Population and genome-wide association studies of Sclerotinia sclerotiorum isolates collected from diverse host plants throughout the United States

Authors: SHARMA POUDEL, ROSHAN - North Dakota State University; BELAY, KASSAYE - North Dakota State University; NELSON JR, BERLIN - North Dakota State University; BRUEGGEMAN, ROBERT - Washington State University; Underwood, William

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2023
Publication Date: 9/27/2023
Citation: Sharma Poudel, R., Belay, K., Nelson Jr, B., Brueggeman, R., Underwood, W. 2023. Population and genome-wide association studies of Sclerotinia sclerotiorum isolates collected from diverse host plants throughout the United States. Frontiers in Microbiology. 14. https://doi.org/10.3389/fmicb.2023.1251003.
DOI: https://doi.org/10.3389/fmicb.2023.1251003

Interpretive Summary: White mold caused by the fungal pathogen Sclerotinia sclerotiorum is a significant yield-limiting disease on many crop plants such as soybean, canola, dry edible bean, and sunflower. This pathogen is globally distributed and reproduces primarily by clonal propagation. However, previous reports have indicated moderate to high levels of genetic variation within populations of white mold and differentiation between populations from different geographic areas. This fungus causes disease by killing plant cells, resulting in expanding lesions on susceptible crop plants. Despite the economic impact of white mold on agriculture, relatively little is known about the mechanisms used by the fungus to infect host plants and cause disease. The goals of this study were to utilize a large and diverse collection of white mold isolates obtained from 25 host plants across 27 U.S. states to: 1) evaluate aggressiveness of diverse white mold isolates in causing stem lesions on two sunflower inbred lines; 2) assess the population characteristics of isolates from different regions and climate conditions; and 3) use a genetic mapping technique referred to as genome-wide association to identify candidate genetic factors controlling aggressiveness in causing disease on sunflower. This study identified isolates that were highly aggressive in causing stem lesions on tested sunflower lines and revealed significant differentiation between white mold populations collected from warmer regions of the U.S. compared to those from areas with colder winters. Additionally, this study identified potential genes associated with isolate aggressiveness that will be studied in depth in the future to provide new insights into the strategies used by this fungus to cause disease on host plants.

Technical Abstract: Sclerotinia sclerotiorum is a necrotrophic fungal pathogen causing disease and economic loss on numerous crop plants. This fungus has a broad host range and can infect over 400 plant species, including important oilseed crops such as soybean, canola, and sunflower. S. sclerotiorum isolates vary in aggressiveness of lesion formation on plant tissues. However, the genetic basis for this variation remains to be determined. The aims of this study were to evaluate a diverse collection of S. sclerotiorum isolates collected from numerous hosts and U.S. states for aggressiveness of stem lesion formation on sunflower, to evaluate the population characteristics, and to identify loci potentially contributing to isolate aggressiveness using genome-wide association mapping. We observed a broad range of aggressiveness among 219 isolates evaluated for stem lesion formation on two sunflower inbred lines, and only a moderate correlation between aggressiveness on the two lines. We performed genotyping by sequencing to identify single nucleotide polymorphisms among isolates and used these markers to assess population differentiation across hosts, regions, and climatic conditions. These evaluations revealed genetic differentiation between populations from warmer climate regions compared to cooler regions. Finally, we carried out a genome-wide association study of isolate aggressiveness and identified three loci significantly associated with aggressiveness. Functional characterization of candidate genes at these loci will likely improve our understanding of the virulence strategies used by this pathogen to cause disease on a wide array of agriculturally important host plants.