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Abstract
Phakopsora pachyrhizi causes Soybean Rust (SBR) on soybeans. SBR is a devastating foliar diseases of soybeans, causing yield losses of up to 50%. P. pachyrhizi could overcome common fungicides and adapt to the environment of the continental US. To better understand the behavior of P. pachyrhizi and determine effective management practices, this thesis investigates population structure and diversity of P. pachyrhizi in the Southeastern US. Genotype by sequencing was used to identify single nucleotide polymorphisms in 49 field isolates of P. pachyrhizi collected from four states over ten years (2008-2017). Two clusters of isolates were identified using K-means clustering, discriminant analysis of principal components, and a neighbor-joining tree. These clusters suggested two introductions of P. pachyrhizi into the US and two P. pachyrhizi genotypes are present in the Southeastern US. P. pachyrhizi isolates demonstrated moderate levels of genetic diversity, with no indications of major adaptations to the Southeastern US.