Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Maize coleoptilar node development: WT vs. rtcs

ABSTRACT: 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

ORGANISM(S): Zea mays

SUBMITTER: Frank Hochholdinger

PROVIDER: E-GEOD-25467 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

Project description:Abscisic acid (ABA) is a key hormone for plant growth, development and stress adaptation. Perception of ABA through four types of receptors has been reported. We show here that impairment of ABA perception through the PYR/PYL/RCAR branch reduces vegetative growth and seed production, and leads to a severely open stomata and dramatic ABA insensitive phenotype, even though other branches for ABA perception remain functional. Arabidopsis sextuple mutant impaired in 6 PYR/PYL receptors, namely PYR1, PYL1, PYL2, PYL4, PYL5 and PYL8, was able to germinate and grow even on 100 mM ABA. Whole-rosette stomatal conductance (Gst) measurements revealed that leaf transpiration in the sextuple pyr/pyl mutant was higher than in the ABA-deficient aba3-1 or ABA-insensitive snrk2.6 mutants. The gradually increasing Gst values of plants lacking three, four, five and six PYR/PYLs indicate quantitative regulation of stomatal aperture by this family of receptors. The sextuple mutant lacked ABA-mediated activation of SnRK2s and ABA-responsive gene expression was dramatically impaired as was reported in snrk2.2/2.3/2.6. In summary, these results show that ABA perception by PYR/PYLs plays a major role to regulate seed germination and establishment, basal ABA signaling required for vegetative and reproductive growth, stomatal aperture and transcriptional response to the hormone. Four biological replicates were generated for the 3 genotypes, pyr1pyl1pyl2pyl4pyl5pyl8 sextuple mutant, snrk2.2/2.3/2.6 triple mutant, and Col-0. All the samples were treated with ABA for 3 hours before harvesting. The four Col-0 samples were mix to create an unique reference Col-0 sample. Two comparasion were made, fisrt one, PYR/PYL sextuple mutant versus Col-0 reference sample and second one, SnRK2 triple mutant versus Col-0 reference sample. In each comparasion four biological replicates were made. Replicas number 1 and 2 were labeled with Cy5 for the mutant sample and Cy3 for the Col-0 reference sample, while the other two replicas,#3 and #4, were reversed-labeled.

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Maize coleoptilar node development: WT vs. rtcs

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