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Open Access Highly Accessed Research article

Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

Pankaj Barah1, Naresh Doni Jayavelu2, Simon Rasmussen3, Henrik Bjørn Nielsen3, John Mundy4 and Atle M Bones1*

Author Affiliations

1 Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway

2 Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim N-7491, Norway

3 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby DK 2800, Denmark

4 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark

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BMC Genomics 2013, 14:722  doi:10.1186/1471-2164-14-722

Published: 22 October 2013

Abstract

Background

Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking.

Results

In this study, we report genome-scale transcript response diversity of 10 A. thaliana ecotypes originating from different geographical locations to non-freezing cold stress (10°C). To analyze the transcriptional response diversity, we initially compared transcriptome changes in all 10 ecotypes using Arabidopsis NimbleGen ATH6 microarrays. In total 6061 transcripts were significantly cold regulated (p < 0.01) in 10 ecotypes, including 498 transcription factors and 315 transposable elements. The majority of the transcripts (75%) showed ecotype specific expression pattern. By using sequence data available from Arabidopsis thaliana 1001 genome project, we further investigated sequence polymorphisms in the core cold stress regulon genes. Significant numbers of non-synonymous amino acid changes were observed in the coding region of the CBF regulon genes. Considering the limited knowledge about regulatory interactions between transcription factors and their target genes in the model plant A. thaliana, we have adopted a powerful systems genetics approach- Network Component Analysis (NCA) to construct an in-silico transcriptional regulatory network model during response to cold stress. The resulting regulatory network contained 1,275 nodes and 7,720 connections, with 178 transcription factors and 1,331 target genes.

Conclusions

A. thaliana ecotypes exhibit considerable variation in transcriptome level responses to non-freezing cold stress treatment. Ecotype specific transcripts and related gene ontology (GO) categories were identified to delineate natural variation of cold stress regulated differential gene expression in the model plant A. thaliana. The predicted regulatory network model was able to identify new ecotype specific transcription factors and their regulatory interactions, which might be crucial for their local geographic adaptation to cold temperature. Additionally, since the approach presented here is general, it could be adapted to study networks regulating biological process in any biological systems.

Keywords:
Arabidopsis thaliana; Ecotypes; Cold stress; Natural variation; Adaptation; Gene expression; Regulatory networks; Arabidopsis thaliana 1001 genome; Systems biology; Network component analysis