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Background  Kiwifruit are classified as climacteric since exogenous ethylene (or its analogue propylene) induces rapid ripening accompanied by ethylene production under positive feedback regulation. However, most of the ripening–associated changes (Phase 1 ripening) in kiwifruit during storage and on–vine occur largely in the absence of any detectable ethylene. This ripening behavior is often attributed to basal levels of system I ethylene, although it is suggested to be modulated by low temperature.    Results  To elucidate the mechanisms regulating Phase 1 ripening in kiwifruit, a comparative transcriptome analysis using fruit continuously exposed to propylene (at 20 °C), and during storage at 5 °C and 20 °C was conducted. Propylene exposure induced kiwifruit softening, reduction of titratable acidity (TA), increase in soluble solids content (SSC) and ethylene production within 5 days. During storage, softening and reduction of TA occurred faster in fruit at 5 °C compared to 20 °C although no endogenous ethylene production was detected. Transcriptome analysis revealed 3761 ripening–related differentially expressed genes (DEGs), of which 2742 were up–regulated by propylene while 1058 were up–regulated by low temperature. Propylene exclusively up–regulated 2112 DEGs including those associated with ethylene biosynthesis and ripening such as  AcACS1 ,  AcACO2 ,  AcPL1 ,  AcXET1 ,  Acβ–GAL ,  AcAAT ,  AcERF6  and  AcNAC7 . Similarly, low temperature exclusively up–regulated 467 DEGS including  AcACO3 ,  AcPL2 ,  AcPMEi ,  AcADH ,  Acβ–AMY2 ,  AcGA2ox2 ,  AcNAC5  and  AcbZIP2  among others. A considerable number of DEGs such as  AcPG ,  AcEXP1 ,  AcXET2 ,  Acβ–AMY1 ,  AcGA2ox1 ,  AcNAC6 ,  AcMADS1  and  AcbZIP1  were up–regulated by either propylene or low temperature. Frequent 1–MCP treatments failed to inhibit the accelerated ripening and up–regulation of associated DEGs by low temperature indicating that the changes were independent of ethylene. On–vine kiwifruit ripening proceeded in the absence of any detectable endogenous ethylene production, and coincided with increased expression of low temperature–responsive DEGs as well as the decrease in environmental temperature.    Conclusions  These results indicate that kiwifruit possess both ethylene−dependent and low temperature–modulated ripening mechanisms that are distinct and independent of each other. The current work provides a foundation for elaborating the control of these two ripening mechanisms in kiwifruit.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1264-y) contains supplementary material, which is available to authorized users.

Comparative transcriptome analysis reveals distinct ethylene–independent regulation of ripening in response to low temperature in kiwifruit