Genome-wide analysis and identification of abiotic stress responsive transcription factor family genes and miRNAs in bread wheat (Triticumaestivum L.): Genomic study of bread wheat

Transcription factors (TFs) act as master regulators that directly bind to their respective distinct cis-regulatory elements and activate the expression of many downstream target genes (regulon), and thus play a key regulatory role in plant development and stress tolerance. TF families such as AP2/EREBP, AREB/ABF, bHLH, bZIP, C2H2, C3HIS, HB, DREB1/CBF, HSF, MADS, MYB, MYC, NAC, WRKY, etc., were known to regulate stress responses of plants and were relatively well studied in rice and Arabidopsis. Bread wheat (Triticumaestivum L) draft genome is recently released and is available in Ensembl Plants database. We used known rice TFs and build Hidden Markov Model (HMM) profiles for individual TF protein families. These Profile HMMs in turn were used to search respective wheat homologs. SMART tool was used for domain identification. Our analysis showed that the wheat genome consists of 201, 166, 265, 182, 200, 102, 200, 274, 54, 125, 315, 226 and 199 genes of AP2/EREBP, AREB/ABF, bHLH, bZIP, C2H2, C3HIS, HB, HIS, HSF, MADS, MYB, NAC and WRKY families, respectively. Genome-wide analysis of miRNAs from wheat genome resulted in identification of 4533 miRNAs from wheat. Further, miRNAs targeting abiotic stress responsive TFs is identified. The genome distribution of abiotic stress responsive TFs and miRNAs strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of these gene families in wheat.