Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled byRps genes. However, little is known regarding the Rps-induced molecular responses to P. sojaeand 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.


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.


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 individualRps-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.


This is the publisher pdf of Feng Lin, Meixia Zhao, Douglas D Baumann, Jieqing Ping, Lianjun Sun, Yunfeng Liu, Biao Zhang, Zongxiang Tang, Elisa Hughes, Rebecca W Doerge, Teresa J Hughes, Jianxin Ma. Molecular Response to the Pathogen Phytophthora sojae Among Ten Soybean Near Isogenic Lines Revealed by Comparative Transcriptomics. BMC Genomics 2014, 15:18 (10 January 2014) and is available at: [insert doi url or url].


Comparative transcriptomics; Resistance to Phytophthora sojae; Soybean

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