Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat
Research article
- ? Equal contributors
1 Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
2 College of Life Science, China West Normal University, Nanchong 637009, China
3 Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Yaan 625014, Sichuan, China
BMC Genomics 2015, 16:125Â
doi:10.1186/s12864-015-1313-y
Zhen-Yong Chen and Xiao-Jiang Guo contributed equally to this work.
Published: 25 February 2015
Abstract (provisional)
Background Wheat (Triticum aestivum) is one of the most important cereal crops, providing
food for humans and feed for other animals. However, its productivity is challenged
by various biotic and abiotic stresses such as fungal diseases, insects, drought,
salinity, and cold. Transcription factors (TFs) regulate gene expression in different
tissues and at various developmental stages in plants and animals, and they can be
identified and classified into families according to their structural and specialized
DNA-binding domains (DBDs). Transcription factors are important regulatory components
of the genome, and are the main targets for engineering stress tolerance. Results
In total, 2407 putative TFs were identified from wheat expressed sequence tags, and
then classified into 63 families by using Hmm searches against hidden Markov model
(HMM) profiles. In this study, 2407 TFs represented approximately 2.22% of all genes
in the wheat genome, a smaller proportion than those reported for other cereals in
PlantTFDB V3.0 (3.33%–5.86%) and PlnTFDB (4.30%–6.46%). We assembled information from
the various databases for individual TFs, including annotations and details of their
developmental stage- and tissue-specific expression patterns. Based on this information,
we identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs,
accounting for 52.22% and 45.87% of the 2407 wheat TFs, respectively. We identified
338, 269, 262, 175, 49, and 18 tissue-specific TFs in the flower, seed, root, leaf,
stem, and crown, respectively. There were 100, 6, 342, 141, 390, and 278 TFs specifically
expressed at the dormant seed, germinating seed, reproductive, ripening, seedling,
and vegetative stages, respectively. We constructed a comprehensive database of wheat
TFs, designated as WheatTFDB (http://xms.sicau.edu.cn/wheatTFDB/). Conclusions Approximately
2.22% (2407 genes) of all genes in the wheat genome were identified as TFs, and were
clustered into 63 TF families. We identified 1257 developmental stage-specific TFs
and 1104 tissue-specific TFs, based on information about their developmental- and
tissue-specific expression patterns obtained from publicly available gene expression
databases. The 2407 wheat TFs and their annotations are summarized in our database,
WheatTFDB. These data will be useful identifying target TFs involved in the stress
response at a particular stage of development.