Time-course transcriptome and chromatin accessibility analyses reveal the dynamic transcriptional regulation shaping spikelet hull size.

The grains of rice (Oryza sativa) are enclosed by a spikelet hull comprising the lemma and palea. Development of the spikelet hull determines the storage capacity of the grain, thus affecting grain yield and quality. Although multiple signaling pathways controlling grain size have been identified, the transcriptional regulatory mechanisms underlying grain development remain limited. Here, we used RNA-seq and ATAC-seq to characterize the transcription and chromatin accessibility dynamics during the development of spikelet hulls. A time-course analysis showed that more than half of the genes were sequentially expressed during hull development and that the accessibility of most open chromatin regions (OCRs) changed moderately, although some regions positively or negatively affected the expression of their closest genes. We revealed a crucial role of GROWTH-REGULATING FACTORs in shaping grain size by influencing multiple metabolic and signaling pathways, and a coordinated transcriptional regulation in response to auxin and cytokinin signaling. We also demonstrated the function of SCL6-IIb, a member of the GRAS family transcription factors, in regulating grain size, with SCL6-IIb expression being activated by SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 18 (OsSPL18). When we edited the DNA sequences within OCRs upstream of the start codon of BRASSINAZOLE-RESISTANT 1 (BZR1) and SCL6-IIb, we generated multiple mutant lines with longer grains. These findings offer a comprehensive overview of the cis-regulatory landscape involved in forming grain capacity and a valuable resource for exploring the regulatory network behind grain development.