Determination of the effects of pre-harvest bagging treatment on kiwifruit appearance and quality via transcriptome and metabolome analyses

[Display omitted] •Bagging treatment by using single-layer bags of outer and inner yellow can improve the appearance and increase the levels of SSC, carotenoids, and anthocyanins, while decreasing the chlorophyll content of ‘Hongyang’ kiwifruit.•The increase in SSC after bagging treatment is mainly due to the increase in D-Glucosamine metabolite and eight DEGs involved in the amino sugar and nucleotide sugar metabolism pathway.•The decrease in Glutamyl-tRNA reductase may be the main reason for the reduction in chlorophyll, while the down-regulation of Lycopene epsilon cyclase and NCED were the key factors behind the increase in carotenoids.•The increase in Taxifolin-3'-O-glucoside metabolite, Flavonoid 3'-monooxygenase, and some TFs were the key factors behind the increase in anthocyanins. Bagging is an effective cultivation strategy to produce attractive and pollution-free kiwifruit. However, the effect and metabolic regulatory mechanism of bagging treatment on kiwifruit quality remain unclear. In this study, transcriptome and metabolome analyses were conducted to determine the regulatory network of the differential metabolites and genes after bagging. Using outer and inner yellow single-layer fruit bags, we found that bagging treatment improved the appearance of kiwifruit, increased the soluble solid content (SSC) and carotenoid and anthocyanin levels, and decreased the chlorophyll levels. We also identified 41 differentially expressed metabolites and 897 differentially expressed genes (DEGs) between the bagged and control ‘Hongyang’ fruit. Transcriptome and metabolome analyses revealed that the increase in SSC after bagging treatment was mainly due to the increase in D-glucosamine metabolite levels and eight DEGs involved in amino sugar and nucleotide sugar metabolic pathways. A decrease in glutamyl-tRNA reductase may be the main reason for the decrease in chlorophyll. Downregulation of lycopene epsilon cyclase and 9-cis-epoxycarotenoid dioxygenase increased carotenoid levels. Additionally, an increase in the levels of the taxifolin-3′-O-glucoside metabolite, flavonoid 3′-monooxygenase, and some transcription factors led to the increase in anthocyanin levels. This study provides novel insights into the effects of bagging on the appearance and internal quality of kiwifruit and enriches our theoretical knowledge on the regulation of color pigment synthesis in kiwifruit.