Abstract:In order to study the response mechanism of Dongxiang wild rice (Oryza rufipogon) to low temperature stress, its RNA-Seq transcriptional expression profile at seedling stage was studied. The results showed that a total of 10 200 differentially expressed genes (DEGs) under low temperature stress were detected compared with control under normal temperature, among which 5 201 DEGs were up-regulated and 4 999 were down-regulated. There were 426 DEGs located in the reported QTL interval of cold tolerance in rice, and 37 of them were family genes related to cold tolerance regulation. Go functional classification and KEGG metabolic pathway analysis of DEGs indicated that nucleic acid binding transcription factor activity, amino acid biosynthesis and photosynthetic metabolism were involved in the response to low temperature stress. The expression patterns of 12 DEGs, including ABA response protein gene, MYB transcription factor and 40S ribosomal protein SA gene, might be related to low temperature stress response by real-time fluorescence quantitative PCR analysis were consistent with those of RNA-Seq. So, it was suggested that plant hormone transduction pathways and transcription factor-related regulatory genes could play an important role in response to low temperature stress in Dongxiang wild rice seedling stage.