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

Sang He, Yusheng Zhao, Michael Mette, Reiner Bothe, Erhard Ebmeyer, Timothy F. Sharbel, Jochen C. Reif*, Yong Jiang

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Scopus citations

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.

Original languageEnglish (US)
Article number168
JournalBMC genomics
Volume16
Issue number1
DOIs
StatePublished - Mar 11 2015

Keywords

  • Association mapping
  • Elite wheat
  • Intensive simulation
  • Map-dependent imputation
  • Map-independent imputation
  • genomic selection

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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