ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2007
Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Haplotype bias detection using pedigree-based transmission simulation: traces of selection that occurred in apple breeding.Horticulture research · 2026Article
- Transcriptome-Wide Association Analysis of Flavonoid Biosynthesis Genes and Their Correlation With Leaf Phenotypes in Hawk Tea (Ecology and evolution · 2024Article
- Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study.Horticulture research · 2021Article
- Article
- Two novel genomic regions associated with fearfulness in dogs overlap human neuropsychiatric loci.Translational psychiatry · 2019Article
- Genome-wide mapping of quantitative trait loci in admixed populations using mixed linear model and Bayesian multiple regression analysis.Genetics, selection, evolution : GSE · 2018Article
- pLARmEB: integration of least angle regression with empirical Bayes for multilocus genome-wide association studies.Heredity · 2017Article
- Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L.Genetics · 2015Article
- Evaluation of multi-locus models for genome-wide association studies: a case study in sugar beet.Heredity · 2015Article
- Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping.PloS one · 2015Article
- Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: a simulation study in rice.BMC genetics · 2014Article
- Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait mapping and genomic prediction.Genetics, selection, evolution : GSE · 2013Article
- Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia.Breeding science · 2013Article
- Article
- Review
- Epistatic association mapping in homozygous crop cultivars.PloS one · 2011Article
- Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm.Genetica · 2009Article
- Review
- Population structure and linkage disequilibrium in barley assessed by DArT markers.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One way to use a crop germplasm collection directly to map QTLs without using line-crossing experiments is the whole genome association mapping. A major problem with association mapping is the presence of population structure, which can lead to both false positives and failure to detect genuine associations (i.e., false negatives). Particularly in highly selfing species such as Asian cultivated rice, high levels of population structure are expected and therefore the efficiency of association mapping remains almost unknown. Here, we propose an approach that combines a Bayesian method for mapping multiple QTLs with a regression method that directly incorporates estimates of population structure. That is, the effects due to both multiple QTLs and population structure were included in our statistical model. We evaluated the efficiency of our approach in simulated- and real-trait analyses of a rice germplasm collection. Simulation analyses based on real marker data showed that our model could suppress both false-positive and false-negative rates and the error of estimation of genetic effects over single QTL models, indicating that our model has statistically desirable attributes over single QTL models. As real traits, we analyzed the size and shape of milled rice grains and found significant markers that may be linked to QTLs reported previously. Association mapping should have good prospects in highly selfing species such as rice if proper methods are adopted. Our approach will be useful for the whole genome association mapping of various selfing crop species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.