Article
Licensed
Unlicensed
Requires Authentication
Regression-Based Multi-Trait QTL Mapping Using a Structural Equation Model
-
Xiaojuan Mi
Published/Copyright:
October 19, 2010
Quantitative trait loci (QTL) mapping often results in data on a number of traits that have well-established causal relationships. Many multi-trait QTL mapping methods that account for the correlation among multiple traits have been developed to improve the statistical power and the precision of QTL parameter estimation. However, none of these methods are capable of incorporating the causal structure among the traits. Consequently, genetic functions of the QTL may not be fully understood. Structural equation modeling (SEM) allows researchers to explicitly characterize the causal structure among the variables and to decompose effects into direct, indirect, and total effects. In this paper, we developed a multi-trait SEM method of QTL mapping that takes into account the causal relationships among traits related to grain yield. Performance of the proposed method is evaluated by simulation study and applied to data from a wheat experiment. Compared with single trait analysis and the multi-trait least-squares analysis, our multi-trait SEM improves statistical power of QTL detection and provides important insight into how QTLs regulate traits by investigating the direct, indirect, and total QTL effects. The approach also helps build biological models that more realistically reflect the complex relationships among QTL and traits and is more precise and efficient in QTL mapping than single trait analysis.
Published Online: 2010-10-19
©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
You are currently not able to access this content.
You are currently not able to access this content.
Articles in the same Issue
- Article
- Epistatic Interactions
- Testing for Gene-Gene Interaction with AMMI Models
- A Bayesian Hierarchical Model for Quantitative Real-Time PCR Data
- Informative or Noninformative Calls for Gene Expression: A Latent Variable Approach
- Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium
- Optimisation of HMM Topologies Enhances DNA and Protein Sequence Modelling
- The Apportionment of Total Genetic Variation by Categorical Analysis of Variance
- Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies
- An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data
- Parameter Estimation in Multiple-Hidden I.I.D. Models from Biological Multiple Alignment
- Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula
- Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
- An Internal Calibration Method for Protein-Array Studies
- Weighted-LASSO for Structured Network Inference from Time Course Data
- Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations
- Sparse Partial Least Squares Classification for High Dimensional Data
- Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases
- Sub-Modular Resolution Analysis by Network Mixture Models
- Space Oriented Rank-Based Data Integration
- The Generalized Odds Ratio as a Measure of Genetic Risk Effect in the Analysis and Meta-Analysis of Association Studies
- Network Enrichment Analysis in Complex Experiments
- Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression
- Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data
- A Random Coefficients Model for Regional Co-Expression Associated with DNA Copy Number
- Locating Multiple Interacting Quantitative Trait Loci with the Zero-Inflated Generalized Poisson Regression
- Classification of Genomic Sequences via Wavelet Variance and a Self-Organizing Map with an Application to Mitochondrial DNA
- Confidently Estimating the Number of DNA Replication Origins
- Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics
- Lasso Logistic Regression, GSoft and the Cyclic Coordinate Descent Algorithm: Application to Gene Expression Data
- Granger Causality Analysis of Human Cell-Cycle Gene Expression Profiles
- Mapping Quantitative Trait Loci in a Non-Equilibrium Population
- On the Optimal Design of Genetic Variant Discovery Studies
- On Optimal Selection of Summary Statistics for Approximate Bayesian Computation
- Assessment of LD Matrix Measures for the Analysis of Biological Pathway Association
- Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis
- The Detection of Blur in Affymetrix GeneChips
- Regression-Based Multi-Trait QTL Mapping Using a Structural Equation Model
- Spatial Clustering of Array CGH Features in Combination with Hierarchical Multiple Testing
- Predicting Patient Survival from Longitudinal Gene Expression
- Including Probe-Level Measurement Error in Robust Mixture Clustering of Replicated Microarray Gene Expression
- Reader's Reaction
- An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes
- Letter to the Editor
- Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn
Articles in the same Issue
- Article
- Epistatic Interactions
- Testing for Gene-Gene Interaction with AMMI Models
- A Bayesian Hierarchical Model for Quantitative Real-Time PCR Data
- Informative or Noninformative Calls for Gene Expression: A Latent Variable Approach
- Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium
- Optimisation of HMM Topologies Enhances DNA and Protein Sequence Modelling
- The Apportionment of Total Genetic Variation by Categorical Analysis of Variance
- Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies
- An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data
- Parameter Estimation in Multiple-Hidden I.I.D. Models from Biological Multiple Alignment
- Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula
- Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
- An Internal Calibration Method for Protein-Array Studies
- Weighted-LASSO for Structured Network Inference from Time Course Data
- Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations
- Sparse Partial Least Squares Classification for High Dimensional Data
- Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases
- Sub-Modular Resolution Analysis by Network Mixture Models
- Space Oriented Rank-Based Data Integration
- The Generalized Odds Ratio as a Measure of Genetic Risk Effect in the Analysis and Meta-Analysis of Association Studies
- Network Enrichment Analysis in Complex Experiments
- Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression
- Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data
- A Random Coefficients Model for Regional Co-Expression Associated with DNA Copy Number
- Locating Multiple Interacting Quantitative Trait Loci with the Zero-Inflated Generalized Poisson Regression
- Classification of Genomic Sequences via Wavelet Variance and a Self-Organizing Map with an Application to Mitochondrial DNA
- Confidently Estimating the Number of DNA Replication Origins
- Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics
- Lasso Logistic Regression, GSoft and the Cyclic Coordinate Descent Algorithm: Application to Gene Expression Data
- Granger Causality Analysis of Human Cell-Cycle Gene Expression Profiles
- Mapping Quantitative Trait Loci in a Non-Equilibrium Population
- On the Optimal Design of Genetic Variant Discovery Studies
- On Optimal Selection of Summary Statistics for Approximate Bayesian Computation
- Assessment of LD Matrix Measures for the Analysis of Biological Pathway Association
- Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis
- The Detection of Blur in Affymetrix GeneChips
- Regression-Based Multi-Trait QTL Mapping Using a Structural Equation Model
- Spatial Clustering of Array CGH Features in Combination with Hierarchical Multiple Testing
- Predicting Patient Survival from Longitudinal Gene Expression
- Including Probe-Level Measurement Error in Robust Mixture Clustering of Replicated Microarray Gene Expression
- Reader's Reaction
- An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes
- Letter to the Editor
- Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn
