Validation and marker development for a chromosome 2 QTL for fire blight resistance in pear

Abstract Fire blight, caused by the bacterial pathogen Erwinia amylovora , is a persistent problem for pear ( Pyrus spp.) growers across most production regions around the world. Growing resistant varieties is one of the best options for managing fire blight. The resistant P. communis cultivars ‘Potomac’ and ‘Old Home’, and the hybrid selection NJA2R59T69 were used in a previous study to identify quantitative trait loci (QTLs) linked to the resistance. The major chromosome 2 QTLs identified in the ‘Potomac’ and ‘Old Home’ sources overlap with QTLs that were previously identified in ‘Harrow Sweet’ and ‘Moonglow’, while that of NJA2R59T69 (through P. ussuriensis ‘Pai Li’) mapped to a nearby location on chromosome 2. In the current study, genes associated with disease resistance in the two chromosome 2 QTL regions were cloned in 23 accessions representing resistant and susceptible cultivars, and progeny from the three sources. Alleles unique to resistant cultivars in these genic regions were targeted by SeqSNP and used to genotype a diversity set of 382 pear accessions with known fire blight disease responses from multiple sources. Association mapping was conducted across subsets of the 382 accessions based on the shared fire blight resistance source. In the 48 accessions with the ‘Potomac’ source of resistance, association mapping identified a marker (Chr2_3601869) that was predictive with 80.8% and 96.0% accuracy in ‘Potomac’ and ‘Pai Li’, respectively. However, Chr2_3601869 was only 57.0% accurate in ‘Old Home’ derived accessions. This marker was converted to a PACE assay that was predictive in both ‘Pai Li’ and ‘Potomac’ -derived accessions but not ‘Old Home’-sourced resistance. Resistance appears to be dominant, with the majority of accessions being heterozygous at the Chr2_3601869 locus. A large proportion of resistant Asian accessions are homozygous for the resistance allele at Chr2_3601869, suggesting these may be excellent sources to introgress resistance. Future work should look to elucidate the critical recombination points within the three mapping populations to further refine the chromosome 2 resistance loci and determine which allele/haplotype corresponds to each unique source of fire blight resistance.