2018 ASHS Annual Conference

Breeding done by today’s apple breeders has been greatly improved by DNA-informed breeding techniques, such as marker-assisted selection. Marker-assisted selection uses DNA-based markers to identify parents and seedlings that have favorable allelic combinations. DNA-based markers are locus-specific tags that reveal polymorphism in DNA sequences. Markers are available for a range of traits including biotic stress resistances, productivity, and fruit quality. For efficiency in marker-assisted seedling selection, trait-predictive markers are usually run a few at a time on families as “DNA tests”, but genetic information about parents is needed first. SNP arrays have become a preferred platform for elite germplasm (cultivars, collection accessions, parents and selections). SNP arrays can provide much more genetic information on germplasm individuals than each DNA test is able to. Currently, SNP data in apple do not automatically provide trait locus genotypes, thus translation of SNP data into haplotypes that are associated with each trait locus allele is needed. This study aimed to associate SNP haplotypes with alleles of fruit quality trait loci of apple, as part of the RosBREED project. Haplotypes spanning trait loci in cultivars from 8K SNP array data were compared with alleles for these cultivars known from previous use of DNA tests or from characterized QTLs. Expected inheritance was confirmed across numerous generations and families. Allelic combinations of each germplasm individual were determined. This information enables breeders to understand the sources of jewels in their germplasm and efficiently reveals the genetic value of each breeding individual.