Identification and classification of the WRKY transcription factors family in barley

Biotic and abiotic stresses are the most important constraints on production by crop plants, including barley. Transcription factors are involved in the regulation of biotic and abiotic stress- response genes and the WRKY transcription factor family encodes a large group of them. Therefore, identification and classification of these factors represent important steps in our quest to find smart strategies for enhancing stress tolerance in plants. In an attempt to identify WRKY transcription factors in barley, multiple searches were done in Plant TFDB and Gramineae TFDB databases. Rice WRKY-conserved sequences were used as the templates for tBLASTN searches in the nr, EST and HTGS datasets for finding new members in barley. An HMM search was used to find sequences containing WRKY conserved domains. The identified 96 HvWRKYs as well as one member of each WRKY subgroup from Arabidopsis, rice and wheat were subjected to multiple alignment using clustalx software and phylogenetic trees were reconstructed using MEGA6 software based on neighborjoining method with a 1000 repeats bootstrap index. Sequences were divided into 3 groups based on the number of WRKY domains and the structure of zinc-finger motifs. Conclusively, there were 13 proteins with 2 WRKY conserved domain in group I, 30 proteins with 1 WRKY conserved domain and Cx7Cx23HxC zinc-finger motif in group III and other proteins with 1 WRKY conserved domain and Cx4-5Cx22-23HxH zinc-finger motif in group II. Regarding the role of group III in plant tolerance to abiotic and biotic stresses, it can be argued that the higher percentage presence of group III members in barley that are similar to rice than to other higher plants can be attributed to duplications in wild monocotyledous ancestors and natural selection for more resistant genotypes in harsh conditions.