Transcriptome analysis of a compatible response by Glycine max to Phakopsora pachyrhizi infection

Soybean is one of the top five agricultural products in the United States. Soybean rust is caused by the obligate fungus Phakopsora pachyrhizi Sydow, an exotic pathogen in the U.S. Extensive screening of soybean germplasm has not identified soybean with resistance to all of the different isolates of soybean rust. A biotechnological approach may help to understand the plant host response at the molecular level and subsequently broaden resistance of soybean to this fungus. Using laser capture microdissection, we isolated susceptible soybean palisade and mesophyll cells showing signs of infection, extracted the RNA and performed transcriptome profiling. A total of 2982 genes were found to be differentially expressed, of which 685 were up-regulated, and 2297 were down-regulated. Eighty-eight percent of our regulated genes are unique to our time-point and our palisade cells. Gene expression data was overlaid on Kyoto Encyclopedia of Genes and Genomes biochemical pathways. In general, up-regulated genes were associated with basic defense while down-regulated genes were associated with many metabolic pathways. These results demonstrate that soybean rust strongly affects plant metabolism at the latest stage of infection and that the plant futilely fights even at the end of the infection process to establish a resistance response.