J Integr Plant Biol. ›› 2013, Vol. 55 ›› Issue (8): 696-709.DOI: 10.1111/jipb.12050

Special Issue: Rice Genomics and Agriculture

• Cell and Developmental Biology • Previous Articles     Next Articles

Transcriptome-wide Analysis of Vernalization Reveals Conserved and Species-specific Mechanisms in Brachypodium

Qing Huan1,2†, Zhiwei Mao1,2†, Jingyu Zhang1, Yunyuan Xu1 and Kang Chong1*   

  1. 1Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
    2University of the Chinese Academy of Sciences, the Chinese Academy of Sciences Beijing 100049, China
  • Received:2013-02-04 Accepted:2013-03-07 Published:2013-06-12
  • About author:*Corresponding author: Tel: +86 10 6283 6695; Fax: +86 10 8259 4821; E-mail: chongk@ibcas.ac.cn
    These authors contributed equally to this work.

Abstract:

Several temperate cereals need vernalization to promote flowering. Little, however, is known about the vernalization-memory-related genes, and almost no comparative analysis has been performed. Here, RNA-Seq was used for transcriptome analysis in non-vernalized, vernalized and post-vernalized Brachypodium distachyon (L.) Beauv. seedlings. In total, the expression of 1,665 genes showed significant changes (fold change ≥4) in response to vernalization. Among them, 674 putative vernalization-memory-related genes with a constant response to vernalization were significantly enriched in transcriptional regulation and monooxygenase-mediated biological processes. Comparative analysis of vernalization-memory-related genes with barley demonstrated that the oxidative-stress response was the most conserved pathway between these two plant species. Moreover, Brachypodium preferred to regulate transcription and protein phosphorylation processes, while vernalization-memory-related genes, whose products are cytoplasmic membrane-bound-vesicle-located proteins, were preferred to be regulated in barley. Correlation analysis of the vernalization-related genes with barley revealed that the vernalization mechanism was conserved between these two plant species. In summary, vernalization, including its memory mechanism, is conserved between Brachypodium and barley, although several species-specific features also exist. The data reported here will provide primary resources for subsequent functional research in vernalization.

Huan Q, Mao Z, Zhang J, Xu Y, Chong K (2013) Transcriptome‐wide analysis of vernalization reveals conserved and species‐specific mechanisms in Brachypodium. J. Integr. Plant Biol. 55(8), 696–709.

Key words: Brachypodium, comparative analysis, RNA-Seq, vernalization

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