Decision support for cost-efficient and logistically feasible marker-assisted seedling selection in fruit breeding

Development of genetically improved new cultivars is expensive, especially for tree fruit which may take years for the organs of economic importance to appear for direct evaluation. A costly and time-consuming part of breeding programs is seedling selection, which involves identifying a few seedlings from among many thousands that have the genetic potential for desired performance levels. New DNA-based diagnostic tools exist that can assist with resource-use efficiency and prediction accuracy of seedling selection, the application of which is known as marker-assisted seedling selection (MASS). However, MASS by fruit breeders is not yet routine, partially because of the lack of decision support for identifying resource-efficient schemes. The MASS Efficiency Calculator version 1.0 described here can be used to model the costs and timing of a breeding program’s traditional operations and combine them with the costs and logistics of DNA testing operations to identify cost-efficient MASS schemes. With this tool, users can explore various possible scenarios to identify conditions in which MASS is predicted to increase cost efficiency—without the need for complicated hand calculations or de novo spreadsheet creation. Users can determine whether enough time will be available for integrating DNA testing into traditional operations. Demonstration of the spreadsheet technology identified logistically feasible and cost-efficient schemes for several scenarios described in an earlier study reported in 2001 with a more realistic complex breeding design modeled here. In these scenarios, up to 43 % of operational costs were predicted to be saved over the first 6–8 years of breeding program operations. These results indicated that MASS can often be very cost efficient, enhancing resource-use efficiency under typical breeding situations with even a single DNA test. When using multiple DNA tests, maximal cost efficiency can be achieved by deploying DNA tests in sequence rather than together. Even when up to 60 % of DNA test results must be disregarded due to technical issues such as failed DNA extractions, substantial savings in resource use can be realized if a high proportion of seedlings are culled. For long-juvenility crops such as apple and grape, breeders have considerable flexibility in choosing when to implement MASS during seedling production while still achieving increased cost efficiency.