MULTI-OMICS APPROACHES TO MAPPING THE GENE REGULATORY NETWORKS BEHIND ANTHOCYANIN AND NUTRIENT ACCUMULATION IN FRUITS AND VEGETABLES: A COMPREHENSIVE REVIEW

Abstract

Quality of fruit and vegetables is mainly determined by two traits: anthocyanin pigmentation and mineral micronutrient content. Both influence consumer attraction, antioxidant property and food security, but neither is controlled by a few genes independently. Instead, they each rely on complex gene regulatory networks (GRNs) integrating developmental, hormonal and environmental signals at transcriptional, post-transcriptional and epigenetic levels. Many years of gene-by-gene studies have revealed the key structural and regulatory genes, particularly the MYB-bHLH-WD40 (MBW) complex, which control anthocyanin biosynthesis, but these studies rarely linked upstream signalling to chromatin status, transcription, protein levels and metabolite outputs in a single system. That is starting to change now that high-throughput, multi-omics platforms are less expensive and more widely available. Genome-wide association studies (GWAS), bulk and single-cell and spatial transcriptomics, epigenomic profiling (WGBS, ChIP-seq, ATAC-seq), proteomics and metabolomics/ionomics in combination with statistical and machine-learning approaches e.g. weighted gene co-expression network analysis (WGCNA) and Bayesian network inference, allow one now to reconstruct GRNs at a resolution not available even 10 years ago and for an increasing number of plant species. This review brings together current knowledge of the anthocyanin biosynthetic pathway and its MBW-centred transcriptional logic; summarizes the major omics technologies and GRN reconstruction pipelines applied in fruit and vegetable crops; provides comparative case studies for apple, grape, citrus, strawberry, blueberry, tomato, eggplant, pepper, potato, sweet potato, lettuce, radish and other horticultural species; and adds a section on ionomics and iron, zinc and provitamin A biofortification. Epigenetic regulation, the role of environmental and hormonal signals, the application of GRN knowledge for precision breeding (e.g., CRISPR/Cas editing), and the health relevance of anthocyanin-rich commodities are also discussed.