Comparative physiological and transcriptomic analysis reveals tissue-specific gene regulation patterns in Micro-Tom tomato in response to graphene quantum dots and graphene oxide

Carbon-based nanomaterials exhibit promising potential in regulating plant growth and development, but their regulatory effects and molecular mechanisms on tomato remain to be systematically explored. This study used Solanum lycopersicum cv. Micro-Tom to investigate the regulatory mechanisms of root-applied graphene quantum dots (GQDs, 100 mg·L⁻¹) and graphene oxide (GO, 200 mg·L⁻¹) on tomato growth, development, and transcriptomic responses. Phenotypic analysis showed both nanomaterials significantly promoted growth, with increases in plant height (11.93%vs 12.93%), stem diameter (4.70%vs 6.44%), leaf area (3.86%vs 5.09%), canopy width (7.13%vs 5.15%), lateral branch number (4.17%vs 9.37%), root length (13.28%vs 13.46%), and root biomass (27.48%vs 81.36%) under GQDs and GO treatments, alongside an early flowering phenotype. Transcriptomic profiling revealed that GQDs induced 7881 differentially expressed genes (DEGs), far more than the 2628 DEGs induced by GO, and the two nanomaterials triggered distinct tissue-specific differential gene expression patterns: GQDs and GO differentially regulated root genes related to glycerolipid metabolism, phenylpropanoid biosynthesis, and transmembrane transport; both affected stem IAA/ABA signaling and substance transport with distinct patterns; GQDs activated leaf zeatin biosynthesis and light-harvesting complex genes, and upregulated flower genes for microtubule assembly, cell wall remodeling, and pectin metabolism. This study reveals tissue-specific transcriptomic responses to GQDs and GO in tomato, providing a theoretical basis for the rational application of carbon-based nanomaterials in sustainable agriculture.