GENOME SCANS

1. 2. Germplasm & Phenotyping TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT GDR, COMPARATIVE GENOMICS Socio-economics information GENOME SCANS Marker priorities Screening services Breeding markers MAB PIPELINING GERMPLASM CHOICE DNA information PBA: crop-wide STANDARDIZED PHENOTYPING New QTLs discovered PBA: breeding program Crossing scheme Efficient routine breeding operations Better fruit MAB PIPELINING Seedling selection scheme Trial MASS BREEDERS’ TOOLBOX DEVELOPMENT

2. Goals for Germplasm Sets • Crop Reference Set • ~480 individuals fruiting in 2010-2012 (cultivars, ancestors, founders, breeding lines, selections, and seedlings) • Genotype and phenotype data to be at www.rosbreed.org as community resource. Tart Cherry Germplasm Set Sweet Cherry Germplasm Set

3. Goals for Germplasm Sets • Breeding Pedigree Sets (BP Set) • ~100-300 extra plants for each breeding program that, together with the CR Set, allow full representation of Important Parents in that program • May remain proprietary with each breeding program; data-sharing improves power Apple Germplasm Set Peach Germplasm Set

4. Goals in Constructing Reference Germplasm Sets • Pedigree-linked individuals • Represent alleles of Important Breeding Parents • Each relative (offspring, ancestors and others) chosen to represent an Important Parent • Goal was >12.5 representation units (e.g. 25 F1 s) for statistical power • F1offspring, full-sibs, and Important Parents used for best genome coverage Strawberry Germplasm Set

5. Goals for Phenotyping • Identify critical fruit quality traits and other important traits • Develop standardized phenotyping protocols to enable data pooling across locations/institutions • Protocols available at www.RosBREED.org • “Fruit Evaluation” tab • Collect best possible data from 2010- 2012 RosBREED

6. RosBREED Cherry Phenotyping • Phenotypic data was collected in 2010. For the sweet cherry set, a subset of 2009 data from a subset of progeny individuals was also added. • In tart cherry our we have 32 phenotypic data columns

7. RosBREED Strawberry Phenotyping • BRS/CRS Planted at all locations • Phenotyping protocol in place • Main challenge is dealing with interrelated issues that are defined where the plants are grown: • Production systems: annual vs perennial matted row • Nursery plant sources: plug with chilling in field vs bareroot w/ chilling at high elevation vs green plant w/ chilling at high latitude or elevation • Market uses for fruit: fresh vs processed

8. RosBREED Peach Phenotyping • 470 accessions phenotyped in both CRS and BRS across three breeding programs: AR, CA and SC. • Additional TX & SC accessions will fruit first time in 2011 and be phenotyped. • Clean pedigree data – many missing or mislabeled pedigrees. • Consistent labeling of all samples for phenotyping and genotyping • All cultivars/accessions listed in peach pedigree file (Pedimap file) and present in demonstration breeders collections to be phenotyped at all sites to estimate environmental effect.

9. RosBREED Apple Phenotyping 792 individuals phenotyped Need to phenotype more individuals held at multiple locations (Pedigree connected or not to estimate environmental effects) Often insufficient fruit for both storage periods Labeling issues DigiTest machine issues