The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.

Yanxiang Zhang,Sanzhen Liu,Christa Lanz,Caroline Marcon,Cheng-Ting Yeh,Frank Hochholdinger,Josefine Nestler,Patrick S Schnable,Nina Opitz,Huanhuan Tai,Anja Paschold

doi:10.1093/jxb/eru249

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.

Highlights

Maize (Zea mays L.) plays an important agronomic role as feed, food, and source of bioethanol
To understand the molecular network regulated by the Auxin/Indole Acetic Acid (Aux/IAA) protein RUM1, ~2 cm long primary roots of the mutant rum1 and homozygous wild-type siblings were subjected to an RNA-Seq analysis (Fig. 1A)
A similar number of genes was expressed in a transcriptome analysis of maize primary roots by SAGE where it was extrapolated from 14 850 expressed genes that ~22 000 genes are active in the root tips of the cultivar FR697 (Poroyko et al, 2005)

Summary

Introduction

Maize (Zea mays L.) plays an important agronomic role as feed, food, and source of bioethanol. The embryonic root system of maize consists of a primary root and a variable number of seminal roots. The post-embryonic root system comprises lateral and shoot-borne roots. In all maize root types lateral roots are initiated from phloem pole pericycle and endodermis cells (Hochholdinger et al, 2004a). The plant hormone auxin is a key regulator of many aspects of plant development. Auxin controls lateral root development (Jansen et al, 2012; Peret et al, 2009a, b), root architecture (Overvoorde et al, 2010) and vascular development (Wilson et al, 1991; Uggla et al, 1996; Mattsson et al, 1999). It was suggested that polar auxin transport controls

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