Stijn Vanderzande, Washington State University, Pullman, WA
Lichun Cai, Michigan State University, East Lansing, MI
David Chagné, The New Zealand Institute for Plant & Food Research Ltd, Palmerston North, New Zealand
Cassia Da Silva Linge, Clemson University, Clemson, SC
Margaret Fleming, Clemson University, Clemson, SC
Ksenija Gasic, Clemson University, Clemson, SC
Seonghee Lee, University of Florida, Wimauma, FL
Youngjae Oh, University of Florida, Wimauma, FL
Natalia Salinas, University of Florida, Wimauma, FL
Christopher Saski, Clemson University, Clemson, SC
Vance M Whitaker, University of Florida, Wimauma, FL
Jason D. Zurn, USDA-ARS NCGR, Corvallis, OR
Amy F. Iezzoni, Michigan State University, East Lansing, MI
Cameron Peace, Washington State University, Pullman, WA
Nahla Bassil, USDA-ARS NCGR, Corvallis, OR
DNA information has been suggested as a means to enhance accuracy, efficiency, creativity, and pace of new cultivar development in fruit breeding. To use DNA information, a thorough understanding of the genetic control of breeding-relevant traits is needed. A first, but by no means final, step towards such understanding is identifying genomic regions controlling the traits of interest. However, many studies do not pursue development of tools for DNA-informed breeding after the discovery of such genomic regions. Before DNA-informed breeding is possible, an identified genomic region must be translated into a trait-predictive DNA test. To perform this translational step, the RosBREED projects (2009-2019) developed a strategy that was applied across eight Rosaceae crops (apple, peach, sweet cherry, tart cherry, strawberry, pear, rose, and blackberry).
Here we present the strategy to develop DNA tests and the extensive set of DNA tests that have been developed, validated, and used in the RosBREED projects. The strategy for DNA test development involves designing assays to evaluate the region of interest, testing each assay on breeding-relevant individuals, tracing allelic inheritance, and disseminating assay details. Key points to include in the dissemination of the DNA tests are the target crop and trait(s) and targeted genomic region(s), marker type of the DNA test, proportion of phenotypic and genotypic variation explained by the DNA test, alleles identified by the DNA test and their effects, frequencies and distribution among common cultivars, and the technical details to run the DNA test. This strategy resulted in more than 50 developed or refined DNA tests and 17 DNA tests under development for key traits, including: fruit quality traits such as fruit texture, fruit flavor, fruit skin coloration, and fruit size; productivity traits such as bloom timing and cross-compatibility; and disease resistance against major pathogens for each crop. These DNA tests are now available to use in DNA-informed fruit breeding and have already been adopted by many Rosaceae breeding programs.
