Marker-assisted backcrossing (MABC) is to date the most successful application of DNA markers in plant breeding. Nevertheless, the large-scale implementation of genome-wide background selection with DNA markers has lagged behind expectations due to the high costs of marker analysis. It has been hypothesized that this problem will be overcome by high-throughput (HT) marker assays which enable genotyping a high number of marker loci at comparatively low cost per individual marker data point. The optimum backcross designs for HT assays have previously not been investigated.The objective of the study was therefore the development of novel selection strategies for the efficient use of HT assays in different applications of MABC. For this purpose, computer simulations were employed.The cost-efficiency of HT assays compared to SM assays was greatest in short, highly intense backcross programs, while it decreased with increasing marker fixation in advanced backcross generations.The optimum breeding designs for SM assays were characterized by increasing marker densities and population sizes. The optimum breeding designs for HT assays were in contrast characterized by few backcross generations, constant marker densities and constant or decreasing population sizes.Combining SM and HT assays at different stages of a backcross program reduced the cost of marker analysis compared to using only HT assays.Using HT assays with a combined selection index for foreground and background selection reduces the logistic efforts and allows more differentiated selection decisions.It can be concluded that HT assays have the potential to increase the relative efficiency of background selection for many applications of MABC.
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