Differential gene expression in foxtail millet during interaction with the smut fungus Ustilago crameri

Foxtail millet smut disease, which is caused by the basidiomycetous fungus Ustilago crameri, has become a severe detriment to millet production. However, little is known about the molecular responses of foxtail millet to infection with U. crameri. In this article, we performed RNA-Seq to investigate transcriptional modulation in the resistant cultivar Jigu20 and the susceptible cultivar Changnong35. In total, 1712 and 1166 differentially expressed genes (DEGs) were identified in Jigu20 and Changnong35, respectively. Our results showed that the pathogenesis-related (PR) genes SiBGL and SiCHI responded positively to inoculation with U. crameri in both Jigu20 and Changnong35. The resistance (R) gene SiRPM1 and its downstream signaling molecules SiSGT1 and SiHSP were also dramatically upregulated upon smut infection in Jigu20. Moreover, we revealed that SiCDPK-SiRbohF-mediated reactive oxygen species (ROS) production might positively contribute to foxtail millet defense against U. crameri. Furthermore, we found that the phenylpropanoid pathway was activated upon smut infection. Taken together, our results suggested that SiBGL, SiCHI, SiRPM1, SiSGT1, SiHSP, SiCDPK, SiRbohF and SiPAL could act as potential candidates in foxtail millet to achieve resistance against smut.