ArticlePloS one2019
Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Article
- A haplotype-layered GWAS identifies a multi-trait grain mold resistance hub on sorghum chromosome 5.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Integration and imputation of GBS-derived and DArTseq-derived SNP markers in assessing genetic diversity of bread wheat genotypes.BMC genomics · 2026Article
- Identification of Iranian bread wheat with superior performance under well-watered and rain-fed conditions using linear selection indices.BMC plant biology · 2026Article
- Interchromosomal linkage disequilibrium analysis reveals strong indications of sign epistasis in wheat breeding families.G3 (Bethesda, Md.) · 2026Article
- Missing genotype imputation in non-model species using self-organizing maps.Molecular ecology resources · 2025Article
- Genome-wide association study (GWAS) uncovers candidate genes linked to the germination performance of bread wheat (Triticum aestivum L.) under salt stress.BMC genomics · 2025Article
- Genetic analyses and prediction for lodging‑related traits in a diverse Iranian hexaploid wheat collection.Scientific reports · 2024Article
- Novel SNP markers for flowering and seed quality traits in faba bean (Frontiers in plant science · 2024Article
- Analysis of genetic diversity and genome-wide association study for drought tolerance related traits in Iranian bread wheat.BMC plant biology · 2023Article
- Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS.Scientific reports · 2023Article
- Utilizing Genomics to Characterize the Common Oat Gene Pool-The Story of More Than a Century of Polish Breeding.International journal of molecular sciences · 2023Article
- Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis.BMC genomics · 2023Article
- Wheat Omics: Advancements and Opportunities.Plants (Basel, Switzerland) · 2023Review
- Interspecific common bean population derived fromFrontiers in plant science · 2023Article
- Genome-wide association mapping and genomic prediction of agronomical traits and breeding values in Iranian wheat under rain-fed and well-watered conditions.BMC genomics · 2022Article
- Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.).BMC plant biology · 2022Article
- Genome-wide association mapping for wheat morphometric seed traits in Iranian landraces and cultivars under rain-fed and well-watered conditions.Scientific reports · 2022Article
- Genome-wide association mapping and genomic prediction for pre‑harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat.BMC plant biology · 2022Article
- Tracking Changes in the Spring Barley Gene Pool in Poland during 120 Years of Breeding.International journal of molecular sciences · 2022Article
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6 authors.
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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.
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