RosBREED Enables Marker-Assisted Breeding for Apple

U.S. apple breeders primarily target consumer-preferred traits of excellent texture, flavor, and appearance. The ability to retain superior fruit quality after storage, so that a year-round domestic supply of nutritious apples is available to the public, is a particular focus. Also considered are traits valued by industry sectors, especially suitability to local production environments. DNA information, if gathered, validated, deployed, and routinely used in breeding decision-making, offers the opportunity for apple genetic improvement to become more efficient and precise in delivering long-term solutions to industry challenges and consumer demands. The multi-institutional RosBREED project (www.rosbreed.org) is enabling such marker-assisted breeding (MAB) for apple. Major public apple breeding programs in Washington, Minnesota, and New York have united in this project to establish a comprehensive crop reference germplasm set of important breeding parents represented by about 500 popular cultivars, ancestors, breeding selections, and breeding populations. This material is connected through many pedigree linkages, which is characteristic of apple breeding germplasm and can be exploited via the statistical approach of Pedigree-Based Analysis. Pedimap software was used to visualize these pedigree connections, revealing unrealized fractions of shared genomes. Large-scale phenotyping and genotyping of this reference germplasm is underway. Standardized phenotyping protocols for apple fruit quality evaluation were conducted since the 2010 season. High-resolution SNP-based genome scans with an 8K array are providing an unprecedented view of cultivated apple genetic diversity, and, through association with phenotypic performance, functional variation for breeding program-specific predictive marker development. Genetic tests for promising trait targets were fast-tracked through RosBREED’s “MAB Pipeline”. Useful outcomes include verification of pedigrees and identification of some incorrect records, with deduction of likely pedigrees in some cases. Markers for fruit storability are assisting seedling selection in the Washington apple breeding program since 2010 to cull inferior seedlings prior to expensive field maintenance and evaluation. Most powerfully, DNA information is informing crossing decisions of U.S. apple breeders, bringing to bear available information to efficiently enrich the next generations of apples with the genetics for superior fruit quality.