Genotype by sequencing SNP dataset for Malus domestica x Malus sieversii F1 populations GMAL4591 and GMAL4592

Fire blight, a bacterial disease caused by Erwinia amylovora, is the most
devastating disease of apples and a major threat to apple production. Most
commercial apple cultivars are susceptible to fire blight driving the need
to develop fire blight resistant cultivars. Although several major fire
blight resistance QTLs have been identified from wild species of Malus,
the challenges of breeding apples due to long juvenile phase and
heterozygosity greatly limit their use. M. sieversii, the primary
progenitor of domesticated apples, is one of the wild Malus species that
is sexually compatible with M. domestica and has some favorable fruit
quality traits. In this study, we performed QTL analysis on two F1 apple
populations of M. domestica cv. ‘Royal Gala’ × M. sieversii (GMAL4591 and
GMAL4592) to identify fire blight resistance QTL. Parental linkage maps
were constructed for each family using marker sets of approximately 20K
GBS-SNPs. Phenotype data was collected from parents and progeny through
controlled fire blight inoculations in the greenhouse for two subsequent
years. A significant (P < 0.0001) moderate-effect fire blight
resistance QTL on linkage group 7 of GMAL4591 was identified from the
paternal parent M. sieversii ‘KAZ 95 17-14’ (Msv_FB7). Msv_FB7 explains
about 48–53% of the phenotyping variance across multiple years and time
points. Additionally, a significant (P < 0.001) minor effect QTL
explaining 18% of the phenotypic variance was identified in population
GMAL4592 on LG10 from ‘Royal Gala’. We developed diagnostic SSR markers
flanking the Msv_FB7 QTL to use in apple breeding. These findings have the
potential to accelerate the development of fire-blight-resistant
cultivars.