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Transcript profiling in rice stem base of wild type and crown root less 1 mutant after auxin treatment

ABSTRACT: Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice and its expression is induced by auxin (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify CRL1-dependant auxin responsive genes. Transcriptome analysis in wild-type and crl1 mutant stem bases after exogenous auxin treatment of plantlets revealed 126 CRL1-dependant auxin responsive genes including a large part of genes encoding proteins involved in signal transduction pathways that may be related to cell division, expansion and differentiation, and root development.

ORGANISM(S): Oryza sativa

PROVIDER: GSE53689 | GEO | 2017/11/30

SECONDARY ACCESSION(S): PRJNA232642

REPOSITORIES: GEO

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Project description:Maize (Zea mays L.) and other monocot cereals develop extensive shoot-borne root systems from nodal structures of the shoot to secure water and nutrient uptake and provide anchorage in the soil. In the present study, the early stages of coleoptilar node (first shoot-node) development of maize were subjected to a detailed morphological and histological analysis followed by a comprehensive microarray profiling via 105 k oligonucleotide microarrays. Expression profiling identified 1,179 microarray features corresponding to 974 unique transcripts which were differentially expressed between three stages of wild-type B73 coleoptilar node development within the first four days after the initiation of this structure. Significantly, all but one of these microarray features were preferentially expressed at day four compared to day zero of coleoptilar node formation. Moreover, comparative microarray profiling of wild-type versus mutant rtcs coleoptilar nodes which do not initiate shoot-borne roots revealed 958 microarray features corresponding to 828 unique transcripts that were expressed in a RTCS dependent fashion. Differential gene expression during wild-type coleoptilar node development and between wild-type and rtcs coleoptilar nodes was confirmed for a subset of 24 genes by qRT-PCR. In order to identify direct downstream targets of RTCS in silico promoter analyses revealed 191 differentially expressed genes that contained at least one LBD motif in a 1 kb promoter region upstream of the ATG start codon. For six promoter sequences containing LBD motives EMSA experiments demonstrated RTCS binding, hence supporting the notion that differentially accumulated genes containing LBD motifs are direct downstream targets of RTCS. The complex RTCS dependent regulation of coleoptilar node development and crown root formation was illustrated by a wide variety of cellular functions represented by the differentially accumulated genes and in particular by the differentially accumulated genes containing LBD promoter motifs. 24 samples in total: 3 developmental stages (0, 2, 4) * 2 genotypes (WT, rtcs) * 4 biological replicates

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Transcript profiling in rice stem base of wild type and crown root less 1 mutant after auxin treatment

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