Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses

Abstract

Background The WRKY transcription factor family plays significant roles in biotic and abiotic stress responses, which has been associated with various biological processes in higher plants. However, very little is known regarding the structure and function of WRKY genes in maize. Results In this study, a total of 140 ZmWRKY proteins encoded by 125 ZmWRKY genes were eventually identified in maize. On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were divided into three main groups (Groups I, II and III) and the Group II was further classified into five subgroups. The characteristics of exon-intron structure of these putative ZmWRKY genes and conserved protein motifs of their encoded ZmWRKY proteins were also presented respectively, which was in accordance with the group classification results. Promoter analysis suggested that ZmWRKY genes shared many abiotic stress-related elements and hormone-related elements. Gene duplication analysis revealed that the segmental duplication and purifying selection might play a significant role during the evolution of the WRKY gene family in maize. Using RNA-seq data, transcriptome analysis indicated that most of ZmWRKY genes displayed differential expression patterns at different developmental stages of maize. Further, by quantitative real-time PCR analysis, twenty-one ZmWRKY genes were confirmed to respond to two different abiotic stress treatments, suggesting their potential roles in various abiotic stress responses. In addition, RNA-seq dataset was used to conduct weighted gene co-expression network analysis (WGCNA) in order to recognize gene subsets possessing similar expression patterns and highly correlated with each other within different metabolic networks. Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential regulatory network. Conclusions Taken together, the present study will serve to present an important theoretical basis for further exploring function and regulatory mechanism of ZmWRKY genes in the growth, development, and adaptation to abiotic stresses in maize.

Genome-Wide Analysis of WRKY Gene Family and the Dynamic Responses of Key WRKY Genes Involved in Ostrinia furnacalis Attack in Zea mays

“…Compared with the previously reported by Zhang et al [ 20 ] and Hu et al [ 21 ], additional new ZmWRKY genes (12 and 9, respectively) were identified and renamed according to the chromosomal distribution, and some previously identified ZmWRKY genes (e.g., GRMZM2G103742) that had no corresponding gene models in maize v4 genome were considered obsolete; moreover, two genes (Zm00001d034475 and Zm00001d044315) identified by Hu et al [ 21 ] were not found in our result based on the same maize genome ( Table S1 ). The WRKY genes were categorized into three groups based on conserved domains and phylogenetic analysis, and the results were consistent with previous findings [ 21 ]. The molecular weights and isoelectric points of the ZmWRKY proteins showed a great deal of variation, likely due to their differing roles across a range of environments.…”

“…In this study, a total of 128 putative non-redundant WRKY genes were identified and characterized using the new maize reference genome, the number of WRKY genes is higher than that identified in the previous studies [ 20 , 21 ]. Compared with the previously reported by Zhang et al [ 20 ] and Hu et al [ 21 ], additional new ZmWRKY genes (12 and 9, respectively) were identified and renamed according to the chromosomal distribution, and some previously identified ZmWRKY genes (e.g., GRMZM2G103742) that had no corresponding gene models in maize v4 genome were considered obsolete; moreover, two genes (Zm00001d034475 and Zm00001d044315) identified by Hu et al [ 21 ] were not found in our result based on the same maize genome ( Table S1 ). The WRKY genes were categorized into three groups based on conserved domains and phylogenetic analysis, and the results were consistent with previous findings [ 21 ].…”

“…In this study, we performed another characterization and analysis of the WRKY gene family using the maize v4 genome. This comprehensive gene list, which revealed a few conflicts with previous studies [ 20 , 21 ], contributes to the understanding of functional and genetic evolution of the entire WRKY gene family in maize. We also integrated transcriptional regulation and expression analyses of WRKY genes to screen candidate key ZmWRKY genes involved in Chinese commercial maize (hybrid Jingke968) defense against the Asian corn borer, Ostrinia furnacalis , which is one of the most destructive pests to maize, and which causes significant yield loss in China [ 25 ].…”

“…In recent years, several studies on genome-wide WRKY identification have been reported in succession using different versions of the maize genome. Zhang et al identified 120 putative WRKY protein-encoding genes in the maize B73 RefGen_v3 genome [ 20 ], and Hu et al identified 125 putative WRKY protein-encoding genes using the new high-quality maize v4 genome [ 21 , 22 ]. Previous studies additionally focused primarily on the roles of WRKY TFs in response to abiotic stress or during developmental processes in maize.…”

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

“…In-depth analysis of the structural characteristics of introns and exons is a key step in the process of gene family evolution [ 60 , 61 ]. A varied number of introns was possessed by AtruWRKY genes, group Ⅰ had more introns in this study, implying that the molecular structure in the group Ⅰ of WRKY genes may be quite conserved in the process of evolution, which conductive to the protein diversity caused evolution [ 62 , 63 ]. It seems that the crucial function of the WRKY gene family in A. truncatum is very much related to group Ⅰ, and similar results were found in eggplant ( Solanum torvum L.) [ 60 ].…”