WRKY53 negatively regulates rice cold tolerance at the booting stage by fine-tuning anther gibberellin levels

Abstract

Cold tolerance at the booting stage (CTB) is a major factor limiting rice (Oryza sativa L.) productivity and geographical distribution. A few cold-tolerance genes have been identified, but they either need to be overexpressed to result in CTB or cause yield penalties, limiting their utility for breeding. Here, we characterize the function of the cold-induced transcription factor WRKY53 in rice. The wrky53 mutant displays increased CTB, as determined by higher seed setting. Low temperature is associated with lower gibberellin (GA) contents in anthers in the wild type but not in the wrky53 mutant, which accumulates slightly more GA in its anthers. WRKY53 directly binds to the promoters of GA biosynthesis genes and transcriptionally represses them in anthers. In addition, we uncover a possible mechanism by which GA regulates male fertility: SLENDER RICE1 (SLR1) interacts with and sequesters two critical transcription factors for tapetum development, UNDEVELOPED TAPETUM1 (UDT1) and TAPETUM DEGENERATION RETARDATION (TDR), and GA alleviates the sequestration by SLR1, thus allowing UDT1 and TDR to activate transcription. Finally, knocking out WRKY53 in diverse varieties increases cold tolerance without a yield penalty, leading to a higher yield in rice subjected to cold stress. Together, these findings provide a target for improving CTB in rice.

R‐loops act as regulatory switches modulating transcription of COLD‐responsive genes in rice

“…This can be achieved by the following ways: (1) It can be mediated by biased R‐loops overlapping TFs, such as OsERF101 , OsWRKY53 and bHLH144 , which can regulate gene transcription in response to COLD through the regulatory network. OsWRKY53 functions as a negative regulator at the rice booting stage under COLD (Tang et al ., 2022), while our preliminary result showed that it can act as a positive regulator at the rice seedling stage of rice under COLD (Fig. 4c), indicating that functions of OsWRKY53 in COLD responses may be developmental stage‐dependent.…”

“…OsWRKY53 has recently been reported to negatively regulate chilling stress at the rice booting stage (Tang et al, 2022), while it had positive roles in the regulation of COLD response at the seedling stage after examining changes in OsWRKY53 expression and R-loop abundance using the same reported transgenic lines ( Figs 4c, S22). According to GRNs constructed, we identified 3953 DEGs (Fig.…”

Dynamic gene regulatory networks improving spike fertility through regulation of floret primordia fate in wheat

“…Meanwhile, the expression of DEGs involved in GA and JA hormone pathways were also induced and upregulated during differentiation phase, particular genes encoding LOX3 rate‐limiting enzyme in JA biosynthesis pathway and GA3ox key enzymes in GA 1 and GA 3 biosynthesis (Figures 8d–f and 9b,c). Genes LOX3 and GA3ox are key factor in JA and GA content, which regulate plant development (Jiao et al, 2018; Tang et al, 2022). Therefore, rapid development of spike and floret primordia was an important environment effect by the IPS treatment: although the 41 MYB and 19 NAC‐related TFs were significantly upregulated in the IPS treatment, only the TaGAM1‐6A TFs (MYB) was predicted to interact with TaHSP70‐4A.1 and TaHSP70‐8, which then interacted with JA pathway‐related genes TaMFP2‐4A, TaOPR‐7B.3, TaOPCL1‐3A.1 (Figure 10b).…”

“…Meanwhile, the expression of DEGs involved in GA and JA hormone pathways were also induced and upregulated during differentiation phase, particular genes encoding LOX3 rate-limiting enzyme in JA biosynthesis pathway and GA3ox key enzymes in GA 1 and GA 3 biosynthesis (Figures 8d-f and 9b,c). Genes LOX3 and GA3ox are key factor in JA and GA content, which regulate plant development (Jiao et al, 2018;Tang et al, 2022) interact with TaHSP70-4A.1 and TaHSP70-8, which then interacted with JA pathway-related genes TaMFP2-4A, TaOPR-7B.3, TaOPCL1-3A.1 (Figure 10b). Thus, in the DEGs analysis between treatments during differentiation phase we worked out rapid response of spike to abiotic stresses by activation of MYB TFs (TaGAM1-6A), genes HSP70 and genes related to JA biosynthesis, which improved assimilates accumulation and then accelerated growth and development of spike (Figure 10b).…”

“…However, to maintain fertile development of floret primordia, all genes involved in these biological processes must be coordinated with one another (Lin et al, 2017; Ye et al, 2010). The expression of several transcription factor genes belonging to the MYB, bHLH, and WRKY families are also important drivers of floret primordia development (Li et al, 2020; Tang et al, 2022). In addition, MIKC‐type MADS‐box genes are proposed to elucidate the molecular mechanism of floral organ specification, which cooperatively regulate the identities of four whorls of floral organs (Honma & Goto, 2001; Murai, 2013; Zhao et al, 2017).…”