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.

Growth Stimulatory Effects and Genome-Wide Transcriptional Changes Produced by Protein Hydrolysates in Maize Seedlings

“…A member of AP2-EREB family, preferentially expressed in coleoptile nodes during maize root development, plays a role in the formation of crown roots (Muthreich et al, 2013). PLETHORA2 in Arabidopsis ( baby boom1 , the homolog in maize) encodes another AP2-EREBP TF required for the formation of root stem cells (Aida et al, 2004).…”

Regulation of plant root system architecture: implications for crop advancement

“…In maize and sorghum brace roots, the most abundant transcripts encode enzymes related to metabolism and energy production [4]. Many additional genes have been identified that are involved in the formation of postembryonic roots in maize and rice [5,6]. The hormone strigolactone has recently been shown to impact various aspects of shoot growth but also appears to be a general mediator of root growth.…”

Structural analysis reveals a “molecular calipers” mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat

“…A DNA-binding study has shown that Arabidopsis LBD proteins, such as LOB, LBD4, and ASYMMETRIC LEAVES2 (AS2), specifically bind a 6-bp consensus LBD-response element (LBD-RE, GCGGCG), which is conserved in the four-nucleotide core sequence CGGC (24). It is well-documented that LBD proteins are nuclear proteins, and the LBD-RE sequence is present in promoters of several target genes of LBD proteins (25)(26)(27)(28)(29)(30). Therefore, LBD proteins are DNA-binding transcription factors.…”