Objective Camellia oleifera ‘Qiufen’ is a unique early-maturing germplasm resource in China. This study aims to elucidate the metabolic profile of its kernels, clarify the dynamic accumulation patterns of important bioactive isoflavonoids, and decipher the key regulatory genes and molecular mechanisms underlying their metabolic pathways. The findings are expected to provide genetic resources and a scientific basis for the molecular design breeding of elite oil-tea varieties with high isoflavonoid content.

Method Fruits of C. oleifera ‘Qiufen’ were collected at three critical developmental stages: fruit growth period (QF0722), oil conversion period (QF0821), and fruit maturity period (QF0920). Following phenotypic observation, their kernels were subjected to untargeted metabolomic and transcriptomic analyses. Through integrated KEGG analysis, association analysis, K-means clustering, and correlation analysis of differentially accumulated metabolites and differentially expressed genes, this study aims to uncover the key genes and potential molecular mechanisms regulating kernel development with a particular focus on isoflavonoid metabolism in C. oleifera ‘Qiufen’.

Result While the fruit peel of C. oleifera ‘Qiufen’ remained green, the epidermal pubescence gradually diminished, and the seed coat color deepened progressively, eventually dehydrating to a brownish hue. Metabolomic and transcriptomic analyses identified 4 698 metabolites and 27 211 differentially expressed genes, respectively. KEGG enrichment and association analyses revealed that pathways such as phenylpropanoid biosynthesis, isoflavone biosynthesis, biosynthesis of various plant secondary metabolites, terpenoid skeleton biosynthesis, glycolysis/glucose production, pyruvate metabolism, alpha linolenic acid metabolism, ascorbic acid and aldehyde metabolism, glycerophospholipid metabolism/glycerolipid metabolism continued to accumulate in three periods. Metabolic pathways such as purine metabolism, pyrimidine metabolism, lysine degradation, butyric acid metabolism, and interconversion of pentose and glucuronic acid were highly enriched in QF0821 vs QF0722; and metabolic pathways such as fatty acid degradation, riboflavin metabolism, glucosinolate biosynthesis, and arginine biosynthesis were highly enriched in QF0920 vs QF0821. These findings indicate that the aforementioned metabolic pathways collectively regulate kernel development in C. oleifera ‘Qiufen’. In addition, by integrating the metabolite gene co expression network, we screened out structural genes such as YCChr15a_016660, YCChr2a_017080 and novel.31123 that are highly correlated with the dynamic changes of 14 isoflavone metabolites, as well as MYB transcription factors including novel.22106, novel.68240, novel.5631 and novel.34569, providing candidate targets for elucidating the transcriptional regulation mechanism of oil tea isoflavone biosynthesis.

Conclusion This study conducted a multi-omics analysis of the seed kernels of C. oleifera ‘Qiufen’ during three key developmental stages, revealing the metabolic changes characteristics of amino acid accumulation in the early stage, secondary metabolism enrichment in the middle stage, and lipid synthesis in the late stage. It also elucidated the transcriptional expression characteristics of carbon metabolism supporting fatty acid assembly and cell membrane construction during the lipid transformation period, as well as the coordinated accumulation of fatty acid modifications and defense substances such as isoflavones during the mature stage. It clarified the systematic coordination of primary metabolism and the phenylpropanoid-isoflavone pathway at the transcriptional and metabolic levels during the development of the C. oleifera ‘Qiufen’ kernels. Moreover, it screened out core genes highly related to isoflavone metabolism, including YCChr15a_016660, YCChr2a_017080, novel.31123, novel.22106, novel.68240, novel.5631 and novel.34569, providing valuable genetic resources and scientific basis for molecular breeding of high-isoflavone Camellia.