The auxin response factor transcription factor family in soybean: Genome-wide identification and expression analyses during development and water stress

Chien Van Ha, Dung Tien Le, Rie Nishiyama, Yasuko Watanabe, Saad Sulieman, Uyen Thi Tran, Keiichi Mochida, Nguyen Van Dong, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, Lam Son Phan Tran

Research output: Contribution to journalArticle

64 Citations (Scopus)

Abstract

In plants, the auxin response factor (ARF) transcription factors play important roles in regulating diverse biological processes, including development, growth, cell division and responses to environmental stimuli. An exhaustive search of soybean genome revealed 51 GmARFs, many of which were formed by genome duplications. The typical GmARFs (43 members) contain a DNA-binding domain, an ARF domain and an auxin/indole acetic acid (AUX/IAA) dimerization domain, whereas the remaining eight members lack the dimerization domain. Phylogenetic analysis of the ARFs from soybean and Arabidopsis revealed both similarity and divergence between the two ARF families, as well as enabled us to predict the functions of the GmARFs. Using quantitative real-time polymerase chain reaction (qRT-PCR) and available soybean Affymetrix array and Illumina transcriptome sequence data, a comprehensive expression atlas of GmARF genes was obtained in various organs and tissues, providing useful information about their involvement in defining the precise nature of individual tissues. Furthermore, expression profiling using qRT-PCR and microarray data revealed many water stress-responsive GmARFs in soybean, albeit with different patterns depending on types of tissues and/or developmental stages. Our systematic analysis has identified excellent tissue-specific and/or stress-responsive candidate GmARF genes for in-depth in planta functional analyses, which would lead to potential applications in the development of genetically modified soybean cultivars with enhanced drought tolerance.

Original languageEnglish
Pages (from-to)511-524
Number of pages14
JournalDNA Research
Volume20
Issue number5
DOIs
Publication statusPublished - Oct 2013
Externally publishedYes

Fingerprint

Indoleacetic Acids
Dehydration
Soybeans
Transcription Factors
Genome
Dimerization
Real-Time Polymerase Chain Reaction
Biological Phenomena
Atlases
Droughts
Growth and Development
Transcriptome
Arabidopsis
Cell Division
Genes
DNA

Keywords

  • ARF transcription factor family
  • Expression analysis
  • Soybean
  • Structural analysis
  • Water stress

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

The auxin response factor transcription factor family in soybean : Genome-wide identification and expression analyses during development and water stress. / Van Ha, Chien; Le, Dung Tien; Nishiyama, Rie; Watanabe, Yasuko; Sulieman, Saad; Tran, Uyen Thi; Mochida, Keiichi; Van Dong, Nguyen; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo; Tran, Lam Son Phan.

In: DNA Research, Vol. 20, No. 5, 10.2013, p. 511-524.

Research output: Contribution to journalArticle

Van Ha, C, Le, DT, Nishiyama, R, Watanabe, Y, Sulieman, S, Tran, UT, Mochida, K, Van Dong, N, Yamaguchi-Shinozaki, K, Shinozaki, K & Tran, LSP 2013, 'The auxin response factor transcription factor family in soybean: Genome-wide identification and expression analyses during development and water stress', DNA Research, vol. 20, no. 5, pp. 511-524. https://doi.org/10.1093/dnares/dst027
Van Ha, Chien ; Le, Dung Tien ; Nishiyama, Rie ; Watanabe, Yasuko ; Sulieman, Saad ; Tran, Uyen Thi ; Mochida, Keiichi ; Van Dong, Nguyen ; Yamaguchi-Shinozaki, Kazuko ; Shinozaki, Kazuo ; Tran, Lam Son Phan. / The auxin response factor transcription factor family in soybean : Genome-wide identification and expression analyses during development and water stress. In: DNA Research. 2013 ; Vol. 20, No. 5. pp. 511-524.
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