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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