Comparative Analysis of miRNA Abundance Revealed the Function of Vvi-miR828 in Fruit Coloring in Root Restriction Cultivation Grapevine (Vitis vinifera L.)

Root restriction cultivation leads to early maturation and quality improvement, especially in the anthocyanin content in grapevine. However, the molecular mechanisms that underlie these changes have not been thoroughly elucidated. In this study, four small RNA libraries were constructed, which included the green soft stage (GS) and ripe stage (RS) of ‘Muscat’ (Vitis vinifera L.) grape berries that were grown under root restriction (RR) and in traditional cultivation (no root restriction, CK). A total of 162 known miRNAs and 14 putative novel miRNAs were detected from the four small RNA libraries by high-throughput sequencing. An analysis of differentially expressed miRNAs (DEMs) revealed that 13 miRNAs exhibited significant differences in expression between RR and CK at the GS and RS stages, respectively. For different developmental stages of fruit, 23 and 34 miRNAs showed expression differences between the GS and RS stages in RR and CK, respectively. The expression patterns of the eight DEMs and their targets were verified by qRT-PCR, and the expression profiles of target genes were confirmed to be complementary to the corresponding miRNAs in RR and CK. The function of Vvi-miR828, which showed the down regulated expression in the RS stage under root restriction, was identified by gene transformation in Arabidopsis. The anthocyanin content significantly decreased in transgenic lines, which indicates the regulatory capacity of Vvi-miR828 in fruit coloration. The miRNA expression pattern comparison between RR and CK might provide a means of unraveling the miRNA-mediated molecular process regulating grape berry development under root restricted cultivation.