Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2014
Publication Date: 1/10/2014
Citation: Lin, F., Zhao, M., Baumann, D.D., Ping, J., Sun, L., Liu, Y., Zhang, B., Tang, Z., Hughes, E., Doerge, R., Hughes, T.J., Ma, J. 2014. Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics. Biomed Central (BMC) Genomics. DOI:10.1186/1471-2164-15-18. Interpretive Summary: Soybeans contains a number of genes that protect it from Phytophthora sojae, the pathogen that causes Phytophthora root and stem rot (PRR). Unfortunately, how these different genes, called “Rps” genes, work to protect soybeans remains largely unclear. Taking advantage of cutting-edge technology, we studied how soybean plants, each with one Rps gene, respond to pathogen attack at the molecular level. We were able to show that the Rps genes provide protection in one of three biochemical ways. These results will help pathologists understand how plants defend themselves against pathogen attack and will provide guidance to soybean breeders in developing soybean plants with multiple Rps genes, which will ultimately increase the duration of protection.
Technical Abstract: Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is effectively controlled by Rps genes in soybean. Rps genes are race-specific, yet the mechanism of resistance, as well as susceptibility, remains largely unclear. Taking advantage of RNA-seq technology, we sequenced the transcriptomes of 10 near isogenic lines (NIL), each with a unique Rps gene, and the recurrent susceptible parent ‘Williams’. A total of 4330 differentially expressed genes (DEGs) were identified in ‘Williams’ while 2075 to 5499 DEGs were identified in each NIL. Comparisons between the NILs and ‘Williams’ allowed classification of two major groups of DEGs of interest: incompatible reaction associated genes (IRAGs) and compatible reaction associated genes (CRAGs). Hierarchical cluster analysis divided 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). Heatmap analysis, along with gene ontology (GO) analysis suggested that the diversity between clusters is likely due to variation in the number of DEGs and the intensity of gene expression, rather than functional differentiation. Further analysis suggested that transcription factors might play a pivotal role in determining cluster pattern, and that members of the WRKY family were strongly associated with incompatible reactions. Analysis of IRAGs and CRAGs with putative functions suggested that the regulation of many phytohormone signaling pathways were associated with incompatible or compatible interactions with potential crosstalk between each other. As such, our study provides an in depth view of both incompatible and compatible interactions between soybean and P. sojae, which provides further insight into the mechanisms involved in host-pathogen interactions.