Pathotype Complexity and Genetic Characterization of Phytophthora sojae Populations in Illinois, Indiana, Kentucky, and Ohio

Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, has been managed with single Rps genes since the 1960s but has subsequently adapted to many of these resistance genes, rendering them ineffective. The objective of this study was to examine the pathotype and genetic diversity of P. sojae from soil samples across Illinois, Indiana, Kentucky, and Ohio by assessing which Rps genes were still effective and identifying possible population clusters. There were 218 pathotypes identified from 473 P. sojae isolates with an average of 6.7 out of 15 differential soybean lines exhibiting a susceptible response for each isolate. Genetic characterization of 103 P. sojae isolates from across Illinois, Indiana, Kentucky, and Ohio with 19 simple sequence repeat markers identified 92 multilocus genotypes. There was a moderate level of population differentiation between these four states, with pairwise F-ST values ranging from 0.026 to 0.246. There were also moderate to high levels of differentiation between fields, with pairwise F-ST values ranging from 0.071 to 0.537. Additionally, cluster analysis detected the presence of P. sojae population structure across neighboring states. The level of pathotype and genetic diversity, in addition to the identification of population clusters, supports the hypothesis of occasional outcrossing events that allow an increase in diversity and the potential to select for a loss in avirulence to specific resistance genes within regions. The trend of suspected gene flow among neighboring fields is expected to be an ongoing issue with current agricultural practices.

Automated summary

This study investigated the pathotype and genetic diversity of Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, in soil samples from Illinois, Indiana, Kentucky, and Ohio. The results showed that there was a moderate level of population differentiation between these states and also between fields within the same state. Cluster analysis detected the presence of P. sojae population structure across neighboring states. The findings support the hypothesis of occasional outcrossing events and highlight the potential impact of gene flow on resistance genes.