Crossing the finish line: how to develop diagnostic DNA tests as breeding tools after QTL discovery

DNA-informed breeding, the integration of DNA-based genetic information into plant breeding programs, can enhance efficiency, accuracy, creativity, and pace of new cultivar development. Most genetic knowledge on key traits for plant breeding has been obtained through QTL analyses. Despite an explosion in QTL discoveries for horticulture crops, very few of those discoveries have been translated into tools for horticultural crop breeding. An example of such tools with direct application in crop genetic improvement are trait-predictive DNA tests. The translation of a promising QTL to a trait-predictive “DNA test” has five steps: (1) choose target QTL; (2) design assay to target locus; (3) assay individuals; (4) trace inheritance; and (5) disseminate DNA test details. Key information to convey to end users about a DNA test are the crop and trait(s) addressed, targeted trait locus or loci, and marker type used; trait heritability and genotypic variance explained by the DNA test; allele effects, frequencies, and germplasm distributions; and technical details for running the test. This paper provides instructions for translating promising QTLs into breeder-friendly, trait-predictive DNA tests, based on our experience with tree fruit. Our intent is to accelerate development of trait-predictive DNA tests and establish a standard framework for reporting them. As scientific understanding of genetic factors controlling breeding-relevant traits continues to expand, systematic and increased DNA test development should help bridge the chasm between academic research and breeding application.