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Background  The main goal of our study was to investigate the implementation, prospects, and limits of marker imputation for quantitative genetic studies contrasting map-independent and map-dependent algorithms. We used a diversity panel consisting of 372 European elite wheat ( Triticum aestivum  L.) varieties, which had been genotyped with SNP arrays, and performed intensive simulation studies.    Results  Our results clearly showed that imputation accuracy was substantially higher for map-dependent compared to map-independent methods. The accuracy of marker imputation depended strongly on the linkage disequilibrium between the markers in the reference panel and the markers to be imputed. For the decay of linkage disequilibrium present in European wheat, we concluded that around 45,000 markers are needed for low cost, low-density marker profiling. This will facilitate high imputation accuracy, also for rare alleles. Genomic selection and diversity studies profited only marginally from imputing missing values. In contrast, the power of association mapping increased substantially when missing values were imputed.    Conclusions  Imputing missing values is especially of interest for an economic implementation of association mapping in breeding populations.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1366-y) contains supplementary material, which is available to authorized users.

Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.)