Haplotype-based validation of genomic regions for breeding of new Nordic apples

When breeding apple cultivars for northern latitudes, early harvest and late flowering are desirable to manage the short growing season and ongoing climatic changes. Depending on the intended use, increased content of polyphenolic compound might be considered desirable (juice and cider) or undesirable (dessert). Thus, we phenotyped a total of 111, 189, and 88 apple genotypes for harvest date, flowering date, and peel concentration of procyanidin B2 (PRB2), respectively, across three Nordic locations in Sweden, Norway, and Finland. Using phased marker data from the 20 K apple Infinium^® SNP array we performed haplotype-based validation of previously described quantitative trait loci (QTL) intervals and genomic regions on Linkage Group (LG) 3 (harvest date), LG 9 and 12 (flowering), and LG16 (PRB2). We assessed the correlation between the traits and historical climate adaptation and identified haplotypes associated with increasing and decreasing effects for the three traits. These results are valuable for Marker Assisted Parent Selection in the Nordic breeding programs, as they support designing crosses to meet the demands of current and future climatic conditions, and fruit quality towards breeding of new dessert cultivars, or cultivars for juice or cider production.