Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of Cytokinin-Responsive Genes Using Microarray Meta-Analysis and RNA-Seq in Arabidopsis

ABSTRACT: Cytokinins are N6-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin, as well as to query the response of genes not represented on microarrays. To this end, we performed a meta- analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis thaliana. Microarray meta-analysis using thirteen microarray experiments combined with empirically-defined filtering criteria identified a set of 226 genes differentially regulated by cytokinin, a subset of which have previously been validated by other methods. RNA-seq validated about 73% of the up-regulated genes identified by this meta-analysis. In silico promoter analysis indicated an over- representation of type-B ARR binding elements, consistent with the role of type-B ARRs as primary mediators of cytokinin-responsive gene expression. RNA-seq analysis identified 73 cytokinin-regulated genes that were not represented on the ATH1 microarray. Representative genes were verified using qRT-PCR and NanoString analysis. Analysis of the genes identified reveals a substantial effect of cytokinin on genes encoding proteins involved in secondary metabolism, particularly those acting in flavonoid and phenylpropanoid biosynthesis, as well as in the regulation of redox state of the cell, particularly a set of glutaredoxin genes. Novel splicing events were found in members of some gene families that are known to play a role in cytokinin signaling or metabolism. The genes identified in this analysis represent a robust set of cytokinin- responsive genes that are useful in the analysis of cytokinin function in plants.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Joseph Kieber

PROVIDER: E-MTAB-4417 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.

Bhargava Apurva A Clabaugh Ivory I To Jenn P JP Maxwell Bridey B BB Chiang Yi-Hsuan YH Schaller G Eric GE Loraine Ann A Kieber Joseph J JJ

Plant physiology 20130322 1

Cytokinins are N(6)-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin as well as to query the response of genes not represented on microarrays. To this end, we performed a meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Microarray meta-analysis using 13 microarray ...[more]

PMID: 23524861

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Project description:The timing of reproductive development determines spike architecture and thus yield in temperate grasses such as barley (Hordeum vulgare L.). Reproductive development in barley is controlled by the photoperiod response gene Ppd-H1 which accelerates flowering time under long-day (LD) conditions. A natural mutation in Ppd-H1 prevalent in spring barley causes a reduced photoperiod response, and thus, late flowering under LD. However, it is not very well understood how LD and Ppd-H1 control pre-anthesis development, and thus spike architecture and yield in barley. We performed a detailed morphological analysis of the pre-anthesis development in the spring barley cultivar Scarlett and its wild barley derived introgression line S42-IL107, carrying the photoperiod responsive Ppd-H1 allele. Characterization of shoot apex development in these genotypes indicated that floral transition and initiation of floral primordia occurred under LD (16h light/ 8h dark) and short day (SD, 8h light/ 16h dark) conditions, while inflorescence and seed development strictly required LDs. Additionally, a fast photoperiod response in the presence of the dominant Ppd-H1 allele promoted floret fertility under LDs. To characterize the effects of the photoperiod and allelic variation at Ppd-H1 on gene expression during pre-anthesis development we performed RNA sequencing of leaves and developing main shoot apices during the vegetative phase and early stages of inflorescence development in Scarlett and S42-IL107 grown under SD and LD conditions. Main shoot apices of both genotypes were sampled at defined developmental stages, i.e. Waddington stage W0.5, W1.0, W2.0 and W3.5, respectively. Leaf samples were harvested from plants before (W1.0) and after floral transition (W2.0). We identified genes that were specifically regulated at floral transition independent of day-length and Ppd-H1 and thus may serve as markers for the staging of floral transition. Furthermore, we identified transcripts differentially expressed between photoperiods and between genotypes in leaves and in shoot apices. This set of transcripts might act as candidates downstream of Ppd-H1 and are correlated with the promotion of shoot apex development and higher floret fertility under LD and in the presence of the photoperiod responsive Ppd-H1 allele.

Dataset Information

Identification of Cytokinin-Responsive Genes Using Microarray Meta-Analysis and RNA-Seq in Arabidopsis

Publications

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.

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