The Endosperm-Specific Gene OsEnS-42 Regulates Seed Vigor and Grain Quality

Seed vigor critically determines sowing performance, while grain quality fundamentally influences commercial value. Elucidating the genetic mechanisms governing these traits is critical for enhancing both seed vigor and grain quality in rice cultivation. Here, we demonstrate that the endosperm-specific gene OsEnS-42 is highly expressed in germinating seeds and developing seeds at the early filling stage. OsEnS-42 is localized in the nucleus and cytoplasm. The seed vigor of OsEnS-42 knockout plants decreased, manifested as decreases in germination rate, seedling length, and root length. In addition, OsEnS-42 knockout plants showed increased chalkiness and amylose content. The transcriptome and physiological indicators showed that OsEnS-42 regulates seed vigor through soluble sugars and redox metabolism, and regulates grain quality via soluble sugars and seed development-related enzymes. Haplotype analysis of OsEnS-42 across global rice germplasm revealed four distinct haplotypes (Hap 1-4) with subspecies-specific distributions. Crucially, accessions with Hap 4 exhibit a lower percentage of grain with chalkiness than accessions with Hap 1 (predominantly indica), enabling marker-assisted introgression to reduce chalkiness without subspecies barriers. Meanwhile, accessions with Hap 2 show lower amylose content, providing targets for specialty rice breeding. Our findings elucidate the pathways through which OsEnS-42 regulates seed vigor and grain quality, and provide new molecular breeding targets for improving seed vigor and grain quality in rice.