High temperature often leads to failure of grain filling in rice (Oryza sativa) causing yield loss, but the underlying mechanisms are still not elucidated. Here, we report that two genes encoding seed-specific NAM/ATAF/CUC (NAC) domain transcription factors, ONAC127 and ONAC129, are responsive to heat stress and involved in the grain filling process of rice. ONAC127 and ONAC129 are dominantly expressed in the pericarp and can form a heterodimer during rice grain filling. CRISPR/Cas9 induced mutants and overexpression lines were then generated to investigate the function of these two transcription factors. Interestingly, both knock-out and overexpression plants showed incomplete grain filling and shrunken grains, which became more severe under heat stress. Transcriptome analysis revealed that ONAC127 and ONAC129 mainly regulate stimulus response and nutrient transport. ChIP-seq analysis identified that the direct target genes of ONAC127 and ONAC129 in developing rice seeds include monosaccharide transporter gene OsMST6, sugar transporter gene OsSWEET4, calmodulin-like protein gene OsMSR2 and AP2/ERF factor gene OsEATB. These results suggest that ONAC127 and ONAC129 regulate grain filling by affecting sugar transportation and abiotic stress responses. Overall, this study demonstrates a transcriptional regulatory network with ONAC127 and ONAC129 coordinating multiple pathways to modulate seed development and heat stress responses at rice reproductive stages.
