Comparative Transcriptomic Analysis Reveals the Underlying Mechanism of Piriformospora indica-Enhanced Root Rot Resistance in Gerbera hybrida

Gerbera hybrida, a model plant for studying the development and evolution of complex inflorescences, has been recognized as a valuable source of colorants and natural coatings. Previously, we demonstrated that inoculation with Piriformospora indica, an endophytic fungus, could enhance the resistance of gerbera to Phytophthora cryptogea, which causes root rot disease. Here, to dissect the underlying molecular mechanism, comparative transcriptomic analyses of gerbera roots from P. indica-colonized (PI), P. cryptogea-inoculated (PC), and P. cryptogea-inoculated P. indica-colonized (PP), along with the non-inoculated control (CK) groups were conducted. In total, we identified 15,763 differentially expressed genes (DEGs) among CK vs. PI, CK vs. PC, and PI vs. PP comparisons, together with PC vs. PP comparisons. Of them, 743 DEGs encode transcription factor (TF) proteins, with the AP2/ERF family members occupying the majority. An ERF gene (GhERF) was identified as one of the 30 common DEGs among the four comparisons. Notably, its transient overexpression in tobacco leaves reduced the lesion area caused by P. cryptogea inoculation to 65.36% of the empty vector control. Many defense response- and secondary metabolism-related DEGs were expressed higher in the PP group than in the PC group. Moreover, P. indica-colonization up-regulated the expression of hormone signaling- and MAPK signaling-related genes, thereby activating the defense responses against the pathogen infection. Our study is helpful for understanding the molecular mechanism underlying P. indica-enhanced root rot resistance in gerbera.