Abstract
Background: Soybean downy mildew (SDM), caused by the obligate parasite Peronospora manshurica (Pm), is a global fungal disease that significantly reduces soybean yield and quality by inducing early leaf drop and decreasing both 100-seed weight and seed oil content. Therefore, investigating the molecular mechanisms underlying early resistance to Pm infection in soybean, along with its key regulatory networks, is of paramount importance for developing effective strategies to combat Pm invasion. Results: This study employed transcriptome sequencing at six time points before and after Pm inoculation in a highly resistant (HR) soybean accession, Jiaohe xiaoheidou (JH), and a highly susceptible (HS) accession, Jilin 5 (JL). Differentially expressed genes (DEGs) in both accessions were assigned to 58 transcription factors (TFs) families, including the v-myb avian myeloblastosis viral oncogene homolog (MYB), WRKY domain-containing transcription factor (WRKY) and basic leucine zipper (bZIP). The mitogen-activated protein kinase (MAPK) signaling pathway-plant and plant-pathogen interaction was significantly enriched in both the transcriptome analysis and the blue module of weighted gene co-expression network analysis (WGCNA). Additionally, isoflavonoid biosynthesis was also enriched in the transcriptome analysis, while flavonoid biosynthesis and phenylalanine metabolism were enriched in the WGCNA blue module, both of which are associated with the phenylpropanoid metabolic pathway. Furthermore, six hub genes were identified within the specificity module of WGCNA. Conclusions: This study demonstrates that soybean resistance to Pm involves multiple TF families and diverse metabolic pathways. These findings provide novel insights into the molecular regulatory network governing soybean resistance to Pm and lay the groundwork for further investigation of the molecular mechanisms underlying SDM resistance.