Approaches Enabling Molecular Breeding of Sweet Cherry

Sweet cherry is an important horticultural crop in United States with a production value of $834 million in 2011. Breeding of sweet cherry is complicated by a prolonged juvenility stage that typically lasts several years and self-incompatibility of most varieties. Advances of genetic and genomic research in sweet cherry are critical to provide the knowledge base to facilitate effective molecular breeding. The Sweet Cherry Genome Sequencing Consortium has developed an early draft of this ~225Mb diploid genome. Sequencing data have been leveraged in both reference based mapping to the peach genome (2010) and de novo approaches. The reference mapping has identified several genes involved in ripening that appear to be non-functional in sweet cherry compared to their peach counterpart opening the door to potentially using these genes to predict ripening of sweet cherry varieties. The de novo obtained contigs have been shown to contain sequences with similarity to 96% of flowering related proteins from Arabidopsis demonstrating their utility.

In addition to genomic approaches, transcriptomic analyses have been developed that are useful for molecular breeding. From cDNA assemblies, 2200 single nucleotide polymorphisms (SNPs) were identified and developed into markers. These gene-based SNP markers were then utilized to determine genetic differences among a population of sweet cherry including differentiation of closely related varieties that are unresolved through the standard SSR markers. We have also developed a computer program, CisSERS, to expedite the conversion of SNPs into CAPS markers. Currently, RNA sequencing is being undertaken to identify candidate genes involved in the differential abscission zone development seen in current sweet cherry cultivars. Long term, this research is expected to facilitate gene based breeding for either stem-free cherries or stem-retaining cherries.