Identification of microRNAs and target genes in apple (Malus domestica) scion and rootstock with grafted interstock

Apple (Malus domestica) is an important multi-functional horticultural crop. However, thus far, there have been few reports concerning the molecular mechanism by which interstock regulates rootstock and scion growth. MicroRNAs (miRNAs) are a type of post-transcriptional regulator that regulates apple growth and development, fruit quality, hormone signal transduction, and stress response. Interstock grafting resulted in differences in miRNA distribution between apple tissues. The regulatory roles of miRNAs in the grafting of apples are not yet clear. In this study, 15 libraries were constructed using the phloem of an apple grafted on two types of interstock and rootstock by high-throughput sequencing. A total of 281 miRNAs were catalogued into 80 families, and 159 novel ones were identified. Compared with the control, the grafting combination with the interstock resulted in 79 differentially expressed miRNAs (DEMs) in the scion, with 36 up-regulated and 43 down-regulated miRNAs, and 57 DEMs in the rootstock, including 22 up-regulated and 35 down-regulated miRNAs. Grafting with the dwarfing interstock led to DEMs in the whole plant, including a decrease in the expression of mdm-miR156 in the scion and mdm-miR172 in the rootstock. Predictive analysis of the DEMs and their target genes suggested that miRNAs mediate scion growth through several aspects, such as plant hormone synthesis and signal transduction, and nutrient absorption and balance. Through combined miRNA and mRNA analysis, the dwarfing effect of the interstock may affect the expression of genes related to the starch and sucrose metabolism pathways in the rootstock and the plant hormone signal transduction pathway in the scion. The available evidence facilitates a better understanding of the role of miRNAs in the response of apples after grafting interstock. One possible reason for the stunting of apple trees and the promotion of early flowering caused by the dwarfing interstock is the decrease in expression levels of mdm-miR156 and mdm-miR172.