The genomic design of fruit metabolomes

As a major source of vitamins, minerals, and dietary fiber, fruits are critical to global nutritional security. Domestication and crop improvement have increased fruit yield and disease resistance but reduced flavor and aroma. With the rapid development of multi-omics, including genomics and metabolomics, and gene-editing technologies such as CRISPR-Cas9, it has become feasible to improve fruit quality through genome design. However, the sensory traits of fruits, including sweetness, sourness, aroma, and color, are complex and regulated by multiple genes, presenting challenges for the study of their genetic basis. Metabolomics, when combined with reverse genetics, reflects gene expression and protein-protein interactions underlying fruit sensory traits more intuitively than other omics approaches. Establishing correlations between metabolites and phenotypic changes and integrating metabolomics with other omics data are crucial aspects of metabolomics research on fruit quality and genomics-assisted breeding. This paper provides a comprehensive review of research on the metabolomics of fruit sensory traits, alongside future prospects for integrating genomic design with metabolomics. It aims to deepen the understanding of multi-omics technologies, promote the application and advancement of metabolomics in fruit research, and establish a robust theoretical foundation for improving fruit sensory quality.