Introgressing blue mold resistance into elite apple germplasm by rapid cycle breeding and foreground and background DNA-informed selection

Apple blue mold causes significant postharvest economic losses worldwide. A blue mold resistance locus, qM-Pe3.1, was previously identified on chromosome 3 of Malus sieversii PI 613981, a wild accession with inferior fruit quality. Introgression of the resistance allele into elite breeding germplasm is difficult and success of introgression and the effect of the PI 613981 genome on fruit quality cannot be phenotypically evaluated until fruiting, which occurs approximately 5 years from seed. In this study, introgression of the qM-Pe3.1 resistance allele was achieved by rapid cycle breeding, utilizing the transgenic line T1190 constitutively expressing the BpMADS4 early-flowering gene. This was supported by DNA-based diagnostic information that enabled marker-assisted selection for blue mold resistance using a locus-specific DNA test developed to detect the qM-Pe3.1 resistance allele in offspring (foreground selection). Of 75 second-generation ([‘Gala’ × PI 613981] × T1190) offspring carrying BpMADS4, 43 also carried the qM-Pe3.1 resistance allele. DNA tests for other trait loci were used to identify other desirable alleles related to fruit quality in progeny and 6874 genome-wide SNP markers (from an apple 20K Illumina® SNP array) were used to identify undesirable genomic segments of PI 613981 (background selection). Three individuals identified with favorable recombination close to qM-Pe3.1 and less than 25% of M. sieversii unimproved genome were selected as best suited for the elimination of unimproved DNA segments in subsequent generations. Our pipeline for introgression of qM-Pe3.1, facilitated by marker-assisted foreground and background selection, successfully advanced this promising germplasm in readiness for the next generation.