Abstract: In order to investigate the mechanism of miRNA response to Botrytis cinerea in tomato，two JA deficient mutants def1 and spr2，and the wild type（Castlemart）plant had been used in this study. miRNA database were conducted following RNA-seq and bioinformatics analysis after B.cinerea inoculation on plant materials at 0 h and 48 h.The qRT-PCR was performed to examine the target miRNA and its predicted target gene expression levels.The results showed that JA defective mutants were more sensitive than wild type to B. cinerea. And H2O2 content was also lower compared to that of wild type. One hundred and thirty known miRNAs and 811 new miRNAs had been identified by RNA-seq，and 8 conserved miRNAs（Sly-miR156e-3p，Sly-miR166c-5p，Sly-miR171f，Sly-miR172b，Sly-miR319a，Sly-miR390b-5p，Sly-miR399b and Sly-miR482d-5p）showed different expression patterns which had been selected in 6 samples. Altogether 122 predicted target genes were obtained，and the expression level of 8 miRNAs and their target genes have been verified by qRT-PCR which showed consistent results with RNA-seq.Therefore，Sly-miR156e-3p，Sly-miR390b-5p，Sly-miR399b and Sly-miR482d-5p may involve in B. cinerea resistance through JA pathway.

Key words: tomato, microRNA, JA, mutant, def1, spr2, Botrytis cinerea