ArticleHeredity2018
pKWmEB: integration of Kruskal-Wallis test with empirical Bayes under polygenic background control for multi-locus genome-wide association study.
Article in Heredity, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
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Who cites it
127 citing papers in PubMed.
- Association mapping integrated with image-based phenomics identifies SNPs and candidate genes underpinning fruit morphology and development in chile pepper (Capsicum annum L.).G3 (Bethesda, Md.) · 2026Article
- Genetic dissection of gluten characteristics based on single- and multi-locus genome-wide association studies in wheat (Food chemistry. Molecular sciences · 2026Article
- Multi-locus GWAS to unravel the genetic architecture of grain iron, zinc and protein contents in wheat (Triticum aestivum L.) genotypes evaluated over multiple locations and years.BMC plant biology · 2026Article
- Multi-locus genome-wide association mapping reveals loci underlying malt quality traits in heterogeneous Ethiopian Barley (Hordeum vulgare L.) germplasm.Scientific reports · 2026Article
- Integrated single marker scanning and sparse Bayesian learning improves performance of detection for GWAS.Plant methods · 2026Article
- Multi-locus genome-wide association studies of aluminum stress indices in shoot and root traits at seedling stage in Ethiopian durum wheat (Triticum turgidum ssp. durum) genotypes.BMC plant biology · 2026Article
- Genome-wide association study identifies consistent genomic loci for yield and nutritional quality in Ethiopian sorghum landraces.The plant genome · 2026Article
- Genome-wide association studies and candidate gene identification under salinity stress in bread wheat (Frontiers in plant science · 2026Article
- Unraveling the genetic architecture of anti-nutritional factors in soybean (Glycine max.) for nutritional enhancement.Scientific reports · 2025Article
- A natural allelic variation of TaIAA10-6A confers pre-harvest sprouting resistance in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Exploring the polygenic landscape of wool traits in Turkish merinos through multi-locus GWAS approaches: Karacabey Merino.BMC veterinary research · 2025Article
- Genome-wide identification of QTNs and candidate genes in Ethiopian sorghum (Sorghum bicolor (L.) moench) landraces using SNP-based approaches.BMC genomic data · 2025Article
- Multi-locus genome-wide association studies for root system architectural traits in Ethiopian sorghum (Sorghum bicolor L.) landraces.BMC plant biology · 2025Article
- Multi-locus genome-wide association study reveals genomic regions underlying root system architecture traits early growth stage of sorghum germplasm.Scientific reports · 2025Article
- Investigation of growth traits in Turkish Merino lambs using multi-locus GWAS approaches: Karacabey Merino.BMC veterinary research · 2025Article
- Development and Validation of Multi-Locus GWAS-Based KASP Markers for MaizePlants (Basel, Switzerland) · 2025Article
- Multi-Locus GWAS Mapping and Candidate Gene Analysis of Anticancer Peptide Lunasin in Soybean (Plants (Basel, Switzerland) · 2025Article
- Conditional QTL/QTN mapping for seed width and mining candidate genes based on soybean FW-RIL population.Molecular genetics and genomics : MGG · 2025Article
- Multi-Experiment and Multi-Locus Genome-Wide Association Mapping for Grain Arsenic in Rice Population.Plant direct · 2025Article
- Discovery of host genetic factors through multi-locus GWAS against toxoplasmosis in sheep: addressing one health perspectives.BMC veterinary research · 2025Article
67 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although nonparametric methods in genome-wide association studies (GWAS) are robust in quantitative trait nucleotide (QTN) detection, the absence of polygenic background control in single-marker association in genome-wide scans results in a high false positive rate. To overcome this issue, we proposed an integrated nonparametric method for multi-locus GWAS. First, a new model transformation was used to whiten the covariance matrix of polygenic matrix K and environmental noise. Using the transferred model, Kruskal-Wallis test along with least angle regression was then used to select all the markers that were potentially associated with the trait. Finally, all the selected markers were placed into multi-locus model, these effects were estimated by empirical Bayes, and all the nonzero effects were further identified by a likelihood ratio test for true QTN detection. This method, named pKWmEB, was validated by a series of Monte Carlo simulation studies. As a result, pKWmEB effectively controlled false positive rate, although a less stringent significance criterion was adopted. More importantly, pKWmEB retained the high power of Kruskal-Wallis test, and provided QTN effect estimates. To further validate pKWmEB, we re-analyzed four flowering time related traits in Arabidopsis thaliana, and detected some previously reported genes that were not identified by the other methods.
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