Gene editing unlocks superior mutants from once detrimental RFL for enhanced rice yield traits

RICE FLORICULA LEAFY/ABERRANT PANICLE ORGANIZATION 2 (RFL/APO2) is a master regulator of panicle morphogenesis and development in rice. Traditionally, mutations in RFL have led to severe growth phenotypes and decreased rice yield, labeling it as detrimental. However, the present study challenged this perception by utilizing CRISPR/Cpf1 and single-base gene-editing technologies to generate a series of site-directed rfl mutants. Our findings revealed that the evolutionarily conserved sterile alpha motif (SAM) domain and DNA-binding domain (DBD), as well as the intron region of RFL, all play roles in regulating rice morphological development and yield traits. Specifically, introns and the SAM domain are primarily involved in panicle development, whereas the DBD and its key functional sites are closely associated with morphological development and yield. Notably, the amino acid at position 266 was found to be a critical site for RFL regulation of grain shape, significantly affecting grain weight, with changes in the expression levels of genes involved in grain length and panicle weight regulation, such as GRF1 and SPL16. This study not only expands our understanding of the role of RFL in monocot plants but also provides a novel perspective on how gene editing can transform a gene once considered detrimental to improve yield traits in cereal crops. These findings suggest that the number of genes available for optimizing rice phenotypes through gene editing can be significantly increased.