S., Zwiesler-Vollick, J., Gopalan, S., Tang, X., Zhou, J. 2006. Rar1, a central player in plant immunity, is targeted by pseudomonas syringae effector avrb. Proceedings of the National Academy of Sciences.  PNAS vol. 103 no. 50 pg. 19200-19205CONSTRUCTION AND CHARACTERIZATION OF TWO BAC LIBRARIES FROM BRACHYPODIUM DISTACHYPON, A NEW MODEL FOR GRASS GENOMICS

- (Peer Reviewed Journal)Gu, Y., Lazo, G., Vogel, J., Coleman-Derr, D., Luo, M.C., Thilmony, R., Garvin, D., Anderson, O., Huo, N. 2006.  Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome. 49(9):1099-1108.PGPRO 1, A NOVEL BINARY VECTOR FOR MONOCOT PROMOTER CHARACTERIZATION

- (Peer Reviewed Journal)Thilmony, R.L., Guttman, M.E., Chiniquy, D., Blechl, A.E. 2006. Pgpro 1, a novel binary vector for monocot promoter characterization. Plant Molecular Biology Reporter. 24:1-13, March 2006GENOME-WIDE TRANSCRIPTIONAL ANALYSIS OF THE ARABIDOPSIS THALIANA INTERACTION WITH THE PLANT PATHOGEN PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 AND THE HUMAN PATHOGEN ESCHERICHIA COLI 0157:H7.

- (Peer Reviewed Journal)Thilmony, R.L., Underwood, W., He, S. 2006. Genome-wide transcriptional analysis of the compatible arabidopsis thaliana-psuedomonas syringae pv. tomato dc3000 interaction. Plant Journal. 46(1):34-53.A FAMLIY OF CONSERVED BACTERIAL EFFECTORS INHIBITS SALICYLIC ACID-MEDITATED BASAL IMMUNITY AND PROMOTES DISEASE NECROSIS IN PLANTS

- (Peer Reviewed Journal)Debroy, S., Thilmony, R.L., Kwack, Y., Nomura, K., He, S. 2004. A famliy of conserved bacterial effectors inhibits salicylic acid-meditated basal immunity and promotes disease necrosis in plants. Proceedings of the National Academy of Sciences. 101: 9927-9932
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