Integrated transcriptomic and metabolomic analyses reveal the mechanism of shoot growth in grafted Camellia oleifera seedlings.

Shoot flushing is a critical determinant of grafted seedling quality in Camellia oleifera, with key evaluation metrics including flushing timing, new shoot number and growth rate, and seedling height uniformity. To elucidate the molecular mechanisms governing shoot development, we conducted integrated analyses of endogenous hormones, metabolomics, and transcriptomics across three Camellia species (C. oleifera, C. meiocarpa, and C. weiningensis). Hormonal profiling revealed that shoot-flushing plants exhibited elevated levels of GA24, GA9, salicylic acid, IAA, IAAla, IPA, and abscisic acid compared to non-flushing plants, while DZ, tZ, and tZR levels were reduced. Metabolomic analysis identified 89 commonly differentially abundant metabolites among the three species. KEGG enrichment and correlation analyses demonstrated significant enrichment of these differentially abundant metabolites and differentially expressed genes in phenylpropanoid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis pathways. Collectively, our findings indicate that shoot flushing is coordinately regulated by multiple metabolic pathways—including plant hormone signal transduction, phenylalanine metabolism, nitrogen metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis—along with expression modulation of key genes such as PAL6, CYP73A4, PER42, GH3.6, and LAX2. These results provide novel insights into the molecular basis of shoot development and offer potential targets for improving grafted seedling quality in C. oleifera.