Integrated Transcriptome and Metabolome Analysis Reveals Molecular Mechanisms Underlying Resistance to Root Rot.

Soybean production is significantly impacted by root rot (PRR), which is caused by . The nucleotide-binding leucine-rich repeat (NLR) gene family plays a crucial role in plant disease resistance. However, current understanding of the function of soybean genes in resistance to PRR is limited. To address this knowledge gap, transgenic soybean plants overexpressing the gene () were generated to elucidate the molecular mechanism of resistance. Here, transcript changes and metabolic differences were investigated at three time points (12, 24, and 36 h) after infection in hypocotyls of two soybean lines, Dongnong 50 (susceptible line, WT) and overexpression line (resistant line, OE). Based on the changes in differentially expressed genes (DEGs) in response to infection in different lines and at different time points, it was speculated that HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), valine, leucine, and isoleucine degradation, and phytohormone signaling may be involved in the defense response of soybean to at the transcriptome level by GO term and KEGG pathway enrichment analysis. Differentially accumulated metabolites (DAMs) analysis revealed that a total of 223 and 210 differential metabolites were identified in the positive ion (POS) and negative ion (NEG) modes, respectively. An integrated pathway-level analysis of transcriptomics (obtained by RNA-seq) and metabolomics data revealed that isoflavone biosynthesis was associated with disease resistance. This work provides valuable insights that can be used in breeding programs aiming to enhance soybean resistance against PRR.