Prediction of resistance, virulence, and host-by-pathogen interactions using dual genome prediction models

Authors: OWEN, HUDSON - University Of Florida; RESENDE, M - University Of Florida; MESSINA, C - University Of Florida; Holland, Jim - Jim; BRAWNER, J - University Of Florida

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2024
Publication Date: 8/6/2024
Citation: Owen, H., Resende, M., Messina, C., Holland, J.B., Brawner, J. 2024. Prediction of resistance, virulence, and host-by-pathogen interactions using dual genome prediction models. Theoretical and Applied Genetics. 137:196. https://doi.org/10.1007/s00122-024-04698-7.
DOI: https://doi.org/10.1007/s00122-024-04698-7

Interpretive Summary: Disease resistance in crops involves an interaction between host plants and infectious pathogens. Both host and pathogen genetics can impact the severity of disease, and interactions between specific host varieties and pathogen strains can also modify disease severity. Here, we measured disease symptoms of a large number of corn varieties in combination each with several fungal disease pathogen isolates. This allowed us to measure the relative importance of host genetics, pathogen genetics, and their interaction for disease severity, which turned out to be of similar magnitude. We showed that applying genomic markers to both host and pathogen permitted prediction of disease severity.

Technical Abstract: Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective.