Identification of miRNAs mediating shoot growth of grafted sweet cherry through small RNA and degradome sequencing

Sweet cherry (Prunus avium L) is an economically important fruit tree in the worldwide, in which grafting is widely used for plant propagation. Rootstock plays a vital role in shoot growth. However, thus far there have been few reports concerning the molecular mechanism of how rootstock regulates scion growth. MicroRNAs (miRNAs) are crucial small RNAs involved in multiple biological processes. The regulatory roles of miRNAs in the grafting of sweet cherry are not yet clear. In the current work, twelve libraries were constructed using the leaves and stems of sweet cherry grafted on two types of Chinese cherry (Prunus pseudocerasus) rootstocks by high-throughput sequencing. A total of 238 known miRNAs were cataloged into 61 families, and 40 novel ones were identified. Among these miRNAs, 13 and 21 miRNAs were differentially expressed in leaves and stems, respectively. The degradome results and prediction analysis of differentially expressed miRNAs and their targets indicated that miRNAs mediate the growth of scion via several aspects: the shoot apical meristem development, phytohormone synthesis and signal transduction, the absorption and balance of nutrient elements. The available evidence facilitates a better understanding of the role of miRNAs in the response of sweet cherry scion to Chinese cherry rootstock after grafting.