ARS | Publication request: Using a next generation sequencing strategy to understand Glycine max-Phakopsora pachyhrizi interaction

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: March 23, 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 entered in the USA in 2004. Its biotrophic life style allows its host to survive but impairs its yield by diminishing the number of seeds per pod and decreasing the number of filled pods per plant. The limited amount of genetic information publicly available about this plant-pathogen interaction brings us to study expression of soybean and SR genes along a time line of the infection process. mRNA was extracted and isolated from soybean leaves 7, 48 and 240 hours after infection (hai) as well as right after inoculation of SR spores on soybean plant (time-zero). cDNA was synthesized and used as sequencing template in a deep sequencing strategy. Resulting sequences were aligned to the soybean genome, soybean gene expression was analyzed and the expression of genes encoding enzymes was overlaid on biochemical pathway diagrams from the Kyoto Encylcopedia of Genes and Genomes to provide easier analysis of changes in pathways. Sequences without homology to the soybean genome were assembled into contigs and homology searches against fungal databases were performed to identify these genes. Over 6 million sequences were obtained for each time-point. About two thirds of these sequences were confirmed as soybean genes. Most of the gene encoding proteins involved in carbohydrate, nucleotide, amino acid, lipid and terpenoid metabolisms were generally down-regulated while gene encoding proteins involved in energy and secondary metabolites were generally up-regulated over the infection time-course. Interesting exceptions include genes encoding proteins involved in pyruvate and propanoate metabolisms, wherein gene expression increased at 7 hai, decreased at 48 hai and increased again at 240 hai. Genes encoding transcription factors showed a tendency to be up-regulated at 7 or 48 hai depending on their family but they were always down-regulated at 240 hai. Most genes identified as SR were potentially new genes according to their absence of homology to public nucleotide and protein databases. Some of them shared typical characteristics of microRNA responsible of gene regulation in many eukaryotes. Some of the genes identified in this study may be use to develop new methods to broaden resistance of soybean to soybean rust.