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 language | English |
|---|---|
| Pages (from-to) | 511-524 |
| Number of pages | 14 |
| Journal | DNA Research |
| Volume | 20 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - Oct 2013 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - The auxin response factor transcription factor family in soybean
T2 - Genome-wide identification and expression analyses during development and water stress
AU - Van Ha, Chien
AU - Le, Dung Tien
AU - Nishiyama, Rie
AU - Watanabe, Yasuko
AU - Sulieman, Saad
AU - Tran, Uyen Thi
AU - Mochida, Keiichi
AU - Van Dong, Nguyen
AU - Yamaguchi-Shinozaki, Kazuko
AU - Shinozaki, Kazuo
AU - Tran, Lam Son Phan
PY - 2013/10
Y1 - 2013/10
N2 - 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.
AB - 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.
KW - ARF transcription factor family
KW - Expression analysis
KW - Soybean
KW - Structural analysis
KW - Water stress
UR - http://www.scopus.com/inward/record.url?scp=84885143956&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84885143956&partnerID=8YFLogxK
U2 - 10.1093/dnares/dst027
DO - 10.1093/dnares/dst027
M3 - Article
VL - 20
SP - 511
EP - 524
JO - DNA Research
JF - DNA Research
SN - 1340-2838
IS - 5
ER -