New markers for flowering-time selection in sweet cherry

Sweet cherry (Prunus avium L.) is a fruit tree in the Rosaceae family grown worldwide for its tasty fruit. However, its yield may be threatened in warmer growing regions by insufficient dormancy, which usually occurs in late-blooming genotypes. Conversely, in cold regions, the yield is threatened by late spring frosts, especially for early flowering cultivars. It is therefore necessary to breed cultivars adapted to local weather conditions and avoid potential crop losses. New markers associated with the beginning of flowering were sought to enable molecular marker-assisted selection of genotypes tailored for different climatic conditions. Previously whole-genome sequenced 298 sweet cherry genotypes with nine years of phenotypic evaluation provided the basis for a genome-wide association study that allowed the identification of 163 single nucleotide polymorphisms and indels associated with flowering time, located on all sweet cherry chromosomes. This study confirmed the previously predicted polygenic basis of the trait. Three markers suitable for selection of late-blooming genotypes and one for early-blooming genotypes were selected and validated using independent 128 sweet cherry hybrids from different crossings. Individual markers for late beginning of flowering were able to select genotypes flowering at least three days after the reference (i.e. the earliest flowering) cultivar 'Kisinevskaja'. Accumulation of preferred allele combinations for all three late-blooming markers has a synergistic effect, indicating delay of flowering 7.1 days after the reference cultivar on average. The marker for early beginning of flowering identified accessions flowering maximally five days after the earliest flowering reference cultivar 'Kisinevskaja'. All four markers were integrated into a single base extension assay to help breeders with prediction of beginning of flowering for their breeding materials and cultivars.