A Cost–Benefit Analysis of DNA Informed Apple Breeding

Abstract

<jats:p>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.</jats:p>

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

“…To estimate the cost-effectiveness of DNA-informed breeding in perennial crops with multiple years per generation, RosBREED developed and applied a cost estimation tool to examine impacts from technology changes, in our case DNA-informed breeding, on three breeding programs 159 – 161 , springboarding from a previous RosBREED tool 162 . The decision-support tool, available on the GDR, utilized cost information for the entire breeding process from crossing to cultivar release to provide cost estimates of the effects of new management practices, high-throughput phenotyping, additional procedures, or other variations a breeder might consider for implementation in a program.…”

“…The decision-support tool, available on the GDR, utilized cost information for the entire breeding process from crossing to cultivar release to provide cost estimates of the effects of new management practices, high-throughput phenotyping, additional procedures, or other variations a breeder might consider for implementation in a program. For the apple breeding program studied 159 , the use of MASS to eliminate greenhouse seedlings prior to field planting was identified as cost-effective when a threshold of at least 25% of the seedlings is discarded. However, for the peach 160 and strawberry 161 breeding programs studied, MASS was determined to only be cost-effective at the end of the seedling stage when used to reduce the number of plants advanced to replicated clonal trials.…”

“…The UMABP began using DNA information for MAPS in 2012 after finding it was cost-effective. The costs for DNA testing for specific loci or whole-genome DNA profiling of parents were minimal (~$50 per parent) relative to the cost of growing inferior offspring to fruiting (more than $30 per seedling multiplied by hundreds to thousands of seedlings) 159 , highlighting the benefits of MAPS. The trait loci routinely targeted for MAPS include those posing phenotypic evaluation bottlenecks and accounting for a large proportion of culling in the seedling stage.…”

“…From 2017 through 2019, MASS was employed routinely to screen more than 15,600 seedlings, representing 30–70% of all available seedlings and 24–56% of families each year. Culling rates were 35–53% with a cost per culled seedling of $4.59–$7.94, depending on culling rates and the number of DNA tests employed 159 .…”

A DNA test for high incidence of soft scald and soggy breakdown postharvest disorders in Malus domestica Borkh

“…Use of this DNA test in parental selection could allow breeders to make more informed crossing decisions that avoid crosses that might result in seedlings with two HDI haplotypes. Parent selection can be especially useful when making crosses to produce very large numbers of seedlings, as the cost of screening seedlings increases with the size of a cross, while the cost of screening parents is a one-time expense (Wannemuehler et al 2019). Several generations of crossing will result in marker-trait linkage deterioration.…”