Transcriptome-based resistance analysis of susceptible and resistant tomato cultivars against Meloidogyne incognita infection

Tomatoes are widely cultivated worldwide and contribute substantially to vegetable production. However, the root-knot nematode (RKN) disease caused by Meloidogyne incognita poses a serious threat to tomato cultivation. The most economical and effective way to control this disease is to deploy resistant cultivars. While the disease resistance provided by the original Mi-1 gene is gradually weakening, highlighting the need to identify new resistance genes for tomato breeding. In this study, RNA sequencing (RNA-seq) was performed on root samples from the resistant tomato cultivar 'Jinpeng M6' and the susceptible cultivar ‘Jinpeng No.1’, with sampling conducted at Stage 1 and 2 for ‘Jinpeng M6’ and Stage 1-6 for ‘Jinpeng No.1’ based on characterized M. incognita infection dynamics. Comparative transcriptome analysis identified differentially expressed genes (DEGs), and qRT PCR validated the expression patterns of 12 selected DEGs. A total of 9,673 DEGs were identified, with Stage 2 representing a critical period for distinguishing the infection-responsive patterns between the two cultivars. KEGG enrichment analysis revealed a dominant “Plant-pathogen interaction” pathway in resistant cultivar, while the susceptible cultivar showed enriched “Plant hormone signal transduction” and “Circadian rhythm - plant” pathways. qRT PCR confirmed DEG expression consistency with RNA-seq, and the shared phenylpropanoid biosynthesis pathway in both cultivars showed significant DEG expression divergence at Stage 2. The results indicate that the phenylpropanoid biosynthesis pathway exhibits cultivar-specific responses to nematode infection and potential roles in tomato resistance. This study provides a theoretical foundation forelucidating the molecular mechanism of tomato resistance to M. incognita , and a scientific basis for screening RKN-resistant tomato germplasm resources.