Comparative Transcriptome and sRNAome Analyses Reveal the Regulatory Mechanisms of Fruit Ripening in a Spontaneous Early-Ripening Navel Orange Mutant and Its Wild Type

A complex molecular regulatory network plays an important role in the development and ripening of fruits and leads to significant differences in apparent characteristics. Comparative transcriptome and sRNAome analyses were performed to reveal the regulatory mechanisms of fruit ripening in a spontaneous early-ripening navel orange mutant (‘Ganqi 4’, Citrus sinensis L. Osbeck) and its wild type (‘Newhall’ navel orange) in this study. At the transcript level, a total of 10792 genes were found to be differentially expressed between MT and WT at the four fruit development stages by RNA-Seq. Additionally, a total of 441 differentially expressed miRNAs were found in the four periods, and some of them belong to 15 families. An integrative analysis of the transcriptome and sRNAome data revealed some factors that regulate the mechanisms of formation of early-ripening traits. First, secondary metabolic materials, especially endogenous hormones, carotenoids, cellulose and pectin, obviously changed during fruit ripening in MT and WT. Second, we found a large number of differentially expressed genes (PP2C, SnRK, JAZ, ARF, PG, and PE) involved in plant hormone signal transduction and starch and sucrose metabolism, which suggests the importance of these metabolic pathways during fruit ripening. Third, the expression patterns of several key miRNAs and their target genes during citrus fruit development and ripening stages were examined. csi-miR156, csi-miR160, csi-miR397, csi-miR3954, and miRN106 suppressed specific transcription factors (SPLs, ARFs, NACs, LACs, and TCPs) that are thought to be important regulators involved in citrus fruit development and ripening. In the present study, we analyzed ripening-related regulatory factors from multiple perspectives and provide new insights into the molecular mechanisms that operate in the early-ripening navel orange mutant ‘Ganqi 4’.