Whole genome sequencing to decrypt the population structure and host-driven adaptation of Cercospora beticola in Germany

Authors: YANG, YIXUAN - International Institute For Sugar Beet Research; Wyatt, Nathan; MARTINEZ, ANA LAURA - North Dakota State University; Bolton, Melvin; VARRELMANN, MARK - International Institute For Sugar Beet Research; LIEBE, SABASTIAN - International Institute For Sugar Beet Research; LENNEFORS, BRITT-LOUISE - Dlf Seeds, Sro; KEUNECKE, HARALD - Kws Saat Ag; REINEKE, HEINRICH - Sesvanderhave; KOHLER, MARIA - Strube Research Gmbh & Co Kg

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/8/2026
Publication Date: N/A
Citation: N/A

Interpretive Summary: Cercospora leaf spot (CLS), caused by the fungal pathogen Cercospora beticola, is a destructive disease across global sugarbeet production regions. Understanding how plant pathogen populations change in response to planting new resistant crop varieties is important for effective management of crop diseases. In this study, we monitored Cercospora populations at four locations in Germany over three years using susceptible and resistant sugarbeet varieties planted at each location. We used whole genome sequencing and population genetic approaches to examine similarities and differences among the populations collected from each variety at each location across the three consecutive years. We observed that Cercospora populations were similar across the four locations but populations collected from susceptible and resistant sugar beet varieties showed the greatest differentiation. Specifically, the populations collected from the resistant sugar beet varieties showed reduced diversity, indicating that a strong selection pressure was filtering the population. We further observed that signatures of adaptation to the resistant sugar beet varieties could be found in population genomic analysis and these results indicate that Cercospora can rapidly adapt to resistant host varieties in just a few years. These results indicate that sugar beet resistant varieties may not be sufficient to manage CLS and an integrative pest management approach that incorporates fungicide applications and additional cultural practices is necessary. Since these resistant varieties are used in the U.S., this research will help American sugarbeet growers manage CLS.

Technical Abstract: Cercospora leaf spot (CLS), caused by Cercospora beticola, is the most destructive foliar disease of sugar beet. Management has relied heavily on fungicides, but widespread resistance emphasized the need for resistant varieties. To assess if and how varietal resistance shapes pathogen populations, we conducted a three-year field experiment at four locations in Germany using sugar beet varieties ranging from susceptible to highly resistant. Prior to the trial, local C. beticola populations were preserved on infected leaf materials for initial inoculation. Each season , infected leaves were collected separately per variety and location to serve as inoculum for the following year, maintaining variety- and location-specific pathogen populations under controlled selective conditions. A total of 900 isolates were subjected to whole-genome sequencing and population genetic analyses. Isolates collected in 2022 showed extensive admixture among locations. Equal mating-type ratios were observed in some populations but skewed in others, suggesting that sexual reproduction may occur locally. Location-specific re-inoculation preserved population continuity but did not produce detectable local adaptation. However, variety-specific re-inoculation revealed clear host-driven adaptation. Populations from one highly resistant variety formed two divergent lineages with reduced diversity and altered allele frequency spectra. Genome scans identified 26 candidate genes, including two putative effectors. These findings demonstrate rapid C. beticola adaptation to resistant varieties, highlighting the role of host-driven selection in resistance management.