ArticleG3 (Bethesda, Md.)2019
Genotype Imputation in Winter Wheat Using First-Generation Haplotype Map SNPs Improves Genome-Wide Association Mapping and Genomic Prediction of Traits.
Article in G3 (Bethesda, Md.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Integration and imputation of GBS-derived and DArTseq-derived SNP markers in assessing genetic diversity of bread wheat genotypes.BMC genomics · 2026Article
- DArTseq genotyping facilitates identification of Aegilops biuncialis chromatin introgressed into bread wheat Mv9kr1.Plant molecular biology · 2024Article
- Broad-spectrum resistance to fungal foliar diseases in wheat: recent efforts and achievements.Frontiers in plant science · 2024Review
- Skim exome capture genotyping in wheat.The plant genome · 2023Article
- Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.The plant genome · 2022Article
- A joint use of pooling and imputation for genotyping SNPs.BMC bioinformatics · 2022Article
- Genotype imputation for soybean nested association mapping population to improve precision of QTL detection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Development of the Wheat Practical Haplotype Graph database as a resource for genotyping data storage and genotype imputation.G3 (Bethesda, Md.) · 2022Article
- Multi-stage resistance toFrontiers in plant science · 2022Article
- Identification of an Elite Core Panel as a Key Breeding Resource to Accelerate the Rate of Genetic Improvement for Irrigated Rice.Rice (New York, N.Y.) · 2021Article
- SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces.Molecular biology reports · 2021Article
- The Haplotype-Based Analysis ofFrontiers in plant science · 2021Article
- Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization.Frontiers in plant science · 2021Article
- Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.G3 (Bethesda, Md.) · 2020Article
- Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs.BMC plant biology · 2019Article
- SNP and Haplotype-Based Genomic Selection of Quantitative Traits inPlants (Basel, Switzerland) · 2019Article
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11 authors.
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Abstract
Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations.
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