title: Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model.
abstract: Agrobacterium rhizogenes (or Rhizobium rhizogenes) is able to transform plant genomes and induce the production of hairy roots. We describe the use of A. rhizogenes in tomato (Solanum spp.) to rapidly assess gene expression and function. Gene expression of reporters is indistinguishable in plants transformed by Agrobacterium tumefaciens as compared with A. rhizogenes. A root cell type- and tissue-specific promoter resource has been generated for domesticated and wild tomato (Solanum lycopersicum and Solanum pennellii, respectively) using these approaches. Imaging of tomato roots using A. rhizogenes coupled with laser scanning confocal microscopy is facilitated by the use of a membrane-tagged protein fused to a red fluorescent protein marker present in binary vectors. Tomato-optimized isolation of nuclei tagged in specific cell types and translating ribosome affinity purification binary vectors were generated and used to monitor associated messenger RNA abundance or chromatin modification. Finally, transcriptional reporters, translational reporters, and clustered regularly interspaced short palindromic repeats-associated nuclease9 genome editing demonstrate that SHORT-ROOT and SCARECROW gene function is conserved between Arabidopsis (Arabidopsis thaliana) and tomato.
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Mily
authors.initials: M
authors.lastname: Ron
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Kaisa
authors.initials: K
authors.lastname: Kajala
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Germain
authors.initials: G
authors.lastname: Pauluzzi
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Dongxue
authors.initials: D
authors.lastname: Wang
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Mauricio A
authors.initials: MA
authors.lastname: Reynoso
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Kristina
authors.initials: K
authors.lastname: Zumstein
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Jasmine
authors.initials: J
authors.lastname: Garcha
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Sonja
authors.initials: S
authors.lastname: Winte
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Helen
authors.initials: H
authors.lastname: Masson
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Soichi
authors.initials: S
authors.lastname: Inagaki
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Fernán
authors.initials: F
authors.lastname: Federici
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Neelima
authors.initials: N
authors.lastname: Sinha
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Roger B
authors.initials: RB
authors.lastname: Deal
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.).
authors.forename: Julia
authors.identifier: http://orcid.org/0000-0002-8568-7125
authors.initials: J
authors.lastname: Bailey-Serres
authors.affiliation: Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.) sbrady@ucdavis.edu.
authors.forename: Siobhan M
authors.initials: SM
authors.lastname: Brady
mesh_terms: D060054:Agrobacterium / Q000502:physiology*; D001483:Base Sequence; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D018744:DNA, Plant; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics / Q000502:physiology*; D008954:Models, Biological; D008969:Molecular Sequence Data; D018517:Plant Roots / Q000235:genetics / Q000382:microbiology / Q000502:physiology*; D011401:Promoter Regions, Genetic; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018744:DNA, Plant