Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references

PLoS One. 2019 Jan 7;14(1):e0208614. doi: 10.1371/journal.pone.0208614. eCollection 2019.

Abstract

Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged as a popular technology for genetic and breeding applications in bread wheat (Triticum aestivum L.) and many other plant species. Although GBS can discover millions of SNPs, a high rate of missing data is a major concern for many applications. Accurate imputation of those missing data can significantly improve the utility of GBS data. This study compared imputation accuracies among four genome references including three wheat references (Chinese Spring survey sequence, W7984, and IWGSC RefSeq v1.0) and one barley reference genome by comparing imputed data derived from low-depth sequencing to actual data from high-depth sequencing. After imputation, the average number of imputed data points was the highest in the B genome (~48.99%). The D genome had the lowest imputed data points (~15.02%) but the highest imputation accuracy. Among the four reference genomes, IWGSC RefSeq v1.0 reference provided the most imputed data points, but the lowest imputation accuracy for the SNPs with < 10% minor allele frequency (MAF). The W7984 reference, however, provided the highest imputation accuracy for the SNPs with < 10% MAF.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromosomes, Plant / genetics
  • Gene Frequency / genetics
  • Genome, Plant*
  • Genotyping Techniques / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Hordeum / genetics*
  • Polymorphism, Single Nucleotide / genetics
  • Reference Standards
  • Triticum / genetics*

Grants and funding

This project is partly funded by US Wheat and Barley Scab Initiative and the National Research Initiative Competitive Grants 2017-67007-25939 to GB and 2017-67007-25929 to GB from the National Institute of Food and Agriculture, U.S. Department of Agriculture. Funders had no role in the study design, data collection and analysis, decision to publication, or manuscript preparation.