ArticleHeredity2017
pLARmEB: integration of least angle regression with empirical Bayes for multilocus genome-wide association studies.
Article in Heredity, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers.
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Who cites it
165 citing papers in PubMed.
- Genomic insights into end-use grain quality and nutritional traits of an ancient Indian dwarf wheat ( Triticum sphaerococcum Percival) population using a multi-locus genome-wide association study.Journal of the science of food and agriculture · 2026Article
- 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 genome-wide association study on the rheological traits in wheat flour dough.BMC genomics · 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
- Multilocus genome-wide association study reveals genomic regions associated with resistance to red leaf blotch in soybean.BMC plant biology · 2026Article
- Genome-Wide Association Study of Yield-Related Traits and Photoperiod Response in Rice.Plants (Basel, Switzerland) · 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
- Mining genes, genomic selection and simulation breeding on hundred-seed weight using a four-way RIL population.Frontiers in plant science · 2026Article
- Genome-wide and co-expression network dissection ofFrontiers in plant science · 2026Article
- Genome-wide association studies and candidate gene identification under salinity stress in bread wheat (Frontiers in plant science · 2026Article
- Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Food chemistry. Molecular sciences · 2025Article
- 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
105 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multilocus genome-wide association studies (GWAS) have become the state-of-the-art procedure to identify quantitative trait nucleotides (QTNs) associated with complex traits. However, implementation of multilocus model in GWAS is still difficult. In this study, we integrated least angle regression with empirical Bayes to perform multilocus GWAS under polygenic background control. We used an algorithm of model transformation that whitened the covariance matrix of the polygenic matrix K and environmental noise. Markers on one chromosome were included simultaneously in a multilocus model and least angle regression was used to select the most potentially associated single-nucleotide polymorphisms (SNPs), whereas the markers on the other chromosomes were used to calculate kinship matrix as polygenic background control. The selected SNPs in multilocus model were further detected for their association with the trait by empirical Bayes and likelihood ratio test. We herein refer to this method as the pLARmEB (polygenic-background-control-based least angle regression plus empirical Bayes). Results from simulation studies showed that pLARmEB was more powerful in QTN detection and more accurate in QTN effect estimation, had less false positive rate and required less computing time than Bayesian hierarchical generalized linear model, efficient mixed model association (EMMA) and least angle regression plus empirical Bayes. pLARmEB, multilocus random-SNP-effect mixed linear model and fast multilocus random-SNP-effect EMMA methods had almost equal power of QTN detection in simulation experiments. However, only pLARmEB identified 48 previously reported genes for 7 flowering time-related traits in Arabidopsis thaliana.
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