Functional Haplotypes for Fruit Firmness in Sweet Cherry using Pedigree-based Analysis

Maintaining sweet cherry textural quality, in particular firmness is of prime interest to the fruit industries as fruit softening during storage and transportation often results in poor quality fruit being delivered to markets and consumers. Texture maintenance has been partially achieved through an understanding of the importance of ‘optimum’ picking date and  the successful commercial application of postharvest technologies such as stringent cool-chain management and gibberellic acid application before harvest. Additionally, this objective can be met through the development of new cultivars that produce fruit with desirable firmness properties that can be maintained over long storage periods. Hence, fruit firmness is a high priority trait in the Pacific Northwest Sweet Cherry Breeding Program (PNWSCBP). To aid the breeding of firmer-fruited cultivars, we seek to understand the genetic control of fruit firmness. A total of 480 pedigree-linked individuals representing the U.S. sweet cherry Crop Reference Set and the PNWSCBP’s Pedigree Set were used in this study. Firmness was recorded in g/mm on each of five largest fruits harvested at physiological maturity from each individual over two seasons in 2010 and 2011, using a firmness tester. An Infinium array containing 6000 cherry single nucleotide polymorphism (SNP) markers was developed by the RosBREED project (www.rosbreed.org) to provide genome-wide markers for determining marker–locus–trait associations. The FlexQTL™ software was used to integrate both the phenotypic and genotypic data to identify QTLs underlying firmness variation in sweet cherry.  We identified three QTLs on linkage group 2, which mapped between 36.1 cM and 69.6 cM.  Functional haplotypes were then identified for these 3 QTLs combined for use in defining firm, medium-firm, and soft fruit. Because the QTLs were discovered and characterized in germplasm representing important breeding parents in U.S. sweet cherry breeding germplasm and the PNWSCBP with good statistical power, these functional haplotypes can be immediately deployed in the PNWSCBP for marker-assisted parent selection and marker-assisted seedling selection.