title: The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.
abstract: The maize (Zea mays L.) Aux/IAA protein RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEMS 1) controls seminal and lateral root initiation. To identify RUM1-dependent gene expression patterns, RNA-Seq of the differentiation zone of primary roots of rum1 mutants and the wild type was performed in four biological replicates. In total, 2 801 high-confidence maize genes displayed differential gene expression with Fc ≥2 and FDR ≤1%. The auxin signalling-related genes rum1, like-auxin1 (lax1), lax2, (nam ataf cuc 1 nac1), the plethora genes plt1 (plethora 1), bbm1 (baby boom 1), and hscf1 (heat shock complementing factor 1) and the auxin response factors arf8 and arf37 were down-regulated in the mutant rum1. All of these genes except nac1 were auxin-inducible. The maize arf8 and arf37 genes are orthologues of Arabidopsis MP/ARF5 (MONOPTEROS/ARF5), which controls the differentiation of vascular cells. Histological analyses of mutant rum1 roots revealed defects in xylem organization and the differentiation of pith cells around the xylem. Moreover, histochemical staining of enlarged pith cells surrounding late metaxylem elements demonstrated that their thickened cell walls displayed excessive lignin deposition. In line with this phenotype, rum1-dependent mis-expression of several lignin biosynthesis genes was observed. In summary, RNA-Seq of RUM1-dependent gene expression in maize primary roots, in combination with histological and histochemical analyses, revealed the specific regulation of auxin signal transduction components by RUM1 and novel functions of RUM1 in vascular development.
authors.affiliation: INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
authors.forename: Yanxiang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Paschold
authors.affiliation: INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
authors.forename: Caroline
authors.initials: C
authors.lastname: Marcon
authors.affiliation: Department of Agronomy, Iowa State University, Ames 50011-3650, Iowa, USA.
authors.forename: Sanzhen
authors.initials: S
authors.lastname: Liu
authors.affiliation: INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
authors.forename: Huanhuan
authors.initials: H
authors.lastname: Tai
authors.affiliation: INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
authors.forename: Josefine
authors.initials: J
authors.lastname: Nestler
authors.affiliation: Center for Plant Genomics, Iowa State University, Ames 50011-3650, Iowa, USA.
authors.forename: Cheng-Ting
authors.initials: CT
authors.lastname: Yeh
authors.affiliation: INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Opitz
authors.affiliation: Department of Molecular Biology, Max-Planck-Institute for Developmental Biology, 72076 Tuebingen, Germany.
authors.forename: Christa
authors.initials: C
authors.lastname: Lanz
authors.affiliation: Department of Agronomy, Iowa State University, Ames 50011-3650, Iowa, USA Center for Plant Genomics, Iowa State University, Ames 50011-3650, Iowa, USA.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
authors.affiliation: INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany hochholdinger@uni-bonn.de.
authors.forename: Frank
authors.initials: F
authors.lastname: Hochholdinger
mesh_terms: D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D007210:Indoleacetic Acids / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D052584:Xylem / Q000235:genetics / Q000254:growth & development; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D007210:Indoleacetic Acids; D010940:Plant Proteins
keywords: Auxin; RNA-Seq; RUM1; lateral roots; lignification; vasculature; xylem.