ArticlePlant physiology2021
TWAS results are complementary to and less affected by linkage disequilibrium than GWAS.
Article in Plant physiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 74 citations in OpenAlex.
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- OzBarley: A genetic and phenotypic data resource capturing the Australian barley breeding history.Scientific data · 2026Article
- Genetic link between metabolic syndrome and coronary artery disease: Insights from genome-wide cross-trait analysis.Global medical genetics · 2026Article
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- In silico prediction of variant effects: promises and limitations for precision plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Genes and pathways determining flowering time variation in temperate-adapted sorghum.The Plant journal : for cell and molecular biology · 2025Article
- Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism.Plant communications · 2025Article
- Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions.BMC genomics · 2025Article
- Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds.Genome biology · 2025Article
- Comment on 'Systematic Druggable Genome-Wide Mendelian Randomization Identifies Therapeutic Targets for Sarcopenia' by Yin Et Al.Journal of cachexia, sarcopenia and muscle · 2025Article
- Transcriptome-wide association study identifies genes associated with bladder cancer risk.Scientific reports · 2025Article
- Connecting intermediate phenotypes to disease using multi-omics in heart failure.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2025Article
- Multivariate genetic architecture of poor sleep quality.Frontiers in neuroscience · 2025Article
- GWAS for identification of genomic regions and candidate genes in vegetable crops.Functional & integrative genomics · 2024Review
- TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean.Plant communications · 2024Article
- Impact of putatively beneficial genomic loci on gene expression in little brown bats (Evolutionary applications · 2024Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A genome-wide association study (GWAS) is used to identify genetic markers associated with phenotypic variation. In contrast, a transcriptome-wide association study (TWAS) detects associations between gene expression levels and phenotypic variation. It has previously been shown that in the cross-pollinated species, maize (Zea mays), GWAS, and TWAS identify complementary sets of trait-associated genes, many of which exhibit characteristics of true positives. Here, we extend this conclusion to the self-pollinated species, Arabidopsis thaliana and soybean (Glycine max). Linkage disequilibrium (LD) can result in the identification, via GWAS, of false-positive associations. In all three analyzed plant species, most trait-associated genes identified via TWAS are well separated physically from other candidate genes. Hence, TWAS is less affected by LD than is GWAS, demonstrating that TWAS is particularly well suited for association studies in genomes with slow rates of LD decay, such as soybean. TWAS is reasonably robust to the plant organs/tissues used to determine expression levels. In summary, this study confirms that TWAS is a promising approach for accurate gene-level association mapping in plants that is complementary to GWAS, and established that TWAS can exhibit substantial advantages relative to GWAS in species with slow rates of LD decay.
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