Rosbreed's Marker-Assisted Breeding Pipeline

Translation of DNA information arising from genomics research into application in breeding is presently a bottleneck. RosBREED is a large-scale initiative seeking to bridge the chasm between genomics research and breeding programs, centered on breeders and ensuring they can capitalize on genomics discoveries and accelerating technological innovation. RosBREED’s translational approach is the establishment and implementation of a marker-assisted breeding (MAB) “pipeline” consisting of a series of connected stages. At one end, any available marker-locus-trait (M-L-T) associations are objectively prioritized for each breeding program using socio-economically derived relative economic weights. In the next stages, markers are adjusted to match available genetic screening services. Then, each marker is assessed for relevance to breeding germplasm using the Pedigree-Based Analysis approach, determining the distribution of functional alleles in potential parents. Information is used to inform crossing decisions, improving proportions of genetically superior seedlings. Cost-efficient and logistically feasible marker-assisted seedling selection schemes are identified and trialed on several thousand seedlings to cull those predicted to have poor performance potential. Finally, robust genetic tests are routinely integrated into breeding operations, while newly reported M-L-T associations enter the pipeline. In 2010, in addition to the establishment of infrastructure components to powerfully enable each pipeline stage in future years, two major activities are taking place: 1) twelve demonstration breeders will each fast-track the pipelining of several already reported M-L-T associations, up to the stage involving marker-assisted parent selection decisions; 2) RosBREED will coordinate establishment of reference germplasm sets across programs representing U.S. breeding stock, begin standardized phenotyping for high-impact traits, and genotype these sets with genome-wide SNP markers targeting fruit quality candidate genes. The database of this comprehensive phenotypic and genotypic information on key germplasm will serve as the reference resource for future genetic discovery and validation and will exploit homology among genomes of three fruit-bearing genera of Rosaceae: Malus (apple), Prunus (peach and cherry), and Fragaria (strawberry). The archived database is expected to stock the shelf with hundreds of promising predictive M-L-T associations for entry into the MAB pipelines of many Rosaceae breeding programs. Successful demonstration of the RosBREED approach will lead to technology transfer to the wider community of U.S. Rosaceae breeders and international partners, so that, ultimately, new cultivars with superior fruit quality will be efficiently delivered by a powerful breeding network mobilizing modern technologies and exploiting the full extent of Rosaceae’s genetic diversity.