Rice yield and quality are adversely affected by high temperatures.In our previous studies,two near-isogenic lines(the heat-sensitive line S97 and the heat-tolerant line T63)were bred,and different displayed genes and proteins between the heat-sensitive and heat-tolerant lines at early milky stage responding to high temperature stress were analyzed.In this study,we analyzed the transcriptome profiles for rice grain from heattolerant and heat-sensitive lines in response to high night temperatures at the early milky stage using the Illumina Sequencing method.The analysis results for the sequencing data indicated that 35 transcripts showed different expressions between heat-tolerant and heat-sensitive rice.Functional analysis of the differentially expressed transcripts indicated that 21 genes have functional annotation and their functions are mainly involved in oxidation-reduction,metabolic,transport,transcript regulation,defense response and photosynthetic processes.Based on the functional annotation of the differentially expressed genes,the possible process that regulates these differentially expressed transcripts in rice grain responding to high night temperature stress at the early milky stage was further analyzed.This analysis indicated that high night temperature stress disrupts electron transport in the mitochondria,which leads to changes in the concentration of hydrogen ions in the mitochondrial and cellular matrix and influences the activity of enzymes involved in TCA and its secondary metabolism in plant cells.The candidate transcripts may provide genetic resources that may be useful in the improvement of heat-tolerant characters of rice.The model proposed here is based on differences in expression and transcription between two rice lines.In addition,the model may support future studies on the molecular mechanisms underlying plant responses to high night temperatures.