Transcription factors in the core gene list are important for rice stress resistance
Transcription factors (TFs) are master regulators of gene expression. Our RNA-seq detected the expression of 1573 putative TF genes that could be classified into 58 families. Among the M. oryzae- induced 8211 DEGs in both Nipponbare and Hui1586 (Fig. 2D), 313 genes encoded TFs (Supplemental dataset 10). These TFs were further classified into two large clusters in a hierarchical clustering based on the fold-change values (Fig. 7A). Most of the TFs in cluster I (205 TFs) were upregulated, while the majority of TFs in cluster II (108 TFs) were downregulated by M. oryzae (Fig. 7A). Among the cluster I TFs, the WRKY family contained 38 members, which was clearly enriched (Fig. 7B). The MYB family ranked second with 25 members, followed by the NAC, bHLH, and AP2-ERF families with 21, 20, and 19 members, respectively (Fig. 7B). The enrichment of WRKY TFs in upregulated DEGs is consistent with the well-established roles of the WRKY family in plant immunity. The NAC, bHLH and AP2-ERF families were slightly enriched in cluster I, suggesting that these TFs were also involved in rice resistance to blast fungi (Fig. 7B).
Among the 313 rice blast fungi-responsive TFs, 14 members were in the core gene list, including 5 WRKY (OsWRKY19, 28, 31, 45, and 77), 2 bHLH, 2 NAC, 2 MYB (OsMYB30 and OsMYB55), 2 G2-like and 1 C2H2 TFs (Supplemental dataset 7). Notably, 5 of them have been reported to regulate rice resistance to pathogens. For instance, OsMYB30 ,OsWRKY31 and OsWRKY45 positively while OsWRKY28negatively regulates rice resistance to M. oryzae (Chujo et al., 2013; W. Li et al., 2020; Lv et al., 2017; Shimono et al., 2012; J. Zhang, Peng, & Guo, 2008). OsMYB30 also plays a negative role in rice cold tolerance (Lv et al., 2017). In addition,OsMYB55 enhances rice tolerance to high temperature (El-Kereamy et al., 2012). Thus, approximately 36% (5 of 14) of the TFs in core genes have been functionally characterized as being important regulators of rice stress resistance, indicating that the core gene list contains important regulators in rice immunity and merit evaluation in further functional studies.
TFs regulate gene expression by binding to sequence-specificcis -regulatory elements of target genes. Therefore, we investigated the TF binding motifs that were overrepresented within the promoters of the 321 core genes. Motifs corresponding to DNA binding sites of WRKY, bHLH and MYB TFs were overrepresented in the core genes (Fig. 7C, 7D and Supplemental dataset 11). The DNA motifs for B3 and bZIP, especially AP2-ERF-type TFs, were markedly overrepresented among the core genes (Fig. 7C). AP2 (APETALA2) and ERF (ethylene-responsive factor) transcription factors are unique to plants, the distinguishing characteristic of which is their so-called AP2 DNA-binding domain (L. Wang, Ma, & Lin, 2019). AP2-ERF genes form a large multigene family and play a variety of roles in plant developmental processes, as well as in plant responses to various types of biotic and environmental stresses (Mizoi, Shinozaki, & Yamaguchi-Shinozaki, 2012; Rashid, Guangyuan, Guangxiao, Hussain, & Xu, 2012). The DNA binding motifs of many AP2-ERF TFs, such as ORA59 and CBF1 (Fig. 7D), are represented on the promoter of 111 and 87 core genes, respectively (Supplemental dataset 11). InArabidopsis , ORA59 positively regulates resistance to necrotrophic pathogens by direct binding to the promoters of jasmonate- and ethylene-responsive genes (Catinot et al., 2015). CBF1 induces cold-regulated gene expression and increases plant freezing tolerance (Chinnusamy, Zhu, & Zhu, 2007). These findings suggest that AP2-ERF TFs are important regulators in rice resistance to blast fungi.