RICE INDETERMINATE 1 (RID1) plays a critical role in controlling floral transition in rice (Oryza sativa). However, the molecular basis for this effect, particularly the target genes and regu-latory specificity, remains largely unclear. Here, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in young leaves at the pre-floral-transition stage to iden-tify the target genes of RID1, identifying 2,680 genes associated with RID1 binding sites genome-wide. RID1 binding peaks were highly enriched for TTTGTC, the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1. Interestingly, CACGTG and GTGGGCCC, two previously uncharacterized indirect binding motifs, were enriched through the interactions of RID1 with the novel flowering-promoting proteins OsPIL12 and OsTCP11, respectively. Moreover, the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes, such as HEADING DATE 1 (HD1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1). Notably, transcriptome se-quencing (RNA-seq) analysis revealed roles of RID1 in diverse developmental pathways. Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136 (a repressor of rice flowering) and negatively regulates its expression. Overall, our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.

Shuo Zhang;Li Deng;Lun Zhao;Changyin Wu

National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan),Hubei Hongshan Laboratory,Huazhong Agricultural University,Wuhan 430070,China

植物学报（英文版）

[1]Shuo Zhang;Li Deng;Lun Zhao;Changyin Wu-.Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition)[J].植物学报（英文版）,2022(09):1690-1705

Indeterminate,INDETERMINATE,RID1,TTTGTC,CACGTG,GTGGGCCC,OsPIL12,OsTCP11,HEADING,FLAVIN,KELCH,REPEAT,OsFKF1,OsERF#136

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