Identification of pathogenic bacteria in saffron (Crocus sativus L.) by high‐throughput sequencing and the evaluation of the antifungal properties of different plant essential oils

Abstract BACKGROUND Saffron ( Crocus sativus L.), a Chinese herbal medicine of significant medicinal value, is extensively cultivated worldwide. However, fungal pathogen‐induced corm rot disease poses a major challenge to saffron cultivation, causing substantial economic losses and long‐standing concern among researchers and industry professionals. The presemt study aimed to accurately and rapidly identify Fusarium oxysporum f. sp. crocus (FOSC) as a crocus‐specific pathogen using high‐throughput sequencing technology. RESULTS High‐throughput sequencing successfully confirmed FOSC as the pathogen responsible for crocus corm rot, with subsequent tolerance gene predictions indicating its resistance to multiple antibiotics. Among eight tested plant essential oils, Cinnamomum cassia essential oil (CC‐EO) exhibited the strongest antifungal activity against FOSC. Cellular‐level investigations revealed that CC‐EO combats FOSC by compromising spore cell membrane integrity, inducing nuclear DNA fragmentation and promoting reactive oxygen species accumulation. CONCLUSION This study represents the first application of high‐throughput sequencing to identify the crocus‐specific FOSC, and demonstrates that CC‐EO holds significant potential for preventing and controlling saffron corm rot through its multi‐target antifungal mechanism. © 2025 Society of Chemical Industry.