P-type pentatricopeptide repeat protein OsYS6 is essential for chloroplast development in rice through its role in chloroplast RNA processing.

Regulation of plastid gene expression is vital for sustaining plastid function and plant growth and development. Pentatricopeptide repeat (PPR) proteins exert influence across nearly every phase in the regulation of organelle-specific genes, and their functional characterization provides valuable targets for breeding programs aimed at improving photosynthetic efficiency and plant vigor. In this research, we identified a rice (Oryza sativa) PPR protein mutant, osys6, which exhibits yellowing phenotypes and seedling lethality due to defective chloroplast development. Mutations in OsYS6 impaired the splicing of two group II introns (ycf3-intron 1 and petB intron) and the RNA editing of the ycf3-185 site. These defects lead to disrupted biosynthesis of photosystem I (PSI) and cytochrome b (6) f complexes in rice and ultimately influencing the growth of rice seedlings. Our results elucidate a crucial role for OsYS6 in coordinating multiple RNA processing events essential for chloroplast biogenesis, which will deepen our knowledge of PPR-mediated chloroplast development in rice. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-025-01621-w.