Quantitative Trait Locus Mapping for Fire Blight Resistance in an F₂ Population of Malus fusca MAL0045 Uncovers Novel Resistance Loci

Several fire blight resistance loci in Malus genotypes map on different linkage groups (LGs) representing chromosomes of the domesticated apple. Prior genetics studies primarily focused on F(1 )populations. A strong resistance quantitative trait locus (QTL) explained up to 66% of phenotypic variance in an F(1 )progeny derived from crossing the highly resistant wild apple genotype Malus fusca MAL0045 and the highly susceptible apple cultivar 'Idared', which was previously mapped on LG10 (Mfu10) of MAL0045. Strains of the causative bacterial pathogen Erwinia amylovora, notably those that show a single nucleotide polymorphism in the avrRpt2EA effector protein sequence at position 156 (e.g., Ea3049), are more virulent and overcome some known fire blight resistance donors and their QTLs. However, MAL0045 is resistant to Ea3049 and Mfu10 is not overcome, but most of the F(1 )progeny were highly susceptible to this strain. This phenomenon led to the assumption that other putative resistance factors not segregating in the F(1 )progeny might be present in the genome of MAL0045. Here, we crossed F(1 )progeny together to obtain 135 F(2 )individuals. Facilitated by genotyping-by-sequencing and phenotypic assessments, we identified and mapped two novel resistance QTLs in these F(2 )individuals on LGs 4 and 15, which were not identified in the F-1. To our knowledge, these are the first resistance QTLs mapped in F-2 progeny in Malus. In addition, we report that neither MAL0045 nor Mfu10 is broken down by a highly aggressive U.S. strain, LA635, after analyses in the original F-1 individuals.