Enabling Marker-Assisted Seedling Selection in the Washington Apple Breeding Program

Breeding new cultivars is a slow and expensive process, but genetic screening tools exist to improve efficiency. We employed the marker-assisted breeding (MAB) Pipeline approach to facilitate routine use of MAB in the Washington apple breeding program. This study traced the journey of one marker-locus-trait (M-L-T) association from publication through high-throughput PCR-based genetic testing to application. The final stages of the Pipeline involve determining cost-efficient highthroughput marker-assisted seedling selection (MASS) schemes with available genetic tests, followed by a trial run on several thousand seedlings. For maximum cost-efficiency in the Washington apple breeding program, genetic screening should be implemented prior to expensive grafting and field planting operations but usually after inexpensive visual culling for traits such as disease susceptibility. Routine MAB is now enabled for this tree fruit breeding program and we estimate that at least 60% of conventional operating costs for first-stage seedling selection could be saved using the available genetic test. INTRODUCTION Breeding new cultivars is slow, incurring huge operational costs for growing and maintaining inferior seedlings in the field. Although genetic screening tools exist that might reduce these costs, and are used to this effect in many crop plants, little is being applied to tree fruit breeding. The Washington apple breeding program focuses on better eating quality, where flavor and texture are primary targets for improvement, and is a typical program that would benefit from routine marker-assisted breeding (MAB). An initial requirement for MAB is the availability of trait-locus-marker (T-L-M) associations, which describe specific cases of genetic markers for loci controlling particular traits (Bliss, 2010). A multi-stage pipeline approach has been developed that addresses various considerations in converting reported T-L-M associations into routine marker-assisted breeding tools (www.rosbreed.org). The eight-stage “MAB Pipeline” is summarized as follows. First, available T-L-M associations are prioritized according to importance to the breeding program’s objectives. Second, efficient genetic screening methods are identified that allow ready access to the DNA information provided by the T-L-M association. Third, the originally reported genetic marker is adapted to available efficient genetic screening methods. Fourth, the TL-M association is validated in crop-wide germplasm. Fifth, utility of the T-L-M association is evaluated in breeding program-specific germplasm. Sixth, T-L-M association information for parent cultivars is considered for parent crossing decisions. Seventh, cost-efficiency and logistics of MASS in the breeding program is analyzed to identify efficient strategies. Eighth, a MASS trial use is performed in a high-throughput