Advances in Genomic, Transcriptomic, and Metabolomic Analyses of Fruit Quality in Fruit Crops

Fruit quality is the main factor determining market competitiveness; it represents the combination of fruit flavor, color, size, and the contents of aromatic and bioactive substances. Research on the genetic basis of fruit quality can provide new information about fruit biology, promote genomic-assisted breeding, and provide technological support for the regulation of fruit quality via habitat selection and/or the control of environmental conditions. High-throughput sequencing is a powerful research method for studying fruit quality traits, and reference genome sequences for many important fruit crops have provided vast amounts of genomic data. To study fruit quality, it is important to select appropriate omics strategies and to analyze omics data meaningfully. Here, we summarize genomic mechanisms of fruit quality formation: gene duplication, transposable element insertion, structural variations and genome methylation in functional genes. We review the genomic, transcriptomic, and metabolomic strategies that have been used to study the genetic basis of fruit quality traits. We also describe some of the genes associated with fruit traits; these genes are a valuable resource for genomics-assisted breeding and are useful models for deciphering the mechanisms of agronomic traits, such as fruit color, size, hardness, aroma components, sugar and acid content. Finally, to maximize the application of omics information, we propose some further directions for research using omics strategies.