OsSLA4 encodes a pentatricopeptide repeat protein essential for early chloroplast development and seedling growth in rice

In land plants, chloroplast transcripts undergo post-transcriptional modifications, including splicing, editing, trimming, etc., before translation, and a set of nuclear-encoded proteins regulate this essential step. In this study, we characterized a rice (Oryza sativa) seedling-lethal albino mutant sla4 from the progeny of tissue culture plants of the japonica cultivar Zhonghua 11. The sla4 mutant exhibited an albino phenotype from germination through the third-leaf stage, and then gradually died. The sla4 mutants lacked photosynthetic pigments and had severe defects in photosynthesis and early chloroplast development. Map-based cloning showed that a 13-bp deletion in the coding region of OsSLA4 on chromosome 7 resulted in the albino phenotype and albino mutants were also generated by knocking-out OsSLA4 in wild type with the CRISPR/Cas9 system. OsSLA4 encodes a chloroplast-localized pentatricopeptide repeat (PPR) protein with 15 PPR motifs and an atypical DYW-like motif. Loss-of-function of OsSLA4 resulted in severe defects in the intron splicing of atpF, ndhA, petB, rpl2, rpl16, rps12-2, and trnG, as well as a significant reduction in the transcript levels of chloroplast ribosomal RNAs and some chloroplast development- and photosynthesis-related genes. These results indicate that OsSLA4 is indispensable for early chloroplast development and seedling growth in rice, most likely acting by influencing the intron splicing of multiple chloroplast group II introns.