ArticlePlant biotechnology journal2019
Optimising the identification of causal variants across varying genetic architectures in crops.
Article in Plant biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Molecular polymorphisms that underlie trait variation in crops: Lessons learned from soybean.The plant genome · 2026Review
- Genetic architecture of ideotype-related traits in middle American beans through single trait, multi-trait and epistatic genome-wide analyses.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Unveiling shared genetic regulators of plant architectural and biomass yield traits in the Sorghum Association Panel.Journal of experimental botany · 2025Article
- TPS5 and TOR signaling components are determinants ofFrontiers in plant science · 2025Article
- Article
- Quantitative genomics-enabled selection for simultaneous improvement of lint yield and seed traits in cotton (Gossypium hirsutum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding.Frontiers in plant science · 2024Review
- Genome-Wide Association Study Identified Novel SNPs Associated with Chlorophyll Content in Maize.Genes · 2023Article
- GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals.Nucleic acids research · 2023Article
- Genome-wide association study for carcass weight in pasture-finished beef cattle in Hawai'i.Frontiers in genetics · 2023Article
- SNP discovery in proso millet (Plant direct · 2022Article
- Hyperspectral reflectance-based phenotyping for quantitative genetics in crops: Progress and challenges.Plant communications · 2021Review
- Exploiting genetic diversity in two European maize landraces for improving Gibberella ear rot resistance using genomic tools.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Status and prospects of genome-wide association studies in plants.The plant genome · 2021Review
- 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves.PeerJ · 2021Article
- Comparison of Single-Trait and Multi-Trait Genome-Wide Association Models and Inclusion of Correlated Traits in the Dissection of the Genetic Architecture of a Complex Trait in a Breeding Program.Frontiers in plant science · 2021Article
- Increased Power and Accuracy of Causal Locus Identification in Time Series Genome-wide Association in Sorghum.Plant physiology · 2020Article
- Shared Genetic Control of Root System Architecture betweenPlant physiology · 2020Article
- Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat.International journal of molecular sciences · 2020Article
- Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia.PloS one · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Association studies use statistical links between genetic markers and the phenotype variation across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real-world genotype datasets from four crop species with distinct minor allele frequency distributions, population structures and linkage disequilibrium patterns. We demonstrate that different GWAS statistical approaches provide favourable trade-offs between power and accuracy for traits controlled by different types of genetic architectures. FarmCPU provides the most favourable outcomes for moderately complex traits while a Bayesian approach adopted from genomic prediction provides the most favourable outcomes for extremely complex traits. We assert that by estimating the complexity of genetic architectures for target traits and selecting an appropriate statistical approach for the degree of complexity detected, researchers can substantially improve the ability to dissect the genetic factors controlling complex traits such as flowering time, plant height and yield component.
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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.