THEORETICAL AND EMPIRICAL EVALUATION OF EFFICIENCY OF MARKER-ASSISTED SEEDLING SELECTION IN ROSACEAE TREE FRUIT BREEDING
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Most rosaceous tree fruit have long juvenility and large plant sizes, which makes traditional seedling selection (TSS), relying on phenotypic evaluation alone, time-consuming and expensive. Marker-assisted seedling selection (MASS) uses DNA markers to provide an early DNA-based evaluation of genetic potential of seedlings. A major challenge in conducting MASS for rosaceous tree fruit is a lack of knowledge of estimating relative efficiency of various MASS strategies compared to TSS. To overcome this challenge and help facilitate successful MASS in rosaceous tree fruit, this study evaluates key elements of MASS efficiency both theoretically and empirically. This study provides an assessment of the current applications, challenges, and perspectives of MASS in Rosaceae tree fruit breeding, investigates genetic gain from alternative seedling selection strategies through analytical derivation and stochastic simulation modelling, provides software tools to estimate the cost of using MASS, and evaluates the efficiency of applying a DNA test for apple acidity, crispness, and firmness in an apple seedling population. Theoretical evaluation of genetic gain suggests that marker-based strategies tends to achieve higher genetic gain than TSS for a trait where the proportion of genotypic variance explained by marker information is greater than the broad-sense heritability. The cost modeling pipeline and decision support tool provide a solution to streamlining cost estimation for complex MASS schemes. Empirical analysis shows applying DNA tests for apple acidity, crispness, and firmness in an apple seedling population achieved similar genetic gain and up to 13% cost savings compared to TSS, if genotyping costs are under $2 per sample. Results from this study provide rosaceous tree fruit breeders, for the first time, both guidance and tools for designing efficient MASS schemes.