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

Abstract

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 C4model plants, Setaria italica (SiWRKY) and S. viridis (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 SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling.

Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance

“…The decrease in synteny with increase in phylogenetic distance between the Poaceae members demonstrates the degree of genetic-relatedness of the corresponding genomes. This is in agreement to previous genome-wide analyses performed for NAC 34, WD40 35, AP2/ERF 36, C 2 H 2 zinc finger and MYB transcription factors3738, DCL, AGO and RDR 39, 14-3-3  40, secondary cell wall genes and WRKY transcription factors4142, and ADP-ribosylation factor43 in foxtail millet. The effect of Darwinian selection in divergence of these genes is examined by investigating the ratio of rate of non-synonymous substitution (Ka) to synonymous substitution (Ks) for all the orthologous gene pairs.…”

Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress

“…Further, decrease in number of orthologous genes between foxtail millet-sorghum (~98%), -maize (~88%), -rice (~75.5%) and - Brachypodium (~54.6%) reveals the close-evolutionary relationship of foxtail millet with sorghum and maize, followed by rice and Brachypodium. This is in agreement with the comparative maps developed using NAC 15, WD40 16, AP2/ERF 17, C 2 H 2 zinc finger and MYB transcription factors1819, DCL, AGO and RDR 20, 14-3-3 21, secondary cell wall genes and WRKY transcription factors2223, and ADP-ribosylation factor24 gene families of foxtail millet.…”

Both JrWRKY2 and JrWRKY7 of Juglans regia mediate responses to abiotic stresses and abscisic acid through formation of homodimers and interaction

“…In the C 4 model plant Setaria italica , SiWRKY066 and SiWRKY082 responded to dehydration and salinity stress and hormone treatments (ABA, salicylic acid and methyl jasmonate), indicating their putative involvement in stress and hormone signalling (Muthamilarasan et al . ). The expression of PgWRKY1 from Panax ginseng is relatively higher in roots and lateral roots compared with leaves, stems and seeds; it is also significantly increased by salicylic acid, ABA and NaCl, but reduced by methyl jasmonate treatment.…”