Multi-omics reveals the mechanisms underlying the differences in the formation of volatile and non-volatile metabolites of different kiwifruit varieties

The kiwifruit, a globally important fruit crop, is a popular fruit with diverse flesh colors and flavors. This study investigated three kiwifruit varieties with different flesh colors, including the Lvrou (green-fleshed), Hongyang (red-fleshed), and G3 (yellow-fleshed) varieties, to elucidate their physicochemical, metabolic, and genetic differences. The results showed that the Lvrou variety exhibited the highest titratable acidity and vitamin C content, the G3 variety had the largest size, the highest soluble sugars, and dry matter, and the Hongyang variety displayed elevated levels of anthocyanins and polyphenols. Next, non-targeted metabolomics identified 2,659 metabolites, with amino acid metabolism emerging as a key discriminator, supported by 1,781 DAMs. In addition, volatile metabolomics revealed 919 VOCs, dominated by esters and ketones, with the G3 variety showing the highest ester abundance, correlating with intense fruity-pineapple aromas. On the other hand, the transcriptomics data linked the ester synthesis to upregulated PDC and ADH genes in the G3 variety, while the amino acid accumulation was associated with elevated tRNA ligase expression in the Lvrou variety. Collectively, these findings support a better understanding of the flavor basis in kiwifruits and provide key molecular markers for kiwifruit breeding with optimized flavor and nutrition.