Comparative Transcriptome Analysis Reveals Potential Genes Conferring Resistance or Susceptibility to Bacterial Canker in Tomato

Abstract

Bacterial canker of tomato is a systemic disease caused by Clavibacter michiganensis (Cm), which poses a grave threat to tomato production worldwide. Towards the identification of genes underlying resistance to Cm infection, the transcriptome of the resistant inbred backcross line IBL2353 carrying the Rcm2.0 locus derived from Solanum habrochaites LA407 and the susceptible Solanum lycopersicum line Ohio88119 was comparatively analyzed after Cm inoculation, and the analysis focused on the genes with different expression patterns between resistant and susceptible lines. Gene ontology (GO) analysis revealed that top terms of differentially expressed genes comprised ubiquitin protein ligases, transcription factors, and receptor kinases. Then we screened out some genes which are potentially associated with the defense response against Cm infection in IBL2353 including the wall-associated receptor kinase-like 20 (WAKL20), and virus-induced gene silencing showed it contributes resistance to Cm infection. In addition to Cm-induced genes related to resistance, the expression of eight homologs from six susceptibility (S) gene families was analyzed. These putative resistance and susceptibility genes are valuable resources for molecular resistance breeding and contribute to the development of new control methods in tomato.

Keywords

• bacterial canker
• RNA-seq
• comparative transcriptome
• inbred backcross line