Identification of marker-trait associations for resistance to Phytophthora root rot resistance in a genetic diversity panel derived from modern Chinese and Canadian germplasm

Objectives:

• Assemble a Genome Wide Association Study (GWAS) genetic diversity panel derived from modern Canadian and Chinese cultivars and their derivatives.
• Conduct a bioassay for Phytophthora Root Rot (PRR) on the diversity GWAS panel to generate phenotypic resistance data.
• Plant GWAS diversity panel lines in a PRR infected field to assess resistance under natural Phytophthora sojae populations.
• Use GWAS to identify novel marker-trait associations (MTA) and candidate genes for PRR resistance.
• Design Kompetitive Allele Specific PCR (KASP) markers for PRR resistance based on MTAs and candidate genes in their vicinity.
• Marker-assisted selection for PRR resistance using the novel KASP markers.

Expected Impacts:

• Phytophthora root rot (PRR) is the fourth most damaging disease in Ontario soybeans, causing a major loss of 807,000 bushels in 2021. At the current price of around $11/bu, this event represented $8.9 million in crop losses for Ontario soybean growers due to PRR alone. In more recent years, at least 550,000 bu have been lost due to PRR annually.
• The best control of PRR is through use of PRR resistant genes such as the Rps series of genes. However, due to selection pressure when growing soybean varieties, there is a constant need to identify and use novel genes for PRR resistance. This project aims to identify novel PRR resistance genes in exotic germplasm such as Chinese varieties that, when introgressed and deployed in future high yielding soybean varieties, will provide Ontario farmers with protection from yield losses caused by PRR disease.

Scientific Summary:

Pathotypes of the soil-borne oomycete pathogen Phytophthora sojae have been found in every soybean producing region. The pathogen is known to compromise yield by causing root rot, wilting, and stem lesions in infected plants. These symptoms characterize the disease Phytophthora root rot (PRR). The soybean industry currently relies on use of Rps (Resistance Phytophthora sojae) genes to manage losses on the pathotype level. New resistance genes must be employed every 6 to 15 years to prevent infection, as P. sojae populations will evolve to overcome the current resistance mechanisms. New sources of resistance are needed as the currently employed Rps1c and Rps1k were determined to be ineffective by McCoy et al. in 2023. Chinese germplasm may hold undiscovered resistance genes for PRR resistance as the germplasm is very diverse. Identifying marker-trait associations in a panel of Chinese and Canadian germplasm allows for a comprehensive evaluation of exotic germplasm while re-evaluating current cultivars for PRR resistance.

External Funding Partners:

The project was funded in part by the Ontario Agri-Food Innovation Alliance, a collaboration between the Government of Ontario and the University of Guelph.