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Background  Plant plastidic caseinolytic protease (Clp) is a central part of the plastid protease network and consists of multiple subunits. The molecular functions of many Clps in plants, especially in crops, are not well known.    Results  In this study, we identified an albino lethal mutant  al3  in rice, which produces albino leaves and dies at the seedling stage. Molecular cloning revealed that  AL3  encodes a plastid caseinolytic protease, OsClpR1, homologous to  Arabidopsis  ClpR1 and is targeted to the chloroplast. Compared with the wild type, chloroplast structure in the  al3  mutant was poorly developed.  OsClpR1  was constitutively expressed in all rice tissues, especially in young leaves. The  OsClpR1  mutation affected the transcript levels of chlorophyll biosynthesis and chloroplast development-related genes. The RNA editing efficiency of three chloroplast genes ( rpl2 ,  ndhB ,  ndhA ) was remarkably reduced in  al3 . Using a yeast two-hybrid screen, we found that OsClpR1 interacted with OsClpP4, OsClpP5, OsClpP2, and OsClpS1.    Conclusions  Collectively, our results provide novel insights into the function of Clps in rice.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12284-021-00489-6.

Plastid caseinolytic protease OsClpR1 regulates chloroplast development and chloroplast RNA editing in rice