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Background  The large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice.    Results  In this study, we raised a mutant from tissue-culture-derived plants of  Oryza sativa subsp. japonica  ‘Zhonghua 11’, which exhibited a lethal chlorosis phenotype from germination to the third-leaf stage. The mutant was designated  seedling-lethal chlorosis 1  ( slc1 ). The  slc1  mutant leaves showed extremely low contents of photosynthetic pigments and abnormal chloroplast development, and were severely defective in photosynthesis. Map-based cloning of  OsSLC1  revealed that a single base (G) deletion was detected in the first exon of  Os06g0710800  in the  slc1  mutant, which caused a premature stop codon. Knockout and complementation experiments further confirmed that  OsSLC1  is responsible for the seedling-lethal chlorosis phenotype in the  slc1  mutant.  OsSLC1  was preferentially expressed in green leaves, and encoded a chloroplast-localized PPR protein harboring 12 PPR motifs. Loss-of-function of  OsSLC1  affected the intron splicing of multiple group II introns, and especially precluded the intron splicing of  rps16 , and resulted in significant increase in the transcript levels of 3 chloroplast ribosomal RNAs and 16 chloroplast development-related and photosynthesis-related genes, and in significant reduction in the transcript levels of 1 chloroplast ribosomal RNAs and 2 chloroplast development-related and photosynthesis-related genes.    Conclusion  We characterized a novel chloroplast-localized PPR protein, OsSLC1, which plays a vital role in the intron splicing of multiple group II introns, especially the  rps16  intron, and is essential for early chloroplast development and seedling survival in rice.

OsSLC1 Encodes a Pentatricopeptide Repeat Protein Essential for Early Chloroplast Development and Seedling Survival