Integrated multi-omics analysis provides molecular insights into flavor variation in melons grafted onto two different pumpkin rootstocks during fruit development

Abstract

Melon fruit flavor is a key quality characteristic that influences consumer preference. Grafting is an effective technique to enhance fruit quality but yields divergent outcomes in terms of fruit flavor. To address this problem, we analyzed parallel changes in flavor-related metabolite accumulation and gene expression in two pumpkin rootstock grafted melons during four fruit developmental stages. We identified 26 061 expressed genes and 840 metabolites from 21 different compound classes, including carbohydrates, amino acids, and lipids. We also detected 50 aroma volatile compounds in the grafted melons. Results showed that genes and metabolites associated with metabolic pathways (carbohydrate, amino acid, lipid, and phenylpropanoid) play a key role in flavor formation. Compared with ‘Sizhuang 12’, ‘Tianzhen 1’ rootstock improved melon fruit flavor by upregulating sugar-related genes (HK, MPI, MIOX, and STP) and inducing metabolite accumulation (d-ribose-5-phosphate, d-galactose, and trehalose 6-phosphate), whereas decreasing bitterness-related amino acids (l-arginine, l-asparagine, and l-tyrosine) and associated genes (thrC, ACS, and GLUL) expression at ripening stage. Furthermore, ‘Tianzhen 1’ exhibited higher expression levels of enzyme-coding genes (4CL, CSE, and COMT) responsible for aroma volatile synthesis than ‘Sizhuang 12’ rootstock. Taken together, our results decipher the basis of the molecular mechanism underlying fruit flavor in grafted melons and provide valuable information for the melons genetic improvement.