title: Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat.
abstract: 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.
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. chenzhenyong@cwnu.edu.cn.|College of Life Science, China West Normal University, Nanchong, 637009, China. chenzhenyong@cwnu.edu.cn.
authors.forename: Zhen-Yong
authors.initials: ZY
authors.lastname: Chen
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. bangzhanggxj@126.com.
authors.forename: Xiao-Jiang
authors.initials: XJ
authors.lastname: Guo
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. czhongxu@gmail.com.
authors.forename: Zhong-Xu
authors.initials: ZX
authors.lastname: Chen
authors.affiliation: College of Life Science, China West Normal University, Nanchong, 637009, China. 838561924@qq.com.
authors.forename: Wei-Ying
authors.initials: WY
authors.lastname: Chen
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. dcliu7@yahoo.com.
authors.forename: Deng-Cai
authors.initials: DC
authors.lastname: Liu
authors.affiliation: Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Yaan, Sichuan, 625014, China. ylzheng@sicau.edu.cn.
authors.forename: You-Liang
authors.initials: YL
authors.lastname: Zheng
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. yaxi.liu@hotmail.com.
authors.forename: Ya-Xi
authors.initials: YX
authors.lastname: Liu
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. ymwei@sicau.edu.cn.
authors.forename: Yu-Ming
authors.initials: YM
authors.lastname: Wei
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. wangjirui@gmail.com.
authors.forename: Ji-Rui
authors.initials: JR
authors.lastname: Wang
mesh_terms: D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D009928:Organ Specificity; D018515:Plant Leaves / Q000254:growth & development; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012639:Seeds / Q000235:genetics / Q000254:growth & development; D013312:Stress, Physiological / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*; D014908:Triticum / Q000235:genetics* / Q000502:physiology
chemical_list: D014157:Transcription Factors