Improper crop rotation may enrich soil‐borne pathogens of Panax notoginseng

Abstract Soil‐borne diseases are the main cause of yield reduction of Panax notoginseng (Sanqi), and are mainly caused by the enrichment of pathogenic fungi during continuous cropping. In the Wenshan district of Yunnan province, China, where Sanqi is widely cultivated, the rotation of Foeniculum vulgare (fennel) crops with Sanqi crops is assumed to help reduce occurrences of rot in Sanqi roots. However, in a field investigation, we found that this practice actually increased incidences of root rot in Sanqi crops. Using fennel plants obtained from the cropping system, we tested the hypothesis that fennel crops enriched communities of pathogenic fungi of Sanqi. We isolated six endophytic fungi from the roots of fennel plants and identified these based on their morphological characteristics and a sequencing analysis. The isolates were identified as Fusarium oxysporum (FV‐1‐R‐1, FV‐2‐R‐1), Alternaria alternata (FV‐3‐R‐1, FV‐14‐R‐1), Pyricularia grisea (FV‐8‐R‐1) and Colletotrichum truncatum (FV‐11‐R‐4). In a series of inoculation experiments, we verified the pathogenicity of these fungi to Sanqi based on Koch's postulates, and demonstrated that all isolates caused root rot in Sanqi. Our results suggest that fennel is an inappropriate crop choice for rotation with Sanqi because it may serve as an intermediate host for the pathogenic fungi that cause root rot in Sanqi, and thereby exacerbate crop diseases. Our empirical findings provide useful information for enhancing the cultivation of Sanqi and the practice of crop rotation.