Genetic mapping reveals sophisticated responses of Malus domestica to Botryosphaeria dothidea isolates

Infection by the globally distributed pathogenic fungus Botryosphaeria dothidea (Moug.) Ces. et de Not. causes bot canker on the stems, branches and limbs or causes fruit ring rot (FRR) on the fruit in apple. To investigate the relationship between resistance to bot canker and FRR and among resistance mechanisms in response to different pathogen isolates, 34 major gene loci and six quantitative trait loci (QTLs) for bot canker and FRR resistance/susceptibility were genetically mapped on Malus genome using an F1 hybrid population (Jonathan × Golden Delicious) in 2008 and 2009. None of the QTLs for bot canker and FRR overlapped with the region of the major gene loci. Some of the FRR- and bot canker-associated loci either coincided or overlapped, and some were independent, suggesting that the responses of different organs to the pathogen would be correlated but might deviate from each other. Some major gene loci and QTLs associated with different pathogen isolates of bot canker or, FRR were mapped to different regions of the genome. The results indicated that not only did the resistance mechanisms differ between bot canker and FRR but also that genetic differentiation occurred among pathogen isolates.