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Low-temperature is one of the most severe abiotic stresses affecting the potato production as the cultivated potato (Solanum tuberosum) is frost sensitive. MicroRNAs have been identified in response to low-temperature stress in plants. Here, via high throughput sequencing, we described the profiling of low-temperature stress response to miRNA and mRNA in potato. Two small RNA and six mRNA libraries were constructed and sequenced. Exactly 294 known and 211 novel microRNAs were identified, 24 microRNAs had the higher expression quantity in Treatment group (EG) than in Control group (CG), and 80 microRNAs had the lower expression in EG than CG. A total of 3298 differentially expressed genes (DEGs) were detected, with 1629 up-regulated and 1669 down-regulated. The metabolism pathway of phenylpropanoid biosynthesis (ko00940) is the common KEGG pathway in differentially expressed miRNA and mRNA. In this pathway, StuPOD13654 and StuPOD32147 are peroxidase which mainly catalyzes the coniferyl and sinapyl alcohol to form guaiac wood lignin monomer and syringyl lignin monomer, which are controlled by stu-novel-miR28211 and stu-novel-miR43095. These indicated that microRNAs may play essential roles in the low-temperature tolerance of potato. [ABSTRACT FROM AUTHOR]