The 2012 ASHS Annual Conference

The use of a comprehensive germplasm set representing materials that breeders use is critical for efficiently enabling systematic and statistically robust validation and utility assessment of jewels in the genome (high value marker–locus–trait (M-L-T) associations). Therefore, at the onset of the RosBREED project, 12 demonstration breeding programs compiled relevant germplasm to constitute a “Crop Reference Sets” (CR Sets) for validation and utility assessment of M-L-T associations in each crop (apple, peach, strawberry, sweet cherry, and tart cherry). All data for the CR Sets will be archived on the Genome Database for Rosaceae and publicly available. In establishing each CR Set, breeding programs identified important breeding parents and traced their pedigrees. To efficiently represent the genomes of these key individuals, available progeny, intermediate ancestors, and founders were included. In addition to the CR Sets, additional Breeding Pedigree Sets (BP Sets) specific to each breeding program were established so that, together with the CR Sets, there was full representation of further important breeding parents. The CR and BP Sets have been phenotyped since 2010 for fruit quality traits and other critical traits using standardized phenotyping protocols developed by the breeding teams. SNP genome scans provided high-resolution genetic data that is being used to validate known M-L-T associations and identify new ones. Genetic tests for several reported M-L-T associations in each crop were fast-tracked through the validation and utility assessment process to demonstrate the use of reference germplasm sets. The visualization of pedigree, phenotypic, and genotypic data for these germplasm sets is enabled for any fruit and nut crop with the publicly available software, Pedimap.