Soybean (Glycine max) is a major crop, serving as a staple for many parts of the world for human consumption and for domesticated animals. It is susceptible to the fungus Phakospora pachyrhizi which causes soybean rust, as you can see in this image.
It is of interest, therefore, to discover which genes convey resistance to this pathogen. There are two obvious ways to attack this problem. First, you could take two strains of Soybean, one (Hawaii 94-1) is resistant and one (Taiwan 80-2) is susceptible to the fungus, infect both and look for differences. The problem with this approach is that the two soybean strains might have a large number of differences which don't relate to their resistances.
In this case, therefore, the alternate approach is used; a single strain of Soybean is used and two strains of fungus: one infective and one not. As we have a single soybean genome, differences in gene expression following infection might be involved in the response to this infection.