ArticlePLoS genetics2020
Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 29 citations in OpenAlex.
- Discovering common and population-specific QTLs for leaf rust resistance in different Barley populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Improvement in genomic prediction of maize with prior gene ontology information depends on traits and environmental conditions.The plant genome · 2025Article
- Identifying QTLs involved in hybrid performance and heterotic group complementarity: new GWAS models applied to factorial and admixed diallel maize hybrid panels.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
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- Allopatric divergence of cooperators confers cheating resistance and limits effects of a defector mutation.BMC ecology and evolution · 2022Article
- Usefulness of temperate-adapted maize lines developed by doubled haploid and single-seed descent methods.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
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- Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci.G3 (Bethesda, Md.) · 2022Article
- Interpreting coronary artery disease GWAS results: A functional genomics approach assessing biological significance.PloS one · 2022Article
- Review
- Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease.American journal of human genetics · 2021Article
- Perspectives on Applications of Hierarchical Gene-To-Phenotype (G2P) Maps to Capture Non-stationary Effects of Alleles in Genomic Prediction.Frontiers in plant science · 2021Article
- Article
- Accounting for Group-Specific Allele Effects and Admixture in Genomic Predictions: Theory and Experimental Evaluation in Maize.Genetics · 2020Article
- Haplotype-Based, Genome-Wide Association Study Reveals Stable Genomic Regions for Grain Yield in CIMMYT Spring Bread Wheat.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred "Flint-Dent" panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species.
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