Identification of bloom date QTLs and haplotype analysis in tetraploid sour cherry (Prunus cerasus)

Bloom date is an important production trait in sour cherry (Prunus cerasus L.) as the risk of crop loss to floral freeze injury increases with early bloom time. Knowledge of the major loci controlling bloom date would enable breeders to design crosses and select seedlings with late bloom date. As sour cherry is a segmental allotetraploid, quantitative trait locus (QTL) analysis for bloom date was performed based on haplotype reconstruction by identifying the parental origins of marker alleles in sour cherry. A total of 338 sour cherry individuals from five F1 populations were genotyped using the cherry 6K Illumina Infinium® SNP array and phenotyped for bloom date in 3 years. A total of four QTLs were identified on linkage group (G)1, G2, G4, and G5, respectively. For these QTLs, 14 haplotypes constructed for the QTL regions were significantly associated with bloom date, accounting for 10.1–27.9% of the bloom date variation within individual populations. The three most significant haplotypes, which were identified for the G4 (G4-k), G2 (G2-j), and G1 (G1-c) QTLs, were associated with 2.8, 1.8, and 1.0 days bloom delay, respectively. These three haplotypes were also demonstrated to have additive effects on delaying bloom date for both individual and multiple QTLs. These results demonstrate that bloom date is under polygenic control in sour cherry; yet, pyramiding late blooming haplotypes for single and multiple QTLs would be an effective strategy to obtain later blooming offspring.