Transcriptome Analysis of a Wild Eggplant Germplasm M239 in Response to Verticillium dahliae Infection

Abstract

In this study, wild eggplant germplasm No. M239, which is highly susceptible to Verticillium wilt, was used as the experimental material. The physiological and biochemical indices (SOD, PAL, MDA and soluble protein) of M239 roots were measured at different times (0, 12, 24, 36, 48, 60 and 72 h) post inoculation with Verticillium dahliae, and the key time points for the M239 response to Verticillium wilt infection were screened. Then, RNA-Seq technology was used to screen the differentially expressed genes (DEGs) in M239 roots at 0, 12 and 48 h post-inoculation (hpi). The transcriptional results of M239 were also compared with those resistance genes from some reported wild relative Solanum species (S. sisymbriifolium and S. aculeatissimum). Then some DEGs were chosen for validation by qRT–PCR. The results showed that 12 and 48 hpi were the turning points in the changes in all physiological and biochemical indices. A total of 6,783 DEGs were identified by RNA-Seq, including 6,141 DEGs (3,046 upregulated and 3,095 downregulated) at the M_12 h vs. M_0 h, 1,903 DEGs (792 upregulated and 1,111 downregulated) at M_48 h vs. M_12 h, and 1,261 DEGs that appeared simultaneously in both stages. KEGG enrichment analysis showed that there were 5 metabolic pathways enriched from DEGs, which were mostly related to primary metabolism, such as glycolysis, amino acid and ribosome biogenesis. Compared with the NCBI non-redundant protein (NR) database, one Ve2 homologous gene and 8 PR protein-related genes were screened. Transcription factor analysis showed that there were a large number of DEGs, such as MYB, AP2-EREBP, bHLH, NAC and Orphans in the two stages. Compared with the reported Verticillium wilt-resistant wild eggplant species, it was found that there were fewer genes and enriched metabolic pathways in the M239 response to Verticillium wilt infection, and it also lacked the response of some known key resistance genes. These results proved that the above resistance genes and metabolic pathways played a key role in the wild eggplant response to V. dahliae infection.