ArticlePloS one2010
Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
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Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it, 152 citations in OpenAlex.
- Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant.Human molecular genetics · 2014Pooled it
- Haplotype-based nested association mapping for net form net blotch response in Australian barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Whole genome sequencing-based multi-locus association mapping for kernel iron, zinc and protein content in groundnut.Scientific reports · 2026Article
- 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
- Decoding Complex Traits in Goats Through Genome-Wide Association Studies: Progress, Challenges, and Perspectives.International journal of molecular sciences · 2026Review
- Haplotype-based genome-wide association study uncovers QTL for fruit-related traits in the 287 tomato accessions.BMC plant biology · 2026Article
- Haplotype GWAS in Swedish warmblood horses for conformation and jumping traits.Journal of animal science · 2026Article
- Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India.BMC genomics · 2024Article
- Genome-wide association study for cashmere traits in Inner Mongolia cashmere goat population reveals new candidate genes and haplotypes.BMC genomics · 2024Article
- Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance toInternational journal of molecular sciences · 2024Article
- Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome.Life science alliance · 2024Article
- TheCells · 2023Review
- Population size in QTL detection using quantile regression in genome-wide association studies.Scientific reports · 2023Article
- Aspergillus flavus genetic structure at a turkey farm.Veterinary medicine and science · 2023Article
- Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets.Frontiers in plant science · 2023Article
- A genome-wide association study of freezing tolerance in red clover (Frontiers in plant science · 2023Article
- Genome-wide association study of agronomical and root-related traits in spring barley collection grown under field conditions.Frontiers in plant science · 2023Article
- Haplotype mining panel for genetic dissection and breeding in Eucalyptus.The Plant journal : for cell and molecular biology · 2023Article
- Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.GigaScience · 2022Article
- Evaluation of Fusarium Head Blight Resistance Effects by Haplotype-Based Genome-Wide Association Study in Winter Wheat Lines Derived by Marker Backcrossing Approach.International journal of molecular sciences · 2022Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association studies (GWAS) may benefit from utilizing haplotype information for making marker-phenotype associations. Several rationales for grouping single nucleotide polymorphisms (SNPs) into haplotype blocks exist, but any advantage may depend on such factors as genetic architecture of traits, patterns of linkage disequilibrium in the study population, and marker density. The objective of this study was to explore the utility of haplotypes for GWAS in barley (Hordeum vulgare) to offer a first detailed look at this approach for identifying agronomically important genes in crops. To accomplish this, we used genotype and phenotype data from the Barley Coordinated Agricultural Project and constructed haplotypes using three different methods. Marker-trait associations were tested by the efficient mixed-model association algorithm (EMMA). When QTL were simulated using single SNPs dropped from the marker dataset, a simple sliding window performed as well or better than single SNPs or the more sophisticated methods of blocking SNPs into haplotypes. Moreover, the haplotype analyses performed better 1) when QTL were simulated as polymorphisms that arose subsequent to marker variants, and 2) in analysis of empirical heading date data. These results demonstrate that the information content of haplotypes is dependent on the particular mutational and recombinational history of the QTL and nearby markers. Analysis of the empirical data also confirmed our intuition that the distribution of QTL alleles in nature is often unlike the distribution of marker variants, and hence utilizing haplotype information could capture associations that would elude single SNPs. We recommend routine use of both single SNP and haplotype markers for GWAS to take advantage of the full information content of the genotype data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.