Infrastructure that will be established for enabling routine marker-assisted breeding (MAB) pipeline consists of a transparent process of prioritizing breeding selection targets that is based on values and preferences from industry sectors and consumers to determine economic weights for traits and market segments (1), development of state-of-the-art crop-specific SNP genome scanning capability for breeding-relevant germplasm that exploits genomic connections among Rosaceae crops (2), and creation of a sustainable data management system with statistical, database, and decision support functionalities (3). Using this infrastructure, an eight-stage MAB Pipeline will be implemented that results in routine MAB in Rosaceae breeding programs (4). An Extension platform engages stakeholders – Rosaceae breeders and allied scientists, the next generation of breeders, producers/processors, marketing groups, trade organizations, and consumers (5).
ACTIVITY 1: Trait and Market Segment Breeding Target Establishment
Economic weights of traits will be determined from information on trait values from key market chain members. Information will be gained with a mix of survey research methods including one-on-one interviews and telephone surveys. Data will be collected for five crops: apple, peach, strawberry, tart cherry, and sweet cherry. Apple will be used as a model to test auction-based economic approaches and one-on-one interviews in which actual tasting of the fruit is required.
ACTIVITY 2: Genome Scans and Comparative Genomics
Develop individual SNP-based genome-scanning capability for each of the crops of apple, peach, strawberry, and cherry, at a resolution of at least one polymorphic SNP marker every 5 cM in any random cross, for use in Pedigree-Based Analysis. The majority of genes targeted for SNP development will be those shared among species, and specific cases of synteny will be exploited to leverage ancestral relatedness at the genomic level.
ACTIVITY 3: Pedigree-Based Breeding Information Management System
A common BIMS aligned with the PBA approach will be established for streamlined collection, archiving, analysis, and interpretation of integrated breeding and genomics data. Statistical programs, component databases, and decision-support tools will be incorporated into this broader BIMS framework, which will be hosted on the Genome Database for Rosaceae (www.rosaceae.org
). Core participating breeding programs will be the alpha-testers for BIMS, ensuring practicality for the wider U.S. Rosaceae breeding community to which BIMS will be delivered. A step-wise process will introduce breeders to this data management system that will ultimately enable programs to leverage genomics advances for improved breeding efficiency.
: MAB Pipeline Implementation
An eight-stage MAB Pipeline will be implemented in core breeding programs by mobilizing Pipeline infrastructure established in activity 3. Implementation of all eight stages in core RosBREED breeding programs will fill the gap between available M-T associations and routine MAB. Core breeding programs will share a common focus of implementing MAB for fruit
Meetings and workshops will be conducted to engage, educate, and train Rosaceae breeders and allied scientists, producers/processors, marketing groups, and trade organizations on RosBREED’s socio-economics and genomics research and application. Extension programming will include short courses and hands-on computer training. Breeding trainees will be broadly trained in integrating breeding, genomics, and socio-economics for crop improvement. RosBREED personnel will actively participate in the eXtension Plant Breeding and Genomics CoP (PBG CoP; PBGworks 2009), and utilize this resource as a vehicle to create educational content for the larger community and public (via a Community of Interest, CoI). External evaluation of extension activities will provide feedback and prompt adjustments in activities.