title: Comparative transcriptome profiling of maize coleoptilar nodes during shoot-borne root initiation.
abstract: Maize (Zea mays) develops an extensive shoot-borne root system to secure water and nutrient uptake and to provide anchorage in the soil. In this study, early coleoptilar node (first shoot node) development was subjected to a detailed morphological and histological analysis. Subsequently, microarray profiling via hybridization of oligonucleotide microarrays representing transcripts of 31,355 unique maize genes at three early stages of coleoptilar node development was performed. These pairwise comparisons of wild-type versus mutant rootless concerning crown and seminal roots (rtcs) coleoptilar nodes that do not initiate shoot-borne roots revealed 828 unique transcripts that displayed RTCS-dependent expression. A stage-specific functional analysis revealed overrepresentation of "cell wall," "stress," and "development"-related transcripts among the differentially expressed genes. Differential expression of a subset of 15 of 828 genes identified by these microarray experiments was independently confirmed by quantitative real-time-polymerase chain reaction. In silico promoter analyses revealed that 100 differentially expressed genes contained at least one LATERAL ORGAN BOUNDARIES domain (LBD) motif within 1 kb upstream of the ATG start codon. Electrophoretic mobility shift assay experiments demonstrated RTCS binding for four of these promoter sequences, supporting the notion that differentially accumulated genes containing LBD motifs are likely direct downstream targets of RTCS.
authors.affiliation: Zentrum für Molekularbiologie der Pflanzen, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: Muthreich
authors.forename: Christine
authors.initials: C
authors.lastname: Majer
authors.forename: Mary
authors.initials: M
authors.lastname: Beatty
authors.forename: Anja
authors.initials: A
authors.lastname: Paschold
authors.forename: André
authors.initials: A
authors.lastname: Schützenmeister
authors.forename: Yan
authors.initials: Y
authors.lastname: Fu
authors.forename: Waqas Ahmed
authors.initials: WA
authors.lastname: Malik
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Piepho
authors.forename: Hajime
authors.initials: H
authors.lastname: Sakai
authors.forename: Frank
authors.initials: F
authors.lastname: Hochholdinger
mesh_terms: D018506:Gene Expression Regulation, Plant; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D018520:Plant Shoots / Q000235:genetics / Q000254:growth & development; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics*
chemical_list: D010940:Plant Proteins