Isolation and Sequence Analysis of Wheat Tissue-Specific cDNAs by Differential Display Ahmed M. El-Shehawi & Mona M. Elseehy & Charles Hedgcoth Published online: 29 May 2010 # Springer-Verlag 2010 Abstract The differential display technology was used to study and isolate tissue-specific cDNA from wheat (Triticum aestivum). cDNA was synthesized by reverse transcription from total RNA from wheat leaves, anthers, and ovaries to search for and isolate tissue-specific cDNAs and use them to screen wheat genomic library to get the corresponding genomic DNA clone. Here, we report the isolation, cloning, and sequencing of various tissue-specific cDNA fragments. Further, we report the isolation of a wheat genomic clone, 18-3. The clone has an unknown open reading frame (ORF238) that is similar to related grain EST sequences, 1,673 bp 5′ flanking region from the ATG and 1321 3′ flanking region. A PlantCARE database search using the 5′ flanking region revealed that there are many cis-acting elements in this region. About 109 cis-acting elements from different plant gene promoters in 24 groups were detected. For example, 26 CAAT elements, a common cis-acting element in promoter and enhancer regions, were detected overall the 5′ flanking region. Multiple TATA-boxes concen- trated in three spots and a putative transcription start site also were detected. In addition, MeJA, DRE, GC-motif, ABRE, GCN4_motif, Skn_1-motif, HSE, A-box, ACE, G-box, I- box, TCCC-motif, P-box, TATC-box, and WUN-motif were detected. The putative function of the reported ORF238 and its promoter is unknown. Keywords Wheat . Anther-specific expression . Promoter . cis-acting elements . Differential display Introduction Plants respond to biotic, abiotic, and developmental signals by the spatial and temporal regulation of gene expression. During plant development, gene expression diverges from the original set of genes expressed in the young seedling tissues through an overlap transition in the gene expression profile in various organs and tissues. This is achieved by the regulation of gene expression through a complicated combination of cis-acting elements in gene promoters and their corresponding trans-acting factors. Precise functional analysis of cis-acting elements and their binding transcrip- tional factors would lead to more understanding of the mechanism by which the expression of these genes leads to specification and organ development as well as plant response to various stresses and signals. This may lead to better exploitation of this information in the recent plant biotechnology to improve plant production and quality. Studying tissue-specific expression is an essential step toward the isolation and characterization of tissue-specific promoters. Many plant promoters have been isolated and characterized including various tissue-specific promoters. For example, seed storage protein promoters have been characterized from wheat (Robert et al. 1989; Thomas and Flavell 1990; Aryan et al. 1991; Lamacchia et al. 2001), rice (Yoshihara et al. 1996; Washida et al. 1999), bean (Bustos et al. 1991), brassica (Ellerstrom et al. 1996), pea (Shirsat et al. 1989), A. M. El-Shehawi (*) Department of Biotechnology, Faculty of Science, Taif University, Taif, Kingdom of Saudi Arabia e-mail: elshehawi@hotmail.com M. M. Elseehy Department of Genetics, Faculty of Agriculture, Alexandria University, Alexandria, Egypt C. Hedgcoth Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA Plant Mol Biol Rep (2011) 29:135–148 DOI 10.1007/s11105-010-0213-1