Transcriptomic and metabolomic analyses reveal flavonoid pathways associated with the resistance of passion fruit to...

Fusarium solani-melongenae-induced stem rot poses a significant threat to passion fruit production. Therefore, the identification of resistant germplasm and disease resistance mechanisms is essential for enhancing disease management strategies. However, resistance mechanisms in passion fruit remain poorly understood. Therefore, in this study, we aimed to systematically assess the core resistance mechanisms of passion fruit to stem rot using multi-omics approaches and gene functional validation by virus-induced gene silencing (VIGS).

After screening 11 passion fruit varieties, we identified DN-2 as resistant and Mantianxing (MTX) as a highly susceptible variety, with lesion length in MTX being 2.9 times greater than in DN-2 at 9 days post-inoculation (dpi). Besides, DN-2 maintained superior photosynthetic performance compared to MTX. Physiological, transcriptomic and metabolomic analyses revealed that the resistance of DN-2 reflected a robust early antioxidant enzyme response and a marked activation of the flavonoid biosynthesis pathway. Notably, silencing three key flavonoid genes (Pe4CL9, PeANR1, and PeFLS5) significantly compromised resistance by increasing lesion lengths by 2.0-, 1.6-, and 1.3-fold, respectively, confirming that these genes positively regulate resistance to stem rot.

The flavonoid biosynthesis pathway serves as a key pathway underlying passion fruit resistance to F. solani-melongenae stem rot. The identification of the resistance genes Pe4CL9, PeANR1, and PeFLS5 provides molecular targets for breeding resistant cultivars, thereby improving the sustainable development of passion fruit production. © 2026 Society of Chemical Industry.