I don't know what kind of molecular markers are you going to apply in your studies and what species are you going to analyse, but below I paste some exemplary studies which can be inspiration for you:
See also Michael Milgroom's excellent textbook: Population Biology of Plant Pathogens: Genetics, Ecology, and Evolution https://apsjournals.apsnet.org/doi/book/10.1094/9780890544525?mobileUi=0