Metabolome–transcriptome association analysis revealed the candidate gene involved in soluble sugar content regulation in cucumber fruits

• Metabolome sequencing was combined with corresponding transcriptome analysis. • 16 differentially expressed genes and three differential metabolites, including sucrose, stachyose, and trehalose, were identified. • Csa_5G322500 may play a crucial role in regulating the soluble sugar content of cucumber fruits. Soluble sugar content is a crucial parameter affecting the taste and flavor of cucumber. Fruit sweetness varies depending on the soluble sugar content. To explore the regulatory mechanism underlying soluble sugar content, we performed metabolome sequencing on diploid (low soluble sugar, CK) and autotetraploid (high soluble sugar, T) cucumber fruits on the day of flowering (S1) and 9 days after flowering (S2). Metabolome sequencing was combined with corresponding transcriptome analysis. In total, 250 and 387 differential metabolites were screened at S1 (T_S1 vs CK_S1) and S2 (T_S2 vs CK_S2), respectively. The combined analysis unveiled that the differentially expressed genes were primarily concentrated in the pathways of starch and sucrose metabolism and galactose metabolism, among others. Overall, 16 differentially expressed genes and three differential metabolites, including sucrose, stachyose, and trehalose, were identified. Csa_5G322500 expressed abundantly and in large differential multiples, as evident from the transcriptome data of diploid and tetraploid cucumber fruits at different developmental stages, indicating that Csa_5G322500 may be the key gene affecting the soluble sugar content of fruits. Agrobacterium -mediated transformation of the plants with Csa_5G322500 revealed significant increases in the soluble sugar content of cucumber at 24, 36, and 48 h after Agrobacterium infection and a significant increase in the expression of Csa_5G322500 at 36 and 48 h after infection. In conclusion, Csa_5G322500 is potentially involved in regulating the soluble sugar content regulation in cucumber fruits.