Natural variation in OsMADS1 transcript splicing affects rice grain thickness and quality by influencing monosaccharide loading to the endosperm

Grain size, which encompasses grain length, width, and thickness, is a critical determinant of both grain weight and quality in rice. Despite the extensive regulatory networks known to determine grain length and width, the pathway(s) that regulate grain thickness remain to be clarified. Here, we present the map-based cloning and characterization of qGT3, a major quantitative trait locus for grain thickness in rice that encodes the MADS-domain transcription factor OsMADS1. Our findings demonstrate that OsMADS1 regulates grain thickness by affecting sugar delivery during grain filling, and we show that OsMADS1 modulates expression of the downstream monosaccharide transporter gene MST4. A natural variant leads to alternative splicing and thus to a truncated OsMADS1 protein with attenuated transcriptional repressor activity. The truncated OsMADS1 protein results in increased expression of MST4, leading to enhanced loading of monosaccharides into the developing endosperm and thereby increasing grain thickness and improving grain quality. In addition, our results reveal that NF-YB1 and NF-YC12 interact directly with OsMADS1, acting as cofactors to enhance its transcriptional activity toward MST4. Collectively, these findings reveal a novel molecular mechanism underlying grain thickness regulation that is controlled by the OsMADS1–NF-YB1–YC12 complex and has great potential for synergistic improvement of grain yield and quality in rice. This study reports that OsMADS1 interacts with NF-YB1 and NF-YC12 to regulate the expression of MST4, a monosaccharide transporter gene. A natural variant results in a truncated OsMADS1 protein with attenuated transcriptional repressor activity, thereby increasing MST4 expression. This leads to enhanced monosaccharide loading into the developing endosperm, ultimately increasing grain thickness and improving grain quality.