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. Rootstock affects the performance of the scion on productivity and fruit quality. Scions on trifoliate orange rootstock could produce better quality of fruits than on other commonly used rootstocks. This phenomenon has been well documented, but genetic factors affecting the fruit quality through interaction of scion and rootstock remained unclear. Fruits in different developmental stages from the Daya mandarin grafted on two genetically divergent rootstocks (Trifoliate orange (Poncirus trifoliata) (Z) and Hongju (Citrus reticulata) (H)) were used for fruit quality, expression of small RNA, and degradome sequencing analysis. Total soluble solids (TSS) of fruit on Z rootstock were significantly higher than those of on H. In contrast, titratable acid (TA) of fruit were lower on Z rootstock. One hundred and eight known and 145 novel microRNAs (miRNA), as well as 555 target genes were identified by in silico analysis and degradome sequencing. One hundred and twenty-nine differentially expressed miRNAs (DEMs) were identified by comparison of miRNA expression between the Daya mandarins grafted on two rootstocks in three different developmental stages. Correlation analysis with the fruits from three navel orange cultivars on two rootstocks showed that four DEMs (Cre-miR159-3p, Cre-miR160a, Cre-miR171b and Cre-miR399-3p) were significant correlated to TSS or TA in some of scion/rootstock combinations. Expressions of Cre-miR399-3p and its target gene INVE demonstrated consistent correlations with fruit quality of four scion varieties grated on Z rootstock, indicating that Cre-miR399–3p and its target gene INVE may be