AUTHOR=Muthamilarasan Mehanathan , Bonthala Venkata S. , Khandelwal Rohit , Jaishankar Jananee , Shweta Shweta , Nawaz Kashif , Prasad Manoj 

TITLE=Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling

JOURNAL=Frontiers in Plant Science

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2015.00910

DOI=10.3389/fpls.2015.00910

ISSN=1664-462X

ABSTRACT=<p>Transcription factors (TFs) are major players in stress signaling and constitute an integral part of signaling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C<sub>4</sub>model plants, <italic>Setaria italica</italic> (SiWRKY) and <italic>S. viridis</italic> (SvWRKY), respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analyzed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II, and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY), followed by group III (39 SiWRKY and 11 SvWRKY) and group I (10 SiWRKY and 6 SvWRKY). Group II proteins were further classified into 5 subgroups (IIa to IIe) based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All <italic>SiWRKY</italic> genes were physically mapped on the <italic>S. italica</italic> genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of <italic>SiWRKY</italic> and <italic>SvWRKY</italic> genes in related C<sub>4</sub> panicoid genomes demonstrated the orthologous relationships between these genomes. <italic>In silico</italic> expression analysis of <italic>SiWRKY</italic> and <italic>SvWRKY</italic> genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate <italic>SiWRKY</italic> genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of <italic>SiWRKY066</italic> and <italic>SiWRKY082</italic> in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling.</p>