Comparative Transcriptome and Targeted Metabolome Profiling Unravel the Key Role of Phenylpropanoid and Glucosinolate Pathways in Defense against Alternaria brassicicola in Broccoli.

() can cause a major yield and quality-limiting disease of called black spot, and the genetic resources conferring complete resistance against have not been identified to date. Here, comparative transcriptome and targeted metabolome analysis were performed utilizing a newly identified resistant (R) line and a broccoli susceptible (S) line at 6, 24, and 72 h post-inoculation (hpi). Kyoto encyclopedia of genes and genomes pathway enrichment and the weighted gene co-expression network analyses showed that the phenylpropanoid pathway regulates the resistance to in broccoli. One metabolite, cinnamic acid, was significantly upregulated in the _inoculated R line compared with the mock treatment but no significant difference in the S line, indicating that the cinnamic acid may cause the resistance difference between R and S lines. Our results also revealed that three indolic glucosinolates of I3G, 4MI3G, and 1MI3G were significantly increased in the _inoculated R line compared with the mock treatment, and some related genes were differentially expressed between the R and S lines. These results provided new insights into the mechanism of defense in and have laid a theoretical foundation for effectively utilizing resistant germplasm resources in broccoli breeding.