ATAC sequencing and transcriptomics reveal OsCHR732 function in regulating chromatin accessibility and gene expression in pollen and ovule development in rice

BACKGROUND: The fertility of pollen and ovules directly influences seed set and overall yield in rice, however, the molecular regulatory mechanisms governing rice pollen and ovule development remain poorly understood. RESULTS: In this study, we discovered that functional knockout mutants of the rice chromatin remodeling factor OsCHR732 exhibited significantly reduced pollen viability, accompanied by abnormal ovule development. Quantitative reverse transcription PCR (qRT-PCR) and β-glucuronidase (GUS) staining revealed that OsCHR732 was highly expressed in young panicles, ovaries, and anthers during the mid-to-late developmental stages. RNA-Seq analysis of young spikelets demonstrated that several genes involved in MAPK signaling and plant hormone signal transduction pathways were significantly down-regulated in the oschr732 mutant. ATAC (Assay for Transposase-Accessible Chromatin)-Seq analysis revealed a decrease in chromatin accessibility at the promoter regions of several genes in the mutant. Integrated ATAC-Seq and transcriptomic analysis further demonstrated that six key genes involved in mitogen-activated protein kinase (MAPK), abscisic acid (ABA), jasmonic acid (JA) and ethylene (ETH) signal transduction were significantly downregulated, including MAP1, WRKY53, ABI5, ABIL1, JAZ11, and ETR2, which expression pattern were similar to that of OsCHR732. CONCLUSIONS: These findings provide a critical foundation for further elucidating the molecular mechanisms by which OsCHR732 regulates pollen and ovule fertility in rice.