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Identification of Novel Strain-Specific and Environment-Dependent Minor QTLs Linked to Fire Blight Resistance in Apples

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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 “Florina” and “Co-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.

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We thank Philip Forsline, formerly with the USDA-ARS Plant Genetics Resources Unit, Geneva, NY, for providing GMAL4593 grafted trees. We also thank Roger Lewis, Wilbur Hershburger, Daniel Silverman, and Trevor Parton of the USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV and Herbert Gustafson of the Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Geneva, NY for their expert technical assistance.


This work was funded in part by the Washington Tree Fruit Research Commission, Wenatchee, WA ( project AP-08-804 “Mapping Malus sieversii: A valuable genetic resource for apple breeding,” project CP-10-101 “Fire blight resistance in Malus sieversii for scion breeding,” and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch project accession number 1011771.

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Correspondence to Awais Khan.

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Desnoues, E., Norelli, J.L., Aldwinckle, H.S. et al. Identification of Novel Strain-Specific and Environment-Dependent Minor QTLs Linked to Fire Blight Resistance in Apples. Plant Mol Biol Rep 36, 247–256 (2018).

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