Why Wait for the Fruit? DNA-informed Breeding in Rosaceae: Prediction of Apple, Peach, and Sweet Cherry Skin Color as a Case Study

Much hype has been generated over the past 30 years regarding the potential positive impact of “molecular markers” on plant breeding. These “molecular markers”, more appropriately termed DNA tests, were expected to have substantial impact in tree fruit breeding, due to long juvenility periods, expensive phenotyping procedures, and space requirements. To date, there are few examples of successful application of DNA tests to enhance breeder decision confidence, termed DNA-informed breeding, for fruit quality traits in perennial crops. A limited number of reliable, predictive DNA tests for breeding-relevant traits is likely a major contributor to this failure to meet expectations. Due to recent dedicated efforts to develop such tools, specifically those of RosBREED and FruitBreedomics projects, the tree fruit breeding community is reaching a point at which this technology can begin to play a valuable role in the breeding process. DNA tests for the prediction of apple, peach, and sweet cherry fruit skin color are examples of some of the tools successfully developed and deployed for direct use in breeding programs. Based on genomic regions discovered by collaborators to be associated with anthocyanin-based fruit color traits, DNA tests were developed. In all three crops, the resulting simple sequence repeat tests differentiated alleles associated with various levels of red skin pigmentation. With the apple and peach tests, it is now possible to select parents with the genetic potential to produce high-blush seedlings and select seedlings predicted to have high-blush levels years before fruit evaluation if desired. In sweet cherry, blush and mahogany skin color are market-defining classes, each having different breeding targets and trait thresholds. Consequently, selecting parents that will produce seedlings of the desired class with the sweet cherry color DNA test can improve crossing outcomes. All three tests developed allow for the synergistic improvement of apple, peach, and sweet cherry fruit color, thanks in part to a conserved MYB10 genetic mechanism in each crop. In addition to the skin color DNA tests, tests are available for the prediction of other valuable fruit quality traits including apple and peach texture and flavor and sweet cherry size and maturity date. So, why wait for the fruit to select germplasm with genetic potential to produce superior quality fruit? With skin color and other fruit quality DNA tests now developed, apple, peach, and sweet cherry breeders are well equipped to take the leap into DNA-informed breeding.