ARS | Publication request: Using Illumina mRNA-Sequencing to understand Glycine max-Phakopsora pachyhrizi interaction

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: April 15, 2011
Publication Date: N/A

Technical Abstract: Soybean is one of the top five agricultural products in the United States and is highly susceptible to soybean rust (SR), an exotic obligate fungus that arrived in the USA in 2004. We used mRNA-Seq by Illumina/Solexa to analyze gene expression pattern of the host and pathogen at different time points during infection. Over 6 million sequences were obtained for each time-point. DNA sequences were aligned to the soybean genome and soybean rust sequences. Tag counts were obtained for each gene and the expression of each gene was compared to the uninfected control. Expression levels of genes encoding enzymes were overlaid on biochemical pathway diagrams from the Kyoto Encylcopedia of Genes and Genomes to provide easier analysis of changes in pathways. For example, we found that genes involved in carbohydrate metabolism were generally down-regulated over the infection time-course. There were some exceptions, such as some genes involved in pyruvate and propanoate metabolism that were up-regulated at 7 hai, but decreased at 48 hai. However, by 240 hai many of these genes were up-regulated again. Genes encoding enzymes in the TCA cycle followed the same pattern but remained down-regulated at 240 hai. Such information may be use to develop new methods to broaden resistance of soybean to soybean rust.