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Seth D. Wannemuehler, James J. Luby, Chengyan Yue, David S. Bedford, R. Karina Gallardo and Vicki A. McCracken

Incorporating DNA-informed breeding techniques can improve selection efficiency for desired traits as compared with conventional breeding methods that do not use DNA-informed techniques. Incorporation of DNA technologies requires additional costs associated with reagents, equipment, and labor. To elucidate the cost-effectiveness of DNA-informed breeding in perennial crops with multiple years per generation, we conducted a cost–benefit analysis examining incorporation of marker-assisted selection (MAS), a type of DNA-informed breeding, applied to an apple breeding program. Annual operational costs for a midwest apple breeding program were used to develop a simulation with inputs including itemized costs and per unit costs for procedures at each breeding program stage. Simulations compared costs of MAS breeding techniques to conventional breeding methods to identify the break-even point (BEP) where cost-savings associated with MAS equals the accrued additional costs. Additional sensitivity analyses were conducted to examine changes in laboratory costs, seedling maintenance costs, and seedling evaluation costs. We found the BEP for this program occurs when MAS results in a removal rate of 13.18%, and changes to other costs (i.e., maintenance costs) result in a smaller percent decrease to the overall program budget. Our findings are useful to perennial crop breeding programs in which managers are considering incorporating DNA-informed breeding techniques.

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Seth D. Wannemuehler, Chengyan Yue, William W. Shane, R. Karina Gallardo and Vicki McCracken

Marker-assisted selection (MAS) use in breeding programs allows for examination of seedlings at an early stage before accumulation of high field costs. However, introducing MAS into a breeding program implies additional costs and uncertainties about effective incorporation. Previous simulations in apple (Malus ×domestica) have shown cost-effective applications of MAS. To further evaluate MAS cost-effectiveness in perennial crops, we conducted a cost-effectiveness analysis examining MAS in an upper midwestern U.S. peach (Prunus persica) breeding program. Breeding program procedures and associated costs were collected and used as input into spreadsheet-based simulations of the breeding program. Simulations compared a conventional breeding program to MAS with varying cull rates of low, medium, and high at multiple stages in the breeding cycle. Cost-effective MAS implementation was identified at the end of seedling trials with a break-even cull rate of 4%. These results inform breeders of cost-effectiveness of MAS use in a peach breeding program.

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Seth D. Wannemuehler, Chengyan Yue, Wendy K. Hoashi-Erhardt, R. Karina Gallardo and Vicki McCracken

DNA-informed breeding techniques allow breeders to examine individual plants before costly field trials. Previous studies with tree fruits such as apple (Malus ×domestica) and peach (Prunus persica) have identified cost-effective implementation of DNA-informed techniques. However, it is unclear whether breeding programs for herbaceous perennials with 1- to 2-year juvenile phases benefit economically from these techniques. In this study, a cost-benefit analysis examining marker-assisted selection (MAS) in a Pacific northwest U.S. strawberry (Fragaria ×ananassa) breeding program was conducted to elucidate the effectiveness of DNA-informed breeding in perennial crops and explore the capabilities of a decision support tool. Procedures and associated costs were identified to create simulations of the breeding program. Simulations compared a conventional breeding program to a breeding program using MAS with low (12.5%), medium (25%), and high (50%) removal rates, and examined different scenarios where MAS had diminishing power to remove individuals as selections reenter the breeding cycle as parent material. We found that MAS application under current costs was not cost-effective in the modeled strawberry program when applied at the greenhouse stage, but cost-effectiveness was observed when MAS was applied at the end of the seedling trials before clonal trials with a removal rate of 12.5%.