ArticlePloS one2018
Quantile regression for genome-wide association study of flowering time-related traits in common bean.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Prioritization of deleterious mutations informs genomic prediction and increases the rate of gain in common bean (Phaseolus vulgaris L.), a simulation study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Enhancing polygenic risk prediction by modeling quantile-specific genetic effects.Scientific reports · 2026Article
- Genome-wide discovery for biomarkers using quantile regression at biobank scale.Nature communications · 2024Article
- Population size in QTL detection using quantile regression in genome-wide association studies.Scientific reports · 2023Article
- Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean.Frontiers in plant science · 2022Article
- Regulation of flowering under short photoperiods based on transcriptomic and metabolomic analysis in Phaseolus vulgaris L.Molecular genetics and genomics : MGG · 2021Article
- Genome-Wide Association Studies of Mineral Content in Common Bean.Frontiers in plant science · 2021Article
- Quantile regression in genomic selection for oligogenic traits in autogamous plants: A simulation study.PloS one · 2021Article
- Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean.Frontiers in plant science · 2021Article
- Article
- Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean.Genetics · 2020Article
- A rank-based normalization method with the fully adjusted full-stage procedure in genetic association studies.PloS one · 2020Article
- Genome-wide association and epistatic interactions of flowering time in soybean cultivar.PloS one · 2020Article
- Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content.Nutrients · 2019Article
- Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans.Genes · 2018Article
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower-DFF; Days for flowering-DTF; Days to end of flowering-DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons. Plants were genotyped for 384 SNPs. Traditional single-SNP and 9 QR models, ranging from equally spaced quantiles (τ) 0.1 to 0.9, were used to associate SNPs to phenotype. Heritabilities were moderate high, ranging from 0.32 to 0.58. Genetic and phenotypic correlations were all high, averaging 0.66 and 0.98, respectively. Traditional single-SNP GWAS model was not able to find any SNP-trait association. On the other hand, when using QR methodology considering one extreme quantile (τ = 0.1) we found, respectively 1 and 7, significant SNPs associated for DFF and DTF. Significant SNPs were found on Pv01, Pv02, Pv03, Pv07, Pv10 and Pv11 chromosomes. We investigated potential candidate genes in the region around these significant SNPs. Three genes involved in the flowering pathways were identified, including Phvul.001G214500, Phvul.007G229300 and Phvul.010G142900.1 on Pv01, Pv07 and Pv10, respectively. These results indicate that GWAS-based QR was able to enhance the understanding on genetic architecture of phenological traits (DFF and DTF) in common bean.
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