Differential host responses of sugarcane to Colletotrichum falcatum reveal activation of probable effector triggered immunity (ETI) in defence responses

The complex polyploidy of sugarcane genome and genetic variations in different cultivars of sugarcane remain a challenge to identify and characterise specific genes controlling the compatible and incompatible interactions between sugarcane and the red rot pathogen, Colletotrichum falcatum. To avoid host background variation in the interaction study, suppression subtractive hybridization (SSH)-based next-generation sequencing (NGS) technology was used in a sugarcane cultivar Co 7805 which is compatible with one C. falcatum pathotype but incompatible with another one. In the incompatible interaction (ICI-less virulent) 10,038 contigs were assembled from similar to 54,699,263 raw reads, while 4022 contigs were assembled from similar to 52,509,239 in the compatible interaction (CI-virulent). The transcripts homologous to CEBiP receptor and those involved in the signalling pathways of ROS, Ca2+ , BR, and ABA were expressed in both interaction responses. In contrast, MAPK, ET, PI signalling pathways and JA amino conjugation related transcripts were found only in ICI. In temporal gene expression assays, 16 transcripts showed their highest induction in ICI than CI. Further, more than 17 transcripts specific to the pathogen were found only in CI, indicating that the pathogen colonizes the host tissue whereas it failed to do so in ICI. Overall, this study has identified for the first time that a probable PAMP triggered immunity (PTI) in both responses, while a more efficient effector triggered immunity (ETI) was found only in ICI. Moreover, pathogen proliferation could be predicted in CI based on transcript expression, which were homologous to Glomerella graminicola, the nearest Glade to the perfect stage of C. falcatum (G. tucumanensis).

Automated summary

The complex polyploidy of sugarcane genome and genetic variations in different cultivars of sugarcane pose a challenge in understanding the interactions between sugarcane and the red rot pathogen. This study used advanced sequencing technology to investigate the genetic responses in compatible and incompatible interactions. The results showed different gene expression and signaling pathways in the two interactions, suggesting the involvement of different immune mechanisms. This study also identified potential genes related to pathogen proliferation and colonization in the host tissue.