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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Citation and License

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

Published: 11 June 2013

Abstract

Background

MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism.

Results

To compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression analysis, induction experiments and qRT-PCR to identify biologically relevant binding sites. In addition, we compared genome-wide target genes of SVP with those published for the MADS domain transcription factors FLC and AP1, which interact with SVP during the vegetative and reproductive phases, respectively.

Conclusions

Our analyses resulted in the identification of pathways that are regulated by SVP including those controlling meristem development during vegetative growth and flower development whereas floral transition pathways and hormonal signaling were regulated predominantly during the vegetative phase. Thus, SVP regulates many developmental pathways, some of which are common to both of its developmental roles whereas others are specific to only one of them.

Keywords:
MADS-box; gene regulation; transcription factors; post transcriptional regulation; ChIP-seq; floral transition; floral development; Arabidopsis thaliana