Abstract：In order to explore the molecular response mechanism of pepper under infection of cucumber
mosaic virus and resistant genes related to this virus，the paper took susceptible material‘Qiemen’and
resistant material‘JJ101’as objectives，and conducted high-throughput transcriptome sequencing
on‘Qiemen’and‘JJ101’ before and after innoculation of CMV，and carried out studies on gene expression
and function by bioinformatics method．The results showed that by using RPKM to calculate gene expression
level，1 158 differentially expressed genes（DEGs）were screened out after ‘Qiemen’and‘JJ101’ were
inoculated with CMV．Among them，643 DEGs were enriched in Gene Ontology（GO）．Their functions
were mainly referred to enzyme activity，metabolic process and defense reaction，etc．While 287 DEGs could
be included into KEGG pathways，including plant pathogen interaction，plant hormone signal transduction，
etc. process．Studies discovered that pepper immunity to CMV was an extreme complicated and multi-pathway
coordinated process，jointly participated by protein metabolism，defense response，hormone regulation and the
other pathways，laying a theoretical foundation for further research on pepper resistant molecular mechanism．
