A study contain both population genomics and GWAS for some important agronomic traits.. Population genetic of fungicide resistance in the wheat head scab pathogen Fusarium graminearum

Fusarium graminearum is a ubiquitous pathogen of cereal crops that causes Fusarium head blight (FHB) on wheat. Genetic variation in F. graminearum can significantly affect the phenotype exhibited on the host, ie aggressiveness, amount of secreted mycotoxin (Desjardin 2006), or resistance to fungicides. The interaction between evolutionary forces and F. graminearum populations over time and space forms the pathogen population structure (McDonald and Linde 2002). Although considerable progress has been made in managing disease through crop rotation, tillage practices, and breeding for FHB resistance, fungicides (eg strobilurin, DMIs, or benzimidazoles) remain an indispensable measure to limit FHB severity and mycotoxin contamination. Fungicide resistance may be monogenic or polygenic. Monogenic resistance (qualitative) can build up rapidly in a population as found for strobilurins or benzimidazole. Polygenic resistance (quantitative) builds up slowly, making it difficult to distinguish between sensitive and resistant sub-populations, especially during the early stages of resistance development, as found for resistance to DMIs. To our knowledge, no studies have evaluated fungicide resistance in natural field populations of F. graminearum, and most reports to date have considered only a few isolates (eg 14 isolates; Klix et al. 2007), which is not sufficient to identify quantitative differences in resistance. However, resistance to both benzimidazole (carbendazim) and DMIs was reported in regional collections originating from many fields (118 isolates F. asiaticum and 41 isolates F. graminearum) (Yin et al. 2009). Genetic analyses of these isolates indicated that resistant isolates for each fungicide group clustered separately from non-resistant isolates. Using sub-lethal doses of DMIs, Becher et al. (2010) addressed the potential to identify different phenotypes, documenting high variation within each phenotype with regard to cross-resistance against other fungicides, aggressiveness, and mycotoxin production. Strobilurin resistance in Microdochium nivale, one of the causal agents of the Fusarium head blight complex, was found across France (Walker et al. 2009). Our main objective is to determine the distribution of resistance to three classes of fungicides within natural field populations of F. graminearum sampled across Europe. The rapidly decreasing cost of Next Generation Sequencing (NGS) will enable us to obtain genomic information across multiple populations. We will use the RAD seq technology coupled with bulk segregant analysis to identify candidate genes, and possibly specific point mutations, associated with fungicide resistance. Point mutations in the identified genes will be screened across the European landscape to establish a base-line for future monitoring of fungicide resistance across Europe