Transcriptome and metabolome profiling reveals key pathways and metabolites involved in defense against Verticillium dahliae in upland cotton

Cotton is the main source of natural fiber in the textile industry, making it one of the most economically important fiber crops in the world. Verticillium wilt, caused by the pathogenic fungus Verticillium dahliae, is one of the most damaging biotic factors limiting cotton production. Mechanistic details of cotton defense responses to Verticillium wilt remain unclear. In this study, GFP-labeled strain of V. dahliae was used to track colonization in cotton roots, and clear conidial germination could be observed at 48 h post-inoculation (hpi), marking this as a crucial time point during infection. Transcriptome analysis identified 1523 and 8270 differentially expressed genes (DEGs) at 24 hpi and 48 hpi, respectively. Metabolomic screening found 78 differentially accumulated metabolites (DAMs) at 48 hpi. Conjoint analysis indicated that the phenylpropanoid biosynthesis pathway was activated in cotton infected with V. dahliae. Five metabolites in the phenylpropanoid biosynthesis pathway, including caffeic acid, coniferyl alcohol, coniferin, scopoletin and scopolin, could significantly inhibit the growth of V. dahliae in vitro, implicating their roles in cotton resistance to Verticillium wilt. The findings expand our understanding of molecular mechanisms underlying the defense response against V. dahliae infection in upland cotton, which may lead to further insights into controlling Verticillium wilt disease.