The dominant lineage of Phakopsora pachyrhizi in the United States of America does not have a Brazilian origin

Asian soybean rust (ASR), caused by the obligate biotrophic fungus, Phakopsora pachyrhizi, was first reported in the continental United States of America (USA) in 2004 and over the years has been of concern to soybean production in the USA. The prevailing hypothesis is that P. pachyrhizi spores were introduced into the USA via hurricanes originating from South America, particularly Hurricane Ivan.

To investigate the genetic diversity and global population structure of P. pachyrhizi, we employed exome-capture based sequencing on 84 field isolates collected from different geographic regions worldwide. We compared the gene-encoding regions from all these field isolates and found that four major haplotypes are prevalent worldwide. Here, we provide genetic evidence supporting multiple incursions that have led to the currently established P. pachyrhizi population of the USA. Phylogenetic analysis of mitochondrial genes further supports this hypothesis.

Notably, we observed limited genetic diversity in P. pachyrhizi populations in Brazil, suggesting a clonal population structure in that country that contrasts to populations from the USA and Africa.

This study provides the first comprehensive characterization of P. pachyrhizi population structures defined by genetic evidence from populations across major soybean growing regions.