At the start of the last five growing seasons (April-May 2019-2023), Minnesota has been above historic average for soil moisture. Saturated soil conditions like these promote the development of a soil-borne, water mold pathogen known as Phytophthora, which attacks soybeans at all growth stages and causes significant yield losses. Together, these may have contributed to seedling emergence issues, damping off, and higher incidences of root and stem rots that have been observed in Minnesota (personal communication with Angie Peltier, David Kee, and Brett Arenz of the UMN Plant Disease Diagnostics Clinic). Phytophthora root and stem rot (PRSR) is caused primarily by Phytophthora sojae (Dorrance et al., 2007), a pathogen belonging to a group of organisms called oomycetes that are closely related to algae and exhibit fungal-like growth habits. They produce motile spores (zoospores) that can ‘swim’ towards roots in films of water in the soil and infect soybean roots. P. sojae is hence often referred to as water molds and are problems generally in water-logged or abnormally wet soils. There is also a second Phytophthora species that can cause PRSR: Phytophthora sansomeana. Dean Malvick has previously identified and surveyed this species in Illinois (Malvick et al., 2004). Although it is present in Minnesota, the current distribution and potential contribution of this species to PRSR is unknown in this state.
There are more than 50 pathotypes (variants) of P. sojae known in the U.S. (Dorrance et al. 2008). The main methods of management are to use soybean varieties that carry either (a) pathotype-specific resistance genes (Rps genes) that confer complete resistance, (b) genes that confer incomplete, partial resistance, (c) genes that confer both complete and incomplete resistance, or (d) effective ‘fungicides’ applied to seed (Matthiesen et al., 2021). In Minnesota, all forms of resistance have been deployed in modern soybean varieties. Ten years ago, when the last P. sojae population was surveyed in Minnesota (2012-2013), it was suggested that many fields were infested with P. sojae pathotypes that could be managed using soybean varieties carrying Rps8 or Rps3a genes, with the Rps6 gene also being somewhat effective (Dorrance et al., 2016). Commercial varieties with these resistance genes were new or uncommon at the time of that study, however. Dorrance et al. (2016) also showed increasing virulence on soybean varieties that carried Rps1 genes, and research in Iowa and Nebraska indicated that over 70% of isolates collected during the 2016-2018 field seasons were virulent on soybean varieties that carried Rps1c or Rps1k genes (Matthiesen et al., 2021).
Indeed, a new study suggests that Rps1a, Rps1c, and Rps1k (the most widely deployed Rps genes) are no longer effective in the U.S., Canada, and Argentina (McCoy et al., 2023). Even though this evidence demonstrates that many current soybean varieties being deployed may be ineffective against P. sojae, seed companies are still screening and testing these varieties in Minnesota. In 2021 and 2022, varieties carrying Rps1c or Rps1k each made up at least 20% of the varieties tested in each year (Lorenz et al., 2021; Lorenz et al., 2022). Many of the soybean varieties being commercially sold, therefore, might be ineffective against the P. sojae populations in soils across Minnesota. Rps-containing soybeans become ineffective because P. sojae can eventually defeat the resistance that the soybean host deploys. Upon root infection, P. sojae secretes Avr molecules to weaken soybean’s immune system. Soybeans, in response, deploy Rps molecules to disarm the effect of Avr, making Avr avirulent. Of note, the soybean Rps and P. sojae Avr must match in order for Rps to disarm Avr. For example, if P. sojae secretes Avr1c, soybean must counter it with Rps1c in order for complete resistance to be achieved. However, because P. sojae continues to gain in Avr complexity and continues to increase in pathotype diversity (McCoy et al., 2023), it is potentially ever more difficult to manage due to the unsuitable Rps-containing soybeans currently being deployed. By knowing the P. sojae population within a field, we would be able to predict which Rps genes could confer complete resistance.
In this proposal, our goal is to understand the P. sojae population in particular fields and region so that the appropriate Rps genes and varieties with high levels of partial resistance are deployed. Interestingly, Rps genes are not effective on other species of Phytophthora such as P. sansomeana. Thus, in addition to understanding the P. sojae pathotype profile, understanding the Phytophthora species profile is also important in fields where soybean is planted. Widely used methods for determining the P. sojae pathotypes in a field are time-consuming and have been known to produce inconclusive and inaccurate results (Dorrance, 2003; Lebreton et al., 2018). In recent research, Avr genes were sequenced and primers were developed to amplify the specific Avr genes that are present in P. sojae isolates (Dussault-Benoit et al., 2020 and Tremblay et al., 2021). In this proposed project, we will use this molecular method to detect which Avr genes are present in the P. sojae isolate. This will allow us to determine the pathotype of that isolate more rapidly and more accurately. AYOS, a Canadian-based company using this molecular method, has started to offer pathotyping and variety recommendations to growers as a private service. However, since this service has received few samples from Minnesota, we aim to validate this service as a tool for growers to make field-specific decisions on which resistant variety to deploy in their field. This proposal aims to provide guidance for soybean breeding programs and Minnesota farmers on Rps genes to manage PRSR, as well as provide information on the potential risk of P. sansomeana as a yield limiting soil-borne disease for which we do not have resistance tools.