title: A set of domain-specific markers in the Arabidopsis embryo.
abstract: We describe a novel set of domain-specific markers that can be used in genetic studies, and we used two examples to show loss of stem cells in a monopteros background. Multicellular organisms can be defined by their ability to establish distinct cell identities, and it is therefore of critical importance to distinguish cell types. One step that leads to cell identity specification is activation of unique sets of transcripts. This property is often exploited in order to infer cell identity; the availability of good domain-specific marker lines is, however, poor in the Arabidopsis embryo. Here we describe a novel set of domain-specific marker lines that can be used in Arabidopsis (embryo) research. Based on transcriptomic data, we selected 12 genes for expression analysis, and according to the observed expression domain during embryogenesis, we divided them into four categories (1-ground tissue; 2-root stem cell; 3-shoot apical meristem; 4-post-embryonic). We additionally show the use of two markers from the "stem cell" category in a genetic study, where we use the absence of the markers to infer developmental defects in the monopteros mutant background. Finally, in order to judge whether the established marker lines also play a role in normal development, we generated loss-of-function resources. None of the analyzed T-DNA insertion, artificial microRNA, or misexpression lines showed any apparent phenotypic difference from wild type, indicating that these genes are not nonredundantly required for development, but also suggesting that marker activation can be considered an output of the patterning process. This set of domain-specific marker lines is therefore a valuable addition to the currently available markers and will help to move toward a generic set of tissue identity markers.
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands.
authors.forename: Jos R
authors.initials: JR
authors.lastname: Wendrich
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands.|Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
authors.forename: Barbara K
authors.initials: BK
authors.lastname: Möller
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands.|Department of Biochemistry and Molecular Biology, Jahangirnagar University, Dhaka, Savar, Bangladesh.|Zentrum für Molekulare Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
authors.forename: Borhan
authors.initials: B
authors.lastname: Uddin
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands.
authors.forename: Tatyana
authors.initials: T
authors.lastname: Radoeva
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands.
authors.forename: Annemarie S
authors.initials: AS
authors.lastname: Lokerse
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands.|Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
authors.forename: Bert
authors.initials: B
authors.lastname: De Rybel
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands. dolf.weijers@wur.nl.
authors.forename: Dolf
authors.initials: D
authors.lastname: Weijers
mesh_terms: D000943:Antigens, Differentiation / Q000235:genetics*; D017360:Arabidopsis / Q000166:cytology / Q000196:embryology* / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018519:Meristem; D018517:Plant Roots / Q000166:cytology; D018520:Plant Shoots / Q000166:cytology; D012639:Seeds / Q000166:cytology / Q000254:growth & development; D013234:Stem Cells / Q000166:cytology / Q000378:metabolism
chemical_list: D000943:Antigens, Differentiation
keywords: Arabidopsis; Embryo development; Stem cells; Tissue markers; monopteros