# Population structure and genetic diversity of Phakopsora pachyrhizi in the Southeastern United States

## TL;DR

This study analyzes the genetic diversity of soybean rust fungus in the southeastern U.S., finding two distinct genotypes introduced in two phases.

## Contribution

The study provides new insights into the population structure and genetic diversity of Phakopsora pachyrhizi in the Southeastern U.S.

## Key findings

- Genetic diversity of Phakopsora pachyrhizi was low to moderately low with no evidence of sexual or parasexual recombination.
- Two genetically distinct groups of isolates were identified, associated with geographic regions in the Southeastern U.S.
- The findings suggest a two-phase introduction of the pathogen into the U.S., with one genotype overwintering in South Georgia and Florida.

## Abstract

Phakopsora pachyrhizi, the causal agent of soybean rust disease (SBR) on Glycine max (soybean), is considered one of the most globally devastating diseases of soybeans and is a particular problem in Brazil, China, Sub-Saharan Africa, and the southern United States. To better understand genetic diversity and epidemiological history of SBR in the United States, 49 P. pachyrhizi isolates collected from soybean fields in four Southeastern states (Alabama, Florida, Georgia, and Louisiana) from the 2008 to 2017 growing seasons were genotyped through restriction site-associated genotype by sequencing (GBS). Rarefaction analysis identified 54 informative SNPs among the P. pachyrhizi isolates. We found no evidence suggesting sexual or parasexual recombination, and measurements of genetic diversity were low to moderately low. Multiple different statistical approaches, including neighbor-joining trees, K-means hierarchical clustering, discriminant analysis of principal components, and principal coordinates analysis (PCoA) all identified two groups of P. pachyrhizi genotypes that associated with geographic location. One group was composed of isolates from south Georgia, and the other with isolates from Alabama, Florida, Georgia (excluding south Georgia), and Louisiana. Our results suggest that two genetically related but distinct genotypes were introduced to the continental United States in a two-phase introduction and overwinter in South Georgia and Florida. The first introduction of one genotype likely occurred in South Georgia in 2004 followed by a later introduction of a second genotype. One genotype remained in South Georgia while the other genotype became established through the Southeastern United States. Future studies are necessary to determine whether SBR in Brazil, China, or Sub-Saharan Africa shows similar patterns of genotype distribution and history or if the United States situation is unique.

Plant pathologists and plant breeders are the target audience for this research. This article provides insight into the genetic diversity and epidemiological history of Phakopsora pachyrhizi in North America that is necessary to effectively manage soybean rust. Forty-nine P. pachyrhizi isolates collected from soybean fields in four Southeastern states for nine growing seasons were genotyped through genotype by sequencing. Clary et al. demonstrated that P. pachyrhizi genetic diversity was low to moderately low, it spread to the Northeastern United States by one of two proposed methods, and the Southeastern United States can harbor new genotypes and generate new pathogenic races which may disperse from Florida and Georgia.