This article is part of a special issue on plant genomics.

Open Access Research

Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis

Veronica Gregis1, Fernando Andrés2, Alice Sessa1, Rosalinda F Guerra1, Sara Simonini1, Julieta L Mateos2, Stefano Torti2, Federico Zambelli1, Gian Marco Prazzoli1, Katrine N Bjerkan3, Paul E Grini3, Giulio Pavesi1, Lucia Colombo14, George Coupland2 and Martin M Kater1*

Author Affiliations

1 Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy

2 Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany

3 Department of Biosciences, University of Oslo, N-0316 Oslo, Norway

4 Consiglio Nazionale delle Ricerche Istituto di Biofisica, 20133 Milan, Italy

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Genome Biology 2013, 14:R56  doi:10.1186/gb-2013-14-6-r56

Published: 11 June 2013

Additional files

Additional data file 1:

contains: Figure S1: Analysis of chromatin sample used for ChIP-seq experiments. Figure S2: qRT-PCR validation of differentially expressed genes between Col-0 and svp-41 plants at the vegetative phase. Figure S3: GO enrichment analysis of differentially expressed genes between Col-0 and svp-41 plants at the vegetative stage. Figure S4: Venn diagram containing the overlapping set of putative targets between SVP and FLC and SVP, AP1, and SEP3. Figure S5: Biologically active SVP-GR fusion. Figure S6: Flower organs of in wdr55-2 -/- mutants show reduced size and asymmetric positioning. Figure S7: In-situ hybridization of wild-type and wdr55-2 inflorescence using AP3 and PI probes. Figure S8: Flower morphology of wdr55-2 ag-1 mutant. Table S1: Summary of sequencing and mapping. Table S3: List of putative targets of SVP related to flowering time. Table S6: List of genes differentially expressed in svp-41 compare to Col-0 and related to auxin, cytokinin, or jasmonate homeostasis. Table S9: List of WDxR motif containing proteins found in SVP DNA binding screen. Table S10: Flower organ count from wdr55-2 -/- mutants. Table S12: Primer pairs used for ChIP-qPCR assays. Table S13: Primer pairs used for the qRT-PCR expression analysis. Methods S1: ChIP protocol. Methods S2: qRT-PCR. Methods S3: In-situ hybridization. Methods S4: Scanning electron microscopy.

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Additional data file 2:

contains Table S2: High confidence targets of SVP in vegetative and reproductive tissues; list of the targets of SVP bound in both vegetative and reproductive tissues; lists of binding regions of SVP in vegetative and reproductive tissues.

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Additional data file 3:

contains Table S4: Lists of putative SVP targets with annotated functions in: meristem development in vegetative and reproductive tissues; response to hormonal stimuli such as auxin, cytokinin, ethylene, abscisic acid, jasmonate, and gibberellins in vegetative tissue.

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Additional data file 4:

contains Table S5: Tiling array expression data obtained using RNA extracted from: wild-type Col-0 and svp-41 plants at the vegetative stage, inflorescences of wild-type Col-0 and svp-41 agl24 ap1-12 and overlap between tiling array and ChIP-seq data.

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Additional data file 5:

contains Table S7: Lists of differentially expressed genes in svp-41 mutant and the available expression-profiling data of seedlings treated with the CK benzyladenine (BA).

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Additional data file 6:

contains Table S8: putative targets for both SVP and AP1 and putative targets for both SVP and SEP3.

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Additional data file 7:

contains Table S8: Comparison of the SVP target list of Tao et al. [37] and the list of high confidence targets of SVP in vegetative tissue presented in this study.

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