Comparative transcriptome analysis of foxtail millet variety JG21 and resistant mutant unravels the key players associated with downy mildew resistance

Abstract Background Foxtail millet downy mildew, incited by the obligate parasite Sclerospora graminicola, represents a highly devastating disease for foxtail millet. The infection of Sclerospora graminicola frequently causes harm to budlets, leaves, and spikes of foxtail millet, thereby substantially influencing its quality and yield. Nevertheless, disease - resistant varieties can effectively reduce the vulnerability to pathogen attacks. Results In this study, we explored Jingu21 (JG21) and the resistant mutant rdm12, which was generated by ethyl methanesulfonate (EMS) mutagenesis. Phenotypic observations revealed that, in comparison with JG21, rdm12 did not display significant disparities in agronomic and quality characteristics. Significantly, rdm12 manifested disease resistance, accompanied by augmented activities of defense enzymes and elevated levels of osmoregulatory substances. Transcriptome analysis of rdm12 mutants and wild-type plants disclosed that the differentially expressed genes were predominantly enriched in pathways such as plant-pathogen interaction, MAPK signaling, phenylpropanoid biosynthesis, and glutathione metabolism signaling. The differential expression of several critical receptor protein kinase genes, WRKY transcription factors, pathogenesis - related (PR) proteins, calmodulin, glutathione S - transferase, and others endows the mutants with enhanced resistance to downy mildew. In particular, WRKY transcription factor 53 encoded by Seita.3G139400, pathogenesis-related protein PRMS encoded by Seita.3G175100and G-type lectin S-receptor-like serine/threonine protein kinase coded by Seita.7G095600, which have played an essential resistant role during the infection by S. graminicola. Conclusions Through this research, we identified the key genes, important products engaged in the resistance process, and their corresponding metabolic pathways, thus unravelling the resistance mechanism of foxtail millet against S. graminicola infection. These findings lay a theoretical groundwork for resistance screening in foxtail millet and the development of new varieties.