ORIGINAL PAPER Identification of Novel Strain-Specific and Environment-Dependent Minor QTLs Linked to Fire Blight Resistance in Apples Elsa Desnoues 1 & John L. Norelli 2 & Herb S. Aldwinckle 1 & Michael E. Wisniewski 2 & Katherine M. Evans 3 & Mickael Malnoy 4 & Awais Khan 1 # Springer Science+Business Media, LLC, part of Springer Nature 2018 Abstract Since its first report almost 200 years ago, fire blight, caused by the gram-negative bacterium Erwinia amylovora, has threatened apple and pear production globally. Identifying novel genes and their functional alleles is a prerequisite to developing apple cultivars with enhanced fire blight resistance. Here, we report 13 strain-specific and environment-dependent minor QTLs linked to fire blight resistance from a segregating Malus sieversii × Malus × domestica mapping population. Interval mapping at 95% confidence and Kruskal –Wallis analysis at P value = 0.005 were used to identify QTLs for three strains of E. amylovora differing in virulence and pathogenicity. The QTLs identified explain a small to moderate part of resistance variability, and a majority was not common between years or E. amylovora strains. These QTLs are distributed in eight linkage groups of apples and comparison of their map position to previously identified fire blight resistance QTLs indicates that most are novel loci. Interaction between experimental conditions in the greenhouse and field, and between years, and differences in virulence levels of strains might be responsible for strain- and year-specific QTLs. The QTLs identified on LG10 for strain Ea273 in 2011 and strain LP101 in 2011, and on LG15 for strain LP101 could be the same QTLs identified previously with strain CFBP1430 in cultivar BFlorina^ and BCo-op16 × Co-op17^ mapping population, respectively. We discuss the potential impact of newly identified minor fire blight QTLs and major gene-based resistance on the rate of mutation in pathogen populations to overcome resistance and durability of resistance. Keywords Fire blight . Erwinia amylovora . Malus domestica . Host resistance . QTL mapping . Durable resistance Introduction New apple cultivars are constantly needed for optimal perfor- mance under changing biotic and abiotic stresses and to meet market demands. Identification of novel genes and their func- tional alleles is essential to breed cultivars with enhanced dis- ease resistance. A wide variety of bacterial diseases cause significant economic loss to fruit growers throughout the world (Harshman et al. 2017); of these, fire blight, caused by the gram-negative bacterium Erwinia amylovora, is a par- ticularly devastating disease of pome fruits, mainly apples and pears (Norelli et al. 2003a). In the USA alone, the economic damage of fire blight to the apple industry was estimated at over $100 million annually through blossom, shoot, or root- stock blight. The actual cost varies yearly and is difficult to estimate due to the recurring cost of sprays and pruning of infected parts, and the multi-year impact of tree and orchard loss. Since its first report in the Hudson Valley, New York almost 200 years ago, fire blight has spread from North America to Europe, western Asia, northern Africa, and New Zealand (van der Zwet et al. 2012). Some preventive mea- sures, including pruning of infected plant parts, restricted movement between infected orchards, and use of antibiotics in combination with fire blight prediction models, and Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11105-018-1076-0) contains supplementary material, which is available to authorized users. * Awais Khan mak427@cornell.edu 1 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA 2 Appalachian Fruit Research Station, USDA-ARS, 2217 Wiltshire Rd., Kearneysville, WV 25430, USA 3 Tree Fruit Research and Extension Center, Washington State University, 1100 N. Western Ave., Wenatchee, WA 98801, USA 4 Foundation Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, TN, Italy Plant Molecular Biology Reporter https://doi.org/10.1007/s11105-018-1076-0