ArticlePLoS computational biology2017
Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers.
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180 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
- A Restricted Two-Stage Multi-Locus Multi-Allele Genome-Wide Association Study Reveals Genomic Loci and Candidate Genes Controlling Plant-Height-Related Traits in Soybean Under Normal and Shade Conditions.International journal of molecular sciences · 2026Article
- Genome-wide association study identifies loci controlling grain yield and protein content in mungbean (Vigna radiata (L.) R. Wilczek var. radiata) using DArTseq SNP markers.BMC plant biology · 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
- Genome-wide association study identifies consistent genomic loci for yield and nutritional quality in Ethiopian sorghum landraces.The plant genome · 2026Article
- Article
- 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
- Mining genes, genomic selection and simulation breeding on hundred-seed weight using a four-way RIL population.Frontiers in plant science · 2026Article
- Genome-wide association study identifies candidate genes associated with leaf morphological traits in grape (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
120 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association study (GWAS) entails examining a large number of single nucleotide polymorphisms (SNPs) in a limited sample with hundreds of individuals, implying a variable selection problem in the high dimensional dataset. Although many single-locus GWAS approaches under polygenic background and population structure controls have been widely used, some significant loci fail to be detected. In this study, we used an iterative modified-sure independence screening (ISIS) approach in reducing the number of SNPs to a moderate size. Expectation-Maximization (EM)-Bayesian least absolute shrinkage and selection operator (BLASSO) was used to estimate all the selected SNP effects for true quantitative trait nucleotide (QTN) detection. This method is referred to as ISIS EM-BLASSO algorithm. Monte Carlo simulation studies validated the new method, which has the highest empirical power in QTN detection and the highest accuracy in QTN effect estimation, and it is the fastest, as compared with efficient mixed-model association (EMMA), smoothly clipped absolute deviation (SCAD), fixed and random model circulating probability unification (FarmCPU), and multi-locus random-SNP-effect mixed linear model (mrMLM). To further demonstrate the new method, six flowering time traits in Arabidopsis thaliana were re-analyzed by four methods (New method, EMMA, FarmCPU, and mrMLM). As a result, the new method identified most previously reported genes. Therefore, the new method is a good alternative for multi-locus GWAS.
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