Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: 5/1/2005
Publication Date: 5/1/2005
Citation: Alkharouf, N., Choi, J.J., Frederick, R.D., Matthews, B.F. 2005. Gene expression changes in soybean after infection with soybean rust (phakopsora pachyrhizi) [abstract]. BARC Poster Day. Paper No. 09.
Technical Abstract: Soybean rust (Phakopsora pachyrhizi) is a fast spreading and highly contagious fungal disease infecting soybean crops in Asia, Africa and more recently south and central America. Losses in yield of 10-80% have been reported in those regions. In late 2004 soybean rust was detected in parts of the southern and southeastern US. It is speculated that an outbreak of this disease in the US is imminent. An outbreak of this disease will have disastrous consequences to soybean farmers. The only effective means of management has been immediate fungicide application when the disease is first detected. This can be too costly to farmers however, and sometimes it isn’t applied early enough rendering the fungicide useless. Understanding gene expression changes in soybean as a result of infection by soybean rust is a first step in elucidating any soybean defensive genes and/or pathways that might be involved in this interaction. This information might be used later to develop an effective control of this pathogen. To this goal microarray experiments were conducted, measuring RNA transcript levels in soybean leaves over 4 time points ranging from 6 to 48 hours post infection (hpi). Over 6000 cDNA inserts were used in these experiments. Data were extracted from images using the software package Spot, and then normalized with the Lowess-print tip method using inhouse tools. Dye swaps were used to account for differential dye binding and a scaling algorithm was used to account for variation across slides. RNA from three independent biological samples was extracted and compared in this study. The results show an abundance of genes differentially expressed in soybean after infection with soybean rust. At 6 hpi genes involved in protein synthesis, signal transduction such as protein kinases, heat shock proteins, ribulose-1,5-biphospate carboxylase, sucrose synthase, and a number of unknown resistance genes were induced. At 12 hpi chalcone synthase, Metallothionein, polyubiquitin and cell wall proteins such as extensin were also induced. At 24 hpi we saw an induction of senescence associated proteins as well as microtubule associated proteins, and a large number of detoxification related proteins such as peroxidases. At 48 hpi stress and disease related proteins SAM22 and EDS1 were induced. A large number of differentially expressed genes are unknown however. Further functional characterization of these genes and others are important in understanding the defense response of soybean. Future plans include the use of laser capture microdisection to isolate only the cells in soybean leaves infected with the rust. The goal is to extract mRNA from those cells and measure localized gene expression changes. This is expected to provide a more concise picture of the molecular pathways and interactions occurring at the sites of infection specifically, as opposed to the whole root.