2019 ASHS Annual Conference

Most commercial apple cultivars are susceptible to fire blight, a bacterial disease caused by Erwinia amylovora that can cause structural damage and tree death. Current management practices are not effective against all disease stages and/or unsustainable. A potential long-term solution is breeding for resistance. Most resistance alleles found at quantitative trait loci (QTLs) associated with fire blight resistance/susceptibility have been identified in genetic backgrounds with poor fruit quality (e.g. Malus × robusta 5, ‘Evereste’). Although introgression of these resistance alleles is possible, improving fruit quality while maintaining resistance would be challenging due to apple’s long generation times and self-incompatibility. This study’s objective was to identify loci associated with fire blight resistance/susceptibility in a pedigree-connected apple reference germplasm set.

Developed during the USDA-SCRI RosBREED project, the pedigree-connected apple reference germplasm set provides efficient allelic representation of important breeding parents (IBPs) in the three US public apple breeding programs. In this study, 27 IBPs were represented in a planting of 556 individuals planted in triplicate in a randomized complete block design. All seedlings, parents and available progenitors were genotyped using the International RosBREED SNP (single nucleotide polymorphism) Consortium Apple 8K Infinium® array.

Using the cut-leaf method, multiple actively growing shoots per tree were inoculated with E. amylovora 153n in 2016 (5×10⁸CFU mL^-1) and 2017 (1×10⁹CFU mL^-1). For each inoculated shoot, the response to E. amylovora was quantified as proportion of current season’s shoot length that was blighted (SLB), calculated from shoot and lesion length measurements. Best linear unbiased predictors (BLUPs), adjusted by the overall SLB mean, were estimated for seedling effects within and across years. Adjusted BLUPs were used as phenotypic values in QTL analyses, which were done using FlexQTL^TM software.

Wide variation in fire blight resistance/susceptibility was observed among seedlings in both years, with responses ranging from highly susceptible to highly resistant; adjusted BLUPs ranged from 0.04 to 0.97 SLB. Most seedlings demonstrated similar levels of resistance/susceptibility in both years with a correlation of ρ = 0.75 (p-value <1 × 10^-4) between years for adjusted BLUPs. Putative QTLs associated with fire blight resistance/susceptibility were identified on chromosomes 6, 7, 8, and 15 in both years, which combined accounted for approximately 42% of phenotypic variation. The loci associated with fire blight resistance/susceptibility identified in this study may enable development of DNA tests, which will aid in more efficient pyramiding of disease resistance/susceptibility alleles and development of high-quality cultivars with lower fire blight susceptibility.