Genome-Wide Identification of microRNAs and Their Targets in Cold-Stored Potato Tubers by Deep Sequencing and Degradome Analysis

Potato tubers, the economically important organ for food, processing raw materials, and seeds, are usually stored at different temperatures for various purposes. A general physiological process during storage is starch hydrolysis and accumulation of reducing sugars as breaking of tuber dormancy. The starch hydrolysis can be accelerated by low temperature. Valuable works have been reported on transcriptional and post-translational regulatory mechanisms that are involved in starch hydrolysis in stored potato tubers. However, little is known whether post-transcriptional events are also involved in this important process. In the present study, two small RNA libraries and two degradome libraries were constructed using 4- and 20 °C-stored potato tubers. Deep sequencing and whole genome-wide data analysis led to the identification of 53 known miRNAs and 60 novel miRNAs, largely increasing the number of miRNAs known in potato. Seventy genes were identified as miRNA targets by degradome analysis, indicating that miRNAs were active in gene expression regulation in the post-harvested tubers. The targets were potentially involved in various biological processes, such as stimulus response, signal transduction, transcriptional regulation, and metabolism. Further expression profiling revealed 11 miRNAs/miRNA*s and 34 targets that showed different patterns between two potato genotypes with distinct response to cold storage in terms of reducing sugar accumulation, implying a role of miRNAs in cold-induced sweetening. This study is the first genome-wide investigation of miRNAs and their targets in cold-stored potato tubers, thus broadening our perspectives on the roles of miRNAs in cold response, dormancy, and carbohydrate metabolism.