Integrated Metabolomics and Transcriptomics Provide Insights into Amino Acid Biosynthesis Mechanisms During Seed Ripening in Three Corylus heterophylla × Corylus avellana Cultivars

The amino acid composition of hazelnut seeds is a critical determinant of nutritional value and flavor. Understanding the biosynthesis mechanisms during seed development is essential for breeding functional varieties. In this study, we analyzed the seed quality characteristics of three Corylus heterophylla × Corylus avellana cultivars (DW, YZ, and B-21) using extensive targeted metabolomics and transcriptomics at the seed enrichment and fruit maturity stages. A total of 273 amino acid-related metabolites—including free proteinogenic amino acids, non-proteinogenic amino acids, small peptides, and their derivatives— were identified. While all cultivars contained a complete profile of essential amino acids, their accumulation patterns varied significantly. Notably, B-21 exhibited significantly higher total amino acid content compared with DW and YZ, although its content decreased during ripening. Integrated metabolomics and transcriptomics analysis, facilitated by Pearson correlation network analysis (PCA), identified 16 key structural genes strongly associated with amino acid synthesis, including PK, ENO, PHGDH, aroA, and trpE. Specifically, IMDH was significantly positively correlated with arginine synthesis, while ilvH, rpiA, and lysC were potential contributors to the synthesis of methionine, histidine, and tryptophan. These findings highlight a putative regulatory network of amino acid biosynthesis in hybrid hazelnuts and provide candidate genes for future functional validation and the genetic improvement of hazelnut nutritional quality.