Combined analysis of carotenoid metabolites and the transcriptome to reveal the molecular mechanism underlying fruit colouration in zucchini (Cucurbita pepo L.)

To reveal the molecular mechanism underlying peel colouration, carotenoid metabolites and the transcriptome were jointly analysed in zucchini peels with three different colours: light green (Lg), yellow (Y), and orange (O). Our results showed that the carotenoid levels in O (157.075 μg/g) and Y (22.734 μg/g) were both significantly higher than in Lg (7.435 μg/g), while the chlorophyll content was highest in Lg (32.326 μg/g), followed by O (7.294 μg/g) and Y (4.617 μg/g). A total of 14 carotenoids were detected in zucchini peels, primarily lutein (103.167 μg/g in Lg, 509.667 μg/g in Y, and 1543.333 μg/g in O). In particular, significant accumulation of antheraxanthin, zeaxanthin, neoxanthin, and β-cryptoxanthin was first reported in orange zucchini in this study. Furthermore, two modules with hub genes related to carotenoid or chlorophyll content were identified through weighted gene coexpression network analysis. Additionally, the transcription level of some hub genes (PIF4, APRR2, bHLH128, ERF4, PSY1, LCYE2, and RCCR3) was highly correlated with pigment content in the peel, which may be responsible for carotenoid accumulation and chlorophyll degradation in the Y and O varieties. Taken together, the results obtained in this study help to provide a novel mechanism underlying peel colouration in zucchini.