Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references
PLoS ONE, ISSN: 1932-6203, Vol: 14, Issue: 1, Page: e0208614
2019
- 42Citations
- 55Captures
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Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
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Metrics Details
- Citations42
- Citation Indexes41
- 41
- CrossRef2
- Patent Family Citations1
- Patent Families1
- Captures55
- Readers55
- 55
Article Description
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.
Bibliographic Details
http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85059649347&origin=inward; http://dx.doi.org/10.1371/journal.pone.0208614; http://www.ncbi.nlm.nih.gov/pubmed/30615624; https://dx.plos.org/10.1371/journal.pone.0208614; https://dx.doi.org/10.1371/journal.pone.0208614; https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208614
Public Library of Science (PLoS)
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