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Background  High temperature affects a broad spectrum of cellular components and metabolism in plants. The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms. Deg proteases are required for the survival of  Escherichia coli  at high temperatures. However, it is still unclear whether rice Deg proteases are required for chloroplast development under high temperatures.    Results  In this study, we reported the first rice  deg  mutant  tcm5  ( thermo-sensitive chlorophyll-deficient mutant 5 ) that has an albino phenotype, defective chloroplasts and could not survive after the 4–5 leaf seedling stage when grown at high temperature (32 °C). However, when grown at low temperatures (20 °C),  tcm5  has a normal phenotype. Map-based cloning showed that  TCM5  encoding a chloroplast-targeted Deg protease protein. The  TCM5  transcripts were highly expressed in all green tissues and undetectable in other tissues, showing the tissue-specific expression. In  tcm5  mutants grown at high temperatures, the transcript levels of certain genes associated with chloroplast development especially PSII-associated genes were severely affected, but recovered to normal levels at low temperatures. These results showed important role of  TCM5  for chloroplast development under high temperatures.    Conclusions  The  TCM5  encodes chloroplast-targeted Deg protease protein which is important for chloroplast development and the maintenance of PSII function and its disruption would lead to a defective chloroplast and affected expression levels of genes associated with chloroplast development and photosynthesis at early rice seedling stage under high temperatures.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0086-5) contains supplementary material, which is available to authorized users.

The Rice TCM5 Gene Encoding a Novel Deg Protease Protein is Essential for Chloroplast Development under High Temperatures