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Background  Phytophthora root and stem rot (PRR) of soybean, caused by  Phytophthora sojae , is controlled by  Rps  genes. However, little is known regarding the  Rps -induced molecular responses to  P. sojae  and how they actually overlap. We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique  Rps  gene/allele, and the susceptible parent Williams, pre- and post-inoculation with the pathogen.    Results  A total of 4,330 differentially expressed genes (DEGs) were identified in Williams versus 2,014 to 5,499 DEGs in individual NILs upon inoculation with the pathogen. Comparisons of the DEGs between the NILs and Williams identified incompatible interaction genes (IIGs) and compatible interaction genes (CIGs). Hierarchical cluster and heatmap analyses consistently grouped the NILs into three clusters: Cluster I ( Rps1-a ), Cluster II ( Rps1-b ,  1-c  and  1-k ) and Cluster III ( Rps3-a ,  3-b ,  3-c ,  4 ,  5 , and  6 ), suggesting an overlap in  Rps -induced defense signaling among certain NILs. Gene ontology (GO) analysis revealed associations between members of the WRKY family and incompatible reactions and between a number of phytohormone signaling pathways and incompatible/compatible interactions. These associations appear to be distinguished according to the NIL clusters.    Conclusions  This study characterized genes and multiple branches of putative regulatory networks associated with resistance to  P. sojae  in ten soybean NILs, and depicted functional “fingerprints” of individual  Rps -mediated resistance responses through comparative transcriptomic analysis. Of particular interest are dramatic variations of detected DEGs, putatively involved in ethylene (ET)-, jasmonic acid (JA)-, (reactive oxygen species) ROS-, and (MAP-kinase) MAPK- signaling, among these soybean NILs, implicating their important roles of these signaling in differentiating molecular defense responses. We hypothesize that different timing and robustness in defense signaling to the same pathogen may be largely responsible for such variations.

Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics