ArticleBMC genetics2014
Association studies including genotype by environment interactions: prospects and limits.
Article in BMC genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Discovering common and population-specific QTLs for leaf rust resistance in different Barley populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genome Wide Association Study Reveals Novel Loci Controlling Agronomic Traits in Tomato (Solanum lycopersicum L.).Biochemical genetics · 2026Article
- Genome-wide association study for agronomic and yield-related traits in spring wheat (Triticum aestivum L.) germplasm.BMC plant biology · 2025Article
- Genetic and molecular approaches for Fusarium wilt resistance in garden pea: advances and future outlook.Plant molecular biology · 2025Review
- Physiologic, Genetic and Epigenetic Determinants of Water Deficit Tolerance in Fruit Trees.Plants (Basel, Switzerland) · 2025Review
- Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.).BMC plant biology · 2024Article
- Genome-wide association study for grain yield and component traits in bread wheat (Frontiers in genetics · 2022Article
- Exploring the legacy of Central European historical winter wheat landraces.Scientific reports · 2021Article
- Editorial: Applied Genetics of Natural Fiber Plants.Frontiers in genetics · 2021Article
- Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management ofPlants (Basel, Switzerland) · 2020Review
- Genome-based breeding approaches in major vegetable crops.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs.BMC plant biology · 2019Article
- Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Identifying favorable alleles for improving key agronomic traits in upland cotton.BMC plant biology · 2019Article
- Genome-Wide Association Study Identifies Candidate Genes Related to Seed Oil Composition and Protein Content inFrontiers in plant science · 2018Article
- From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress.Molecular systems biology · 2017Article
- Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs.Plant biotechnology journal · 2017Article
- Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits.Journal of experimental botany · 2016Article
- Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- An Analytic Solution to the Computation of Power and Sample Size for Genetic Association Studies under a Pleiotropic Mode of Inheritance.Human heredity · 2016Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundAssociation mapping studies offer great promise to identify polymorphisms associated with phenotypes and for understanding the genetic basis of quantitative trait variation. To date, almost all association mapping studies based on structured plant populations examined the main effects of genetic factors on the trait but did not deal with interactions between genetic factors and environment. In this paper, we propose a methodological prospect of mixed linear models to analyze genotype by environment interaction effects using association mapping designs. First, we simulated datasets to assess the power of linear mixed models to detect interaction effects. This simulation was based on two association panels composed of 90 inbreds (pearl millet) and 277 inbreds (maize).
resultsBased on the simulation approach, we reported the impact of effect size, environmental variation, allele frequency, trait heritability, and sample size on the power to detect the main effects of genetic loci and diverse effect of interactions implying these loci. Interaction effects specified in the model included SNP by environment interaction, ancestry by environment interaction, SNP by ancestry interaction and three way interactions. The method was finally used on real datasets from field experiments conducted on the two considered panels. We showed two types of interactions effects contributing to genotype by environment interactions in maize: SNP by environment interaction and ancestry by environment interaction. This last interaction suggests differential response at the population level in function of the environment.
conclusionsOur results suggested the suitability of mixed models for the detection of diverse interaction effects. The need of samples larger than that commonly used in current plant association studies is strongly emphasized to ensure rigorous model selection and powerful interaction assessment. The use of ancestry interaction component brought valuable information complementary to other available approaches.
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