title: Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.).
abstract: 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.
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt, Seeland, Germany. sang@ipk-gatersleben.de.
authors.forename: Sang
authors.initials: S
authors.lastname: He
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt, Seeland, Germany. zhao@ipk-gatersleben.de.
authors.forename: Yusheng
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt, Seeland, Germany. mette@ipk-gatersleben.de.
authors.forename: M Florian
authors.initials: MF
authors.lastname: Mette
authors.affiliation: KWS LOCHOW GMBH, D-29296, Bergen, Germany. Reiner.Bothe@kws.com.
authors.forename: Reiner
authors.initials: R
authors.lastname: Bothe
authors.affiliation: KWS LOCHOW GMBH, D-29296, Bergen, Germany. ebmeyer@kws-lochow.de.
authors.forename: Erhard
authors.initials: E
authors.lastname: Ebmeyer
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt, Seeland, Germany. sharbel@ipk-gatersleben.de.
authors.forename: Timothy F
authors.initials: TF
authors.lastname: Sharbel
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt, Seeland, Germany. reif@ipk-gatersleben.de.
authors.forename: Jochen C
authors.initials: JC
authors.lastname: Reif
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt, Seeland, Germany. jiang@ipk-gatersleben.de.
authors.forename: Yong
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D005787:Gene Frequency; D005819:Genetic Markers; D040641:Quantitative Trait Loci; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers