Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with ‘Honeycrisp’ being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. ‘Honeycrisp’ inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent ‘Frostbite’. The highly resistant IBP ‘Enterprise’ had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.
Fire blight (Erwinia amylovora), a potentially devastating disease in apple, can cause floral, fruit and structural damage and even tree death. Most commercial apple cultivars are susceptible and the resistance/susceptibility of many modern cultivars has not been evaluated. Fire blight resistance/susceptibility is difficult to phenotype due to quantitative resistance, impacts of tree vigour and environment on susceptibility, and the erratic nature of the disease. Resistance/susceptibility levels were determined for 94 apple cultivars and important breeding parents. In 2016 and 2017, multiple actively growing shoots per tree (about three trees per cultivar) were challenged with E. amylovora Ea153n via a cut‐leaf inoculation method. Proportion of current season's shoot length blighted (SLB) was calculated for each shoot. To classify cultivar responses, estimated marginal SLB means were compared to four controls, representing highly susceptible (HS) to highly resistant (HR), via Dunnett's tests. Cultivar responses ranged from HS to HR with estimated marginal SLB means of 0.001–0.995 in 2016 and 0.000–0.885 in 2017. Most cultivars demonstrated similar resistance/susceptibility levels in both years (ρ = 0.657, P < 0.0001). K‐means clustering was used to classify cultivars into three resistance/susceptibility groups based on incidence, average severity (SLB), and maximum severity values (maximum SLB and age of wood infected). Sixteen cultivars were consistently moderately resistant (MR) to HR while the remainder ranged from HS to MR. An updated comparison of susceptibility of important cultivars is provided. Resistance/susceptibility information gained could be used to identify genetic loci associated with resistance/susceptibility and/or inform parental selection in apple scion breeding programmes.
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