Identification of novel cold stress responsive microRNAs and their putative targets in ‘Sultana’ grapevine (Vitis vinifera) using RNA deep sequencing

Cold stress is one of the most important abiotic factors that limit the geographical distribution and productivity of grapevines. MicroRNAs (miRNAs) are known to be involved in plant development and stress responses; so, comprehensive knowledge of their expression pattern under cold stress could improve our knowledge of microRNA-mediated stress tolerance in grapevine. In this study, the effects of gradual chilling on the expression dynamics of miRNAs in grapevine (Vitis vinifera var. ‘white sultana’) were evaluated using high-throughput sequencing. Small RNAs’ libraries were generated from the grapevine leaves under normal and low temperature (4 ◦C) conditions. A total of 158 known and 181 novel miRNAs were detected and among them, 28 and 10 miRNAs were up- and down-regulated, respectively. The predicted target genes of differentially expressed miRNAs predominantly control important transcription factors like ARF, SPL, GRAS, NF-YA, HD-ZIPII. Based on enrichment analysis, we suggest that the networks associated with responses to phosphate starvation, copper ion, leaf growth and development, auxin and abscisic acid signaling are among the important enriched networks which contribute to the procedures of responses to cold stress. These results provide useful information for further efforts and research on the roles of miRNAs in grapevine tolerance to cold stress.