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







James  Thomson

(Jim)
                        Crop Improvement and Genetics Research

                        




                        
                        Research Geneticist
                        Phone: (510) 559-5721
                        
                        
                        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: 444561Therapeutic Molecule Evaluation and Field Delivery Pipeline for Solutions to HLB, Albany, California
                                                    Interagency Reimbursable Agreement
                                                                    (I)Accession Number: 439298Microalgae as a Novel Platform to Improve Honey Bee Nutrition, Microbiome Health, and Pathogen Resistance
                                                    Interagency Reimbursable Agreement
                                                                    (I)Accession Number: 439554Exploiting Pattern Triggered Immunity to Combat Huanglongbing
                                                    Reimbursable Cooperative Agreement
                                                                    (R)Accession Number: 437389Effects on Surrounding Gene Activity Due to Gene Stacking within a Predefined Location of the Soybean Genome
                                                    Trust Fund Cooperative Agreement
                                                                    (T)Accession Number: 435737**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Agrobacterium-mediated Transformation of the dwarf Soybean Minimax
                                                        

- (Peer Reviewed Journal)Shao, M., Mc Cue, K.F., Thomson, J.G. 2024. Agrobacterium-mediated Transformation of the dwarf Soybean Minimax. Plants. 13:1013. https://doi.org/10.3390/plants13071013.Complete genome of Agrobacterium fabrum strain 1D1416
                                                        

- (Peer Reviewed Journal)Alabed, D., Huo, N., Gu, Y.Q., Thomson, J.G. 2023. Complete genome of Agrobacterium fabrum strain 1D1416. Microbiology Resource Announcements. 12(7). https://doi.org/10.1128/mra.00264-23.Complete genome of Agrobacterium fabrum strain 1D1416
                                                        

- (Peer Reviewed Journal)Alabed, D.F., Huo, N., Gu, Y.Q., Thomson, J.G. 2023. Complete genome of Agrobacterium fabrum strain 1D1416. Microbiology Resource Announcements. 12(7). https://doi.org/10.1128/mra.00264-23.Evaluation of novel surfactants for plant transformation
                                                        

- (Peer Reviewed Journal)Huynh, J.N., Hotton, S.K., Chan, R., Syed, Y., Thomson, J.G. 2022. Evaluation of novel surfactants for plant transformation. BMC Research Notes. 15. Article 360. https://doi.org/10.1186/s13104-022-06251-5.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.pdfDraft genome sequence of Agrobacterium fabrum strain 1D1104
                                                        

- (Peer Reviewed Journal)Huo, N., Gu, Y.Q., McCue, K.F., Alabed, D., Thomson, J.G. 2021. Draft genome sequence of Agrobacterium fabrum strain 1D1104. Microbiology Resource Announcements. 10(48). Article e00996-21. https://doi.org/10.1128/MRA.00996-21.Efficient 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.Phenotypic examination of 38 Camelina sativa (L.) Crantz accessions from the USDA – ARS National Genetics Resource Program
                                                        

- (Peer Reviewed Journal)Hotton, S.K., Kammerzell, M., Chan, R., Hernandez, B.T., Young, H.A., Tobias, C.M., Mckeon, T.A., Brichta, J.L., Thomson, N.J., Thomson, J.G. 2020. Phenotypic examination of 38 Camelina sativa (L.) Crantz accessions from the USDA – ARS National Genetics Resource Program. Plants. 9(5). Article 642. https://doi.org/10.3390/plants9050642.Phenotypic examination of camelina sativa (L.) crantz accessions from the USDA – ARS National Genetics Resource Program
                                                        

- (Peer Reviewed Journal)Hotton, S., Kammerzell, M., Chan, R., Hernandez, B.T., Young, H.A., Tobias, C.M., Mckeon, T.A., Brichta, J.L., Thomson, N.J., Thomson, J.G. 2020. Phenotypic examination of camelina sativa (L.) crantz accessions from the USDA – ARS National Genetics Resource Program. Plants. 9(5). https://doi.org/10.3390/plants9050642.Draft genome sequence of Agrobacterium tumefaciens strain 1D1526
                                                        

- (Peer Reviewed Journal)Huo, N., Gu, Y.Q., Mc Cue, K.F., Alabed, D., Thomson, J.G. 2019. Draft genome sequence of Agrobacterium tumefaciens strain 1D1526. Microbiology Resource Announcements. 8(45). https://doi.org/10.1128/MRA.01084-19.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.Complete genome sequence of Agrobacterium fabrum strain 1D159
                                                        

- (Peer Reviewed Journal)Huo, N., Gu, Y.Q., McCue, K.F., Alabed, D., Thomson, J.G. 2019. Complete genome sequence of Agrobacterium fabrum strain 1D159. Microbiology Resource Announcements. 8(19):e00207-19. https://doi.org/10.1128/MRA.00207-19.Draft genome sequence of serratia sp. 1D1416
                                                        

- (Peer Reviewed Journal)Alabed, D.F., Huo, N., Gu, Y.Q., McCue, K.F., Thomson, J.G. 2019. Draft genome sequence of serratia sp. 1D1416. Microbiology Resource Announcements. 8(3):e01354-18. https://doi.org/10.1128/MRA.01354-18.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.RMCE methods of precise plant genome modification

- (Abstract Only)Small serine recombination systems ParA-MRS and CinH-RS2 perform precise excision of plastid DNA

- (Peer Reviewed Journal)Shao, M., Blechl, A.E., Thomson, J.G. 2017. Small serine recombination systems ParA-MRS and CinH-RS2 perform precise excision of plastid DNA. Plant Biotechnology Journal. doi: 10.1111/pbi.12740.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: 10.1080/21645698.2016.1267897Draft 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.Purple is the new Orange

- (Trade Journal)Dasgupta, K., Shao, M., Thomson, J.G. 2016. Purple is the new Orange. Citrograph. 7(3):54-58.Genetic transformation in citrus: Thinking outside the box

- (Abstract Only)Peixoto De Olivei, M.L., Thomson, J.G., Stover, E.W. 2016. Genetic transformation in citrus: Thinking outside the box [abstract]. Annual Meeting of the American Society of Horticulture Science. August 8-11, 2016, Atlanta, GeorgiaHigh-efficiency propagation of mature 'Washington Navel' orange and juvenile "Carrizo" citrange using axillary shoot proliferation

- (Peer Reviewed Journal)De Oliveira, M.L., Thomson, J.G., Stover, E.W. 2016. High-efficiency propagation of mature 'Washington Navel' orange and juvenile "Carrizo" citrange using axillary shoot proliferation. HortTechnology. 26:278-286.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.Agrobacterium-mediated transformation of Mexican lime (Citrus aurantifolia Swingle) using optimized systems for epicotyls and cotelydons

- (Peer Reviewed Journal)De Oliveira, M.L.P, Moore, G., Thomson, J.G., Stover, E.W. 2015. Agrobacterium-mediated transformation of Mexican lime (Citrus aurantifolia Swingle) using optimized systems for epicotyls and cotelydons. Advances in Bioscience and Biotechnology. 6:657-668.Utilization of founder lines for improved Citrus biotechnology via RMCE

- (Trade Journal)Oliveira, M.L., Stover, E.W., Thomson, J.G. 2016. Utilization of founder lines for improved Citrus biotechnology via RMCE. Citrograph.  7:56-60.Gene stacking by recombinases

- (Peer Reviewed Journal)Srivastava, V., Thomson, J.G. 2015. Gene stacking by recombinases. Plant Biotechnology Journal. 14(2):471-482. doi: 10.1111/pbi.12459.A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max

- (Peer Reviewed Journal)Shao, M., Michno, J., Blechl, A.E., Thomson, J.G. 2015. A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. BioMed Central (BMC)Biotechnology. doi: 10.1007/s00299-015-1818-5.The codA gene as a negative selection marker in Citrus

- (Peer Reviewed Journal)Thomson, J.G., Stover, E.W., Peixoto De Olivei, M.L. 2015. The codA gene as a negative selection marker in Citrus. BioMed Central (BMC)Biotechnology. 4:264.Recombinase technology for precise genome engineering

- (Book / Chapter)Thomson, J.G., Blechl, A.E. 2015. Recombinase technology for precise genome engineering. In: Zhang, F., Puchta, H., Thomson, J.G., editors. Advances in new technology for targeted modification of plant genomes. New York, NY: Springer. p. 113-144.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.Development of consumer-friendly transgenic citrus plants with potential broad spectrum resistance to HLB, Citrus canker, Phytopthora and other exotic diseases

- (Trade Journal)Louzada, E., Thomson, J.G. 2015. Development of consumer-friendly transgenic citrus plants with potential broad spectrum resistance to HLB, Citrus canker, Phytopthora and other exotic diseases. Citrograph. 6:3/42-46.Developing exchange/recombinase founder lines to introduce huanglongbing (HLB) resistance genes into citrus

- (Abstract Only)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.Gene targeting in embryonic stem cells, II: conditional technologies

- (Book / Chapter)Down with DON: Strategies for precise transgene delivery and rnai-based suppression of fusarium

- (Abstract Only)Precise excision of plastid DNA by the large serine recombinase Bxb1
                                                        

- (Peer Reviewed Journal)Shao, M., Kumar, S., Thomson, J.G. 2014. Precise excision of plastid DNA by the large serine recombinase Bxb1. Plant Biotechnology Journal. 12:322-329 DOI: 10.1111/pbi.12139.Founder lines for improved citrus biotechnology

- (Trade Journal)Thomson, J.G., Stover, E.W. 2013. Founder lines for improved citrus biotechnology. Citrograph. 38-39.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.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.Pollen-specific transgene excision in tobacco using the codon optimized serine resolvase CinHo-RS2 site-specific recombination system

- (Peer Reviewed Journal)Moon, H.S., Abercrombie, L.L., Eda, S., Blanvillain, R., Thomson, J.G., Ow, D.W., Stewart, N.C. 2011. Pollen-specific transgene excision in tobacco using the codon optimized serine resolvase CinHo-RS2 site-specific recombination system. Plant Molecular Biology. 75(6):621-631.A Rapid and Quantitative Recombinase Activity Assay

- (Abstract Only)Recombinase technology: applications and possibilities

- (Peer Reviewed Journal)Wang, Y., Yau, Y., Perkins-Balding, D., Thomson, J.G. 2010. Recombinase Technology: Applications and Possibilities. Plant Cell Reports. 30(3):267-285.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.Genome Sequencing and Analysis of the Model Grass Brachypodium Distachyon.

- (Peer Reviewed Journal)Vogel, J.P., Garvin, D.F., Gu, Y.Q., Lazo, G.R., Anderson, O.D., Bragg, J.N., Chingcuanco, D.L., Weng, Y., Belknap, W.R., Thomson, J.G., Dardick, C.D., Baxter, I.R. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.Plant defensins: Defense, development and application

- (Peer Reviewed Journal)Stotz, H., Thomson, J.G., Yueju, W. 2009. Plant defensins: Defense, development and application. Plant Signaling and Behavior.4(11):1010-1012.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.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.Germinal transmission of site-specific excised genomic DNA by the bacterial ParA resolvase

- (Abstract Only)Thomson, J.G., Yau, Y., Blanvillian, R., Ow, D.W. 2008. Germinal transmission of site-specific excised genomic DNA by the bacterial ParA resolvase. Plant & Animal Genomes XVI Conference, San Diego, CA, January 13-17, 2008.The parA resolvase performs site-specific genomic excision in Arabidopsis

- (Abstract Only)Thomson, J.G., Blanvillian, R., Yau, Y., Ow, D.W. 2007. The parA resolvase performs site-specific genomic excision in Arabidopsis. Plant & Animal Genomes XIV Conference, San Diego, CA, January 13-17, 2007.Site-Specific Recombination Systems for the Genetic Manipulation of Eukaryotic Genomes

- (Peer Reviewed Journal)Thomson, J.G., Ow, D.W. 2006. Site-Specific Recombination Systems for the Genetic Manipulation of Eukaryotic Genomes. Genesis 44(10):465-476.
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