Linkage Analysis and Gene Mapping
Published on 9. August 2023
530 pages
978-2-7598-3043-5 (ISBN)
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Edition
Digital original
Language
English
Place of publication
Les Ulis
France
Target group
Professional and scholarly
US School Grade: College Graduate Student
Edition type
Digital original
ISBN-13
978-2-7598-3043-5 (9782759830435)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Classification
Content
- Intro
- Linkage Analysis and Gene Mapping
- Preface
- Contents
- Populations in Genetic Studies
- Commonly Used Populations in Genetic Studies
- Bi-Parental Populations
- Multi-Parental Populations
- Considerations in Developing Genetic Populations
- Preliminary Analysis of Genotypic Data
- Collection and Coding of Genotypic Data
- Gene Frequency and Genotypic Frequency
- Fitness Test on Genotypic Frequencies
- Genetic Effect and Genetic Variance
- Calculation of Population Mean and Phenotypic Variance
- One-Locus Additive and Dominance Model
- Population Mean and Genetic Variance at One Locus
- ANOVA on Single Environment Trials
- Linear Decomposition on Phenotypic Observation
- Decomposition of Sum of Squares of Phenotypic Deviations
- Single Environmental ANOVA on Rice Grain Length
- ANOVA on Multi-Environment Trials
- Linear Decomposition on Phenotypic Observation
- Decomposition of Sum of Squares of Phenotypic Deviations
- Multi-Environmental ANOVA on Rice Grain Length
- Estimation of Genotypic Values and the Broad-Sense Heritability
- Genotypic Values and Broad-Sense Heritability from Single Environmental Trials
- Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials
- Estimation of Genotypic Values Under Heterogeneous Error Variances
- Exercises
- Estimation of the Two-Point Recombination Frequencies
- Generation Transition Matrix
- Usefulness of the Transition Matrix in Linkage Analysis
- Transition Matrix of One Generation of Backcrossing
- Transition Matrix of One Generation of Selfing
- Transition Matrix of Doubled Haploid
- Transition Matrix of Repeated Selfing
- Expression of the Two-Locus Genotypic Frequencies in Matrix Format
- Theoretical Genotypic Frequencies at Two Loci
- Theoretical Frequencies of 10 Genotypes at Two Loci
- Theoretical Frequencies of 4 Homozygotes in Permanent Populations
- Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations
- Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations
- Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations
- Genotypic Frequencies of Two Dominant Loci in Temporary Populations
- Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations
- Genotypic Frequencies of Two Recessive Loci in Temporary Populations
- Estimation of Two-Point Recombination Frequency
- Maximum Likelihood Estimation of Recombination Frequency in DH Populations
- General Procedure on the Maximum Likelihood Estimation of Recombination Frequency
- Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 Population
- Initial Values in Newton Algorithm
- EM Algorithm in Estimating Recombination Frequency in F2 Populations
- Effects on the Estimation of Recombination Frequency from Segregation Distortion
- Exercises
- Three-Point Analysis and Linkage Map Construction
- Three-Point Analysis and Mapping Function
- Genetic Interference and Coefficient of Interference
- Mapping Function
- Construction of Genetic Linkage Maps
- Marker Grouping Algorithm
- Marker Ordering Algorithm
- Use of the k-Optimal Algorithm in Linkage Map Construction
- Rippling of the Ordered Markers
- Integration of Multiple Maps
- Comparison of the Recombination Frequency Estimation in Different Populations
- LOD Score in Testing the Linkage Relationship in Different Populations
- Accuracy of the Estimated Recombination Frequency
- Least Population Size to Declare the Significant Linkage Relationship and Close Linkage
- Linkage Analysis in Random Mating Populations
- Linkage Dis-Equilibrium in Random Mating Populations
- Generation Transition Matrix from Diploid Genotypes to Haploid Gametes
- Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating
- Exercises
- Single Marker Analysis and Simple Interval Mapping
- Single Marker Analysis
- Phenotypic Means of Different Genotypes at One Marker Locus
- Single Marker Analysis by t-Test in Populations with Two Genotypes
- Single Marker Analysis by t-Test in Populations with Three Genotypes
- ANOVA in Single Marker Analysis in Populations with Three Genotypes
- Likelihood Ratio Test in Single Marker Analysis
- Problems with Single Marker Analysis
- Simple Interval Mapping
- Frequencies of the QTL Genotypes in a Marker Interval
- Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes
- Testing for the Existence of QTL
- Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance
- Applications of Simple Interval Mapping in DH and F2 Populations
- Phenomenon of 'Ghost' QTL in Simple Interval Mapping
- Other Problems with Simple Interval Mapping
- Threshold Values of LOD Score in QTL Mapping
- Significance Level and Critical Value of One Test Statistic
- Distribution of the LRT Statistic at Single Scanning Positions in the Absence of Any QTL
- Factors Affecting the Distribution of the Genome-Wide Largest LOD Score
- Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping
- Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping
- Exercises
- Inclusive Composite Interval Mapping
- Importance of the Control on Background Genetic Variation in QTL Mapping
- Inclusive Composite Interval Mapping in DH Populations
- Additive Genetic Model of One Single QTL
- Additive Genetic Model for Multiple QTLs
- One-Dimensional Scanning and Hypothesis Testing for Additive QTLs
- Application of ICIM in a DH Mapping Population in Barley
- Inclusive Composite Interval Mapping in F2 Populations
- Additive and Dominant Model of One Single QTL
- Additive and Dominant Model for Multiple QTLs
- One-Dimensional Scanning and Hypothesis Testing in Additive and Dominant QTL Mapping
- Application of ICIM in an F2 Mapping Population
- Type II Error in Hypothesis Testing and Statistical Power in QTL Detection
- Type II Error and Statistical Power in Hypothesis Testing
- Probability of Two Types of Error and the Appropriate Sample Size
- Distribution and Effect Models of QTLs Used in Power Analysis by Simulations
- Calculation of the Detection Power and False Discovery Rate in QTL Mapping
- Comparison of IM and ICIM by Simulation
- QTL Detection Power and FDR from IM
- QTL Detection Power and FDR from ICIM
- Detection Powers Counted by Marker Intervals
- Suitable Population Size Required in QTL Mapping
- Avoiding the Overfitting Problem in the First Step of Model Selection in ICIM
- Exercises
- QTL Mapping for Epistasis and Genotype-by-Environment Interaction
- Epistatic QTL Mapping in DH Populations
- Linear Regression in Epistatic QTL Mapping and the Statistical Properties
- Two-Dimensional Scanning on Di-Genic Epistatic QTLs
- Genetic Variance on Epistatic QTLs with Linkage
- Simulation Study on Epistatic QTL Mapping in DH Populations
- Epistatic QTL Mapping in F2 Populations
- The Di-Genic Epistasis Model in F2 Populations
- Epistatic QTL Mapping Procedure in F2 Population
- Detection Power of Epistatic QTLs in F2 Populations
- Genetic Analysis and Detection Power of the Most Common Di-Genic Interactions
- Genetic Effects in Di-Genic Interactions
- Decomposition of Genetic Variance at the Presence of Di-Genic Epistasis
- Power Simulation of Epistatic QTL Mapping
- Issues in Epistatic QTL Mapping
- Mapping of the QTL by Environment Interactions
- Mapping of the Additive QTL by Environment Interactions
- Mapping of the Epistatic QTL and Environment Interactions
- QTL and Environment Interactions in One Actual RIL Population in Maize
- Exercises
- Genetic Analysis in Hybrid F1 of Two Heterozygous Parents and Double-Cross F1 of Four Homozygous Parents
- Linage Analysis in the Hybrid F1 Derived from Two Heterozygous Parents
- Categories of Polymorphism Markers
- Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci
- Estimation of the Recombination Frequency Between Two Fully-Informative Markers
- Haploid Type Rebuilding in the Heterozygous Parents
- Estimation of the Recombination Frequency for Incompletely Informative Markers
- Theoretical Frequencies of Identifiable Genotypes Between the Complete Marker and Other Three Categories of Markers
- Theoretical Frequencies of Identifiable Genotypes Between Two Markers Belonging to Category II, III, or IV
- Theoretical Frequencies of Identifiable Genotypes Between Two Category IV Markers
- Haploid Type Rebuilding at the Presence of All Categories of Markers
- Linkage Analysis in Double Cross F1 Derived from Four Pure-Line Parents
- Marker Categories and Estimation of Recombination Frequency in the Double Cross F1 Population
- Equivalence Between the Double Cross F1 of Pure-Line Parents and Hybrid F1 of Heterozygous Parents
- Genotypic Frequencies at Three Complete Markers
- Imputation of Incomplete and Missing Marker Information
- QTL Mapping in the Double Cross F1 Population Derived from Four Pure-Line Parents
- One-QTL Genetic Model in Double Cross F1 Population
- The Linear Regression Model of the Phenotype on Marker Type for Multiple QTLs
- Inclusive Composite Interval Mapping (ICIM) in the Double Cross F1 Population
- Exercises
- Genetic Analysis in Multi-Parental Pure-Line Progeny Populations
- Linkage Analysis in Four-Parental Pure-Line Populations
- Development Procedure and Marker Classification in Four-Parental Pure-Line Populations
- Theoretical Frequencies of Genotypes and Estimation of Recombination Frequency at Two Complete Loci
- Estimation of the Recombination Frequency Involving Incomplete Markers
- Situations When Number of Inbred Parents Smaller Than Four
- Linkage Analysis in Eight-Parental Pure-Line Populations
- Development Procedure and Marker Classification in Eight-Parental Pure-Line Populations
- Marker Classification and Genotypic Coding in Eight-Parental Pure-Line Populations
- Theoretical Frequencies of Genotypes at Two Complete Loci
- Estimation of the Recombination Frequency Between Any Two Categories of Markers
- Situations When the Number of Inbred Parents Smaller Than Eight
- QTL Mapping in Four-Parental Pure-Line Populations
- Genetic Constitution at Three Complete Loci
- Imputation of the Incomplete and Missing Marker Information
- The Linear Regression Model of Phenotype on Marker Types
- Inclusive Composite Interval Mapping (ICIM) in Four-Parental Pure-Line Populations
- QTL Mapping in Eight-Parental Pure-Line Populations
- Genetic Constitution at Three Complete Loci
- The Linear Regression Model of Phenotype on Marker Types
- Inclusive Composite Interval Mapping (ICIM) in Eight-Parental Pure-Line Populations
- Exercises
- QTL Mapping in Other Genetic Populations
- Selective Genotyping Analysis and Bulked Segregant Analysis
- Statistical Principles of Selective Genotyping Analysis
- Likelihood Ratio Test and LOD Score Statistics from Selective Genotyping Analysis
- Bulked Segregant Analysis
- Problems with Selective Genotyping Analysis and Bulked Segregant Analysis
- QTL Mapping in Populations of Chromosomal Segment Substitution Lines
- Characteristics of Chromosomal Segment Substitution Lines
- Mapping Methods in Populations of Chromosomal Segment Substitution Lines
- QTL Mapping for Grain Length in a CSSL Population in Rice
- QTL Mapping in Genetic Populations of Multiple Parents Crossed with One Common Parent
- Generalized Linear Regression and Model Selection
- Parameter Estimation and Hypothesis Testing in JICIM
- QTL Mapping for Flowering Time in an Arabidopsis NAM Population
- Mendelization of Quantitative Trait Genes
- Preliminary Mapping of One QTL on Grain Width of Rice in One RIL Population
- Validation of the Grain Width QTL by Chromosomal Segment Substitution Lines
- Mendelization of a Stable QTL on Grain Width
- Fine Mapping and Functional Analysis of the Gene at a Stable Grain Width QTL
- Association Mapping in Natural Populations
- Linkage Disequilibrium is the Prerequisite of Gene Mapping
- Linkage Disequilibrium in Random Mating Populations
- Factors Influencing Linkage Disequilibrium
- Comparison of Linkage and Association Approaches in Gene Mapping
- Exercises
- More on the Frequently Asked Questions in QTL Mapping
- Genetic Variance and Contribution to Phenotypic Variation of the Detected QTL
- Genetic Variance and Phenotypic Contribution from One QTL
- Genetic Variance and Phenotypic Contribution of Linked QTLs
- Phenotypic Contribution and the QTL Detection Power
- On the Use of Composite Traits in QTL Mapping
- Composite Traits and Their Applications in Genetic Studies and Breeding
- QTL Mapping on Component and Composite Traits in One Maize RIL Population
- Genetic Effects and Genetic Variances on Composite Traits
- Power Analysis in QTL Mapping on Composite Traits
- Heritability of Composite Traits
- Effects on QTL Detection by the Increase in Marker Density
- Effects of Denser Markers on Independent QTLs
- Effect of Denser Markers on Linked QTLs
- Imputation of Missing Marker Types and Their Effects in QTL Mapping in Bi-Parental Populations
- Imputation of Missing and Incomplete Marker Types
- QTLs on Plant Height in an F2 Population in Rice
- Effects of Missing Marker Types on QTL Detection
- Effects of Segregation Distortion on Genetic Studies
- Segregation Distortion Loci in One Rice F2 Population
- Effects of Segregation Distortion on QTL Mapping in Populations with Three Genotypes at Each Locus
- Genetic Distance That can be Affected by Segregation Distortion
- Effects of Segregation Distortion on QTL Mapping in Populations with Two Genotypes at Each Locus
- Non-Normality of the Phenotypic Distribution
- Phenotypic Model and Distribution of Quantitative Traits
- QTL Mapping on Phenotypic Traits of the Non-Normal Distributions
- Exercises
- References
- Index
- Appendix A: Journal Articles Making Up This Book (relevant contents to the book are indicated at the end of each journal article)
- Appendix B: Dissertations of Post-Graduates Making Up This Book
- Appendix C: Integrated Software Packages Making Up This Book
