Identification of candidate genes associated with susceptibility to Stemphylium vesicarium in European pear (Pyrus communis L.)

Pear brown spot, caused by Stemphylium vesicarium, is a major constraint on pear production in several European regions, leading to recurrent yield and quality losses and increased costs due to intensive fungicide use and orchard sanitation. Since its emergence in the late 1970s, the disease remains difficult to manage because of the pathogen’s dual saprophytic–pathogenic lifestyle, multiple inoculum sources, and favourable epidemic conditions in modern orchards. Current management combines fungicide applications, sometimes guided by forecasting systems, with cultural practices to reduce inoculum. However, control is often insufficient under favourable weather conditions, and repeated fungicide use has promoted resistance to some active ingredients. Although pathogen biology and epidemiology have been widely studied, less attention has been given to host response, particularly the genetic basis of variable susceptibility among pear cultivars. A large region on chromosome 15 has been associated with susceptibility, but its size has hindered candidate gene identification and limited breeding for resistant cultivars. This doctoral thesis investigates the genetic basis of susceptibility to brown spot in European pear. QTL mapping confirmed and narrowed the Sv-locus on chromosome 15 through phenotyping of two segregating progenies and construction of dense linkage maps using Single Primer Enrichment Technology. A complementary genome-wide association study on a diverse panel of cultivars and local germplasm from Emilia-Romagna combined susceptibility data with Axiom 70K genotyping. Fine mapping with newly developed markers further refined the candidate region. Both QTL and GWAS identified a major susceptibility locus on chromosome 15. Fine mapping restricted this region to a 71.2 kb interval containing 12 annotated genes involved in redox regulation, protein homeostasis, carbohydrate metabolism, and signal transduction. Sequence polymorphisms and in silico expression analyses highlighted candidate genes, including one absent in the resistant cultivar ‘Williams’. These results advance understanding of pear brown spot susceptibility and support future breeding efforts.