GW2-mediated ubiquitination and degradation of YLR regulate grain size and leaf color by coordinating source-sink modulation

The RING-Type E3 ubiquitin ligase GRAIN WIDTH 2 (GW2) is a key regulator of grain size and weight in rice (Oryza sativa). However, its substrates and broader roles, particularly in grain size and photosynthesis, remain largely unknown. Here, we applied EMS mutagenesis to the gw2 background and identified a mutant, ylr, exhibiting altered leaf color and reduced grain yield. We identified YLR as an allele of a divinyl reductase involved in converting chlorophyll-a to monovinyl chlorophyll-a during chlorophyll biosynthesis. Interestingly, non-frameshift mutations in the YLR α-helix structure resulted in lighter leaf coloration and fewer tillers, whereas frameshift mutations in YLR led to dwarf plant height. We confirmed that proper YLR function maintains chlorophyll content and chloroplast integrity, ultimately influencing photosynthesis and grain yield. Scanning electron microscopy and transcriptome analysis showed that YLR positively regulates grain length through the alteration of cell number. We further demonstrated that GW2 interacts with and ubiquitinates YLR, targeting it for degradation. Collectively, these findings establish a GW2-YLR regulatory module that integrates leaf color, photosynthesis, and grain yield, supporting coordination between source- and sink-related genes and offering potential targets for optimizing photosynthesis and crop productivity.