Effects of scion-rootstock interaction on citrus fruit quality related to differentially expressed small RNAs

•Total soluble solids of fruit on Poncirus trifoliata rootstock were significantly higher than those of on Citrus reticulata rootstock, reversely, titratable acid of fruit were lower on Poncirus trifoliata rootstock.•One hundred and twenty-nine differentially expressed miRNAs were identified by comparison of miRNA expression between the ‘Daya’ mandarin grafted on Poncirus trifoliata and Citrus reticulata rootstocks at different developments.•Correlation analysis with the fruits from four citrus cultivars grafted on two rootstocks showed that four differentially expressed miRNAs (Cre-miR159–3p, Cre-miR160a, Cre-miR171b and Cre-miR399–3p) were significant correlated to TSS or TA in some of scion/rootstocks combinations. Cre-miR399–3p and its target gene INVE may be one of the important reasons for improving fruit quality on Poncirus trifoliata rootstock.