| Basic Genetics | p. 1 |
| Introduction | p. 1 |
| Genes and Chromosomes | p. 1 |
| Meiosis | p. 2 |
| Mendel's Laws | p. 3 |
| Mendel's First Law | p. 3 |
| Mendel's Second Law | p. 4 |
| Linkage and Mapping | p. 5 |
| Interference | p. 8 |
| Quantitative Genetics | p. 8 |
| Population Properties of Genes | p. 8 |
| A General Quantitative Genetic Model | p. 9 |
| Genetic Models for the Backcross and F2 Design | p. 10 |
| Epistatic Model | p. 12 |
| Heritability and Its Estimation | p. 12 |
| Genetic Architecture | p. 14 |
| The Estimation of Gene Number | p. 15 |
| Molecular Genetics | p. 16 |
| SNP | p. 18 |
| Exercises | p. 20 |
| Note | p. 20 |
| Modeling Unequal Genetic Effects by the Gamma Function | p. 21 |
| Modeling Unequal Genetic Effects by a Geometric Series | p. 22 |
| Basic Statistics | p. 25 |
| Introduction | p. 25 |
| Populations and Models | p. 25 |
| Samples | p. 27 |
| Likelihood Estimation | p. 27 |
| Hypothesis Testing | p. 31 |
| The Pearson Chi-Squared Test | p. 31 |
| Likelihood Ratio Tests | p. 33 |
| Simulation-Based Approach | p. 37 |
| Bayesian Estimation | p. 38 |
| Exercises | p. 40 |
| Linkage Analysis and Map Construction | p. 43 |
| Introduction | p. 43 |
| Experimental Design | p. 44 |
| Mendelian Segregation | p. 45 |
| Testing Marker Segregation Patterns | p. 45 |
| Segregation Patterns in a Full-Sib Family | p. 46 |
| Two-Point Analysis | p. 49 |
| Double Backcross | p. 50 |
| Double Intercross-F2 | p. 52 |
| Three-Point Analysis | p. 56 |
| Multilocus Likelihood and Locus Ordering | p. 58 |
| Estimation with Many Loci | p. 61 |
| Mixture Likelihoods and Order Probabilities | p. 62 |
| Map Functions | p. 63 |
| Mather's Formula | p. 64 |
| The Morgan Map Function | p. 65 |
| The Haldane Map Function | p. 65 |
| The Kosambi Map Function | p. 66 |
| Exercises | p. 69 |
| Notes: Algorithms and Software for Map Construction | p. 71 |
| A General Model for Linkage Analysis in Controlled Crosses | p. 77 |
| Introduction | p. 77 |
| Fully Informative Markers: A Diplotype Model | p. 78 |
| Two-Point Analysis | p. 78 |
| A More General Formulation | p. 81 |
| Three-Point Analysis | p. 82 |
| A More General Formulation | p. 86 |
| Fully Informative Markers: A Genotype Model | p. 88 |
| Parental Diplotypes | p. 88 |
| Joint modeling of the Linkage, Parental Diplotype, and Gene Order | p. 91 |
| Partially Informative Markers | p. 96 |
| Joint modeling of the Linkage and Parental Diplotype | p. 96 |
| Joint modeling of the Linkage, Parental Diplotype, and Gene Order | p. 98 |
| Exercises | p. 99 |
| One dominant marker | p. 100 |
| One dominant marker and one F2 codominant marker | p. 100 |
| Notes | p. 101 |
| Linkage Analysis | p. 101 |
| The Diplotype Probability | p. 102 |
| Gene Order | p. 105 |
| M-Point Analysis | p. 106 |
| Linkage Analysis with Recombinant Inbred Lines | p. 107 |
| Introduction | p. 107 |
| RILs by Selling | p. 107 |
| Two-Point Analysis | p. 107 |
| Three-Point Analysis | p. 111 |
| RILs by Sibling Mating | p. 117 |
| Two-point Analysis | p. 117 |
| Three-point Analysis | p. 118 |
| Bias Reduction | p. 118 |
| RILs by Selling | p. 118 |
| RILs by Sibling Mating | p. 119 |
| Multiway RILs | p. 120 |
| Exercises | p. 120 |
| Note | p. 122 |
| Linkage Analysis for Distorted and Misclassified Markers | p. 123 |
| Introduction | p. 123 |
| Gametic Differential Viability | p. 123 |
| One-Gene Model | p. 123 |
| Two-Gene Model | p. 127 |
| Simulation | p. 130 |
| Zygotic Differential Viability | p. 132 |
| One-Gene Model | p. 132 |
| Two-Gene Model | p. 133 |
| Simulation | p. 134 |
| Misclassification | p. 134 |
| One-gene Model | p. 134 |
| Two-Gene Model | p. 138 |
| Simulation | p. 141 |
| Exercises | p. 142 |
| Special Considerations in Linkage Analysis | p. 145 |
| Introduction | p. 145 |
| Linkage Analysis with a Complicated Pedigree | p. 145 |
| A Nuclear Family | p. 145 |
| Multipoint Estimation of Identical-By-Descent Sharing | p. 149 |
| A Complex Pedigree | p. 150 |
| Information Analysis of Dominant Markers | p. 160 |
| Introduction | p. 160 |
| Segregation Analysis | p. 161 |
| Linkage Analysis | p. 165 |
| Exercises | p. 168 |
| Marker Analysis of Phenotypes | p. 171 |
| Introduction | p. 171 |
| QTL Regression Model | p. 172 |
| Analysis at the Marker | p. 174 |
| Two-Sample t Test | p. 174 |
| Analysis of Variance | p. 176 |
| Genetic Analysis | p. 179 |
| Moving Away from the Marker | p. 181 |
| Likelihood | p. 181 |
| Power Calculation | p. 184 |
| Marker Interaction Analysis | p. 188 |
| ANOVA | p. 188 |
| Genetic Analysis | p. 192 |
| Whole-Genome Marker Analysis | p. 195 |
| Exercises | p. 198 |
| The Structure of QTL Mapping | p. 203 |
| Introduction | p. 203 |
| The Mixture Model | p. 204 |
| Formulation | p. 204 |
| Structure, Setting, and Estimation | p. 206 |
| Population Genetic Structure of the Mixture Model | p. 207 |
| Backcross/F2 | p. 207 |
| Outbred Crosses | p. 208 |
| Recombinant Inbred Lines | p. 208 |
| Natural Populations | p. 208 |
| Quantitative Genetic Structure of the Mixture Model | p. 208 |
| Additive-Dominance Model | p. 209 |
| Additive-Dominance-Epistasis Model | p. 210 |
| Multiplicative-Epistatic Model | p. 211 |
| Mechanistic Model | p. 212 |
| Experimental Setting of the Mixture Model | p. 213 |
| Estimation in the Mixture Model | p. 214 |
| Computational Algorithms for the Mixture Model | p. 216 |
| EM Algorithm | p. 216 |
| Monte Carlo EM | p. 216 |
| Stochastic EM | p. 217 |
| An EM Algorithm/Newton-Raphson Hybrid | p. 217 |
| Some Cautions | p. 218 |
| Bayesian Methods | p. 218 |
| Estimating the Number of Components in a Mixture Model | p. 220 |
| Exercises | p. 221 |
| Interval Mapping with Regression Analysis | p. 223 |
| Introduction | p. 223 |
| Linear Regression Model | p. 224 |
| Interval Mapping in the Backcross | p. 224 |
| Conditional Probabilities | p. 224 |
| Conditional Regression Model | p. 226 |
| Estimation and Test | p. 228 |
| Interval Mapping in an F2 | p. 230 |
| Remarks | p. 233 |
| Exercises | p. 234 |
| Interval Mapping by Maximum Likelihood Approach | p. 237 |
| Introduction | p. 237 |
| QTL Interval Mapping in a Backcross | p. 238 |
| The Likelihood | p. 238 |
| Maximizing the Likelihood | p. 240 |
| Hypothesis Testing | p. 246 |
| Model for Incorporating Double Recombination | p. 252 |
| Model for Incorporating Interference | p. 252 |
| QTL Interval Mapping in an F2 | p. 254 |
| No Double Recombination | p. 254 |
| Independence | p. 257 |
| Interference | p. 260 |
| Testing Hypotheses | p. 262 |
| Factors That Affect QTL Detection | p. 262 |
| Procedures for QTL Mapping | p. 263 |
| The Number of QTLs | p. 263 |
| Locations of Individual QTLs | p. 266 |
| Exercises | p. 267 |
| Threshold and Precision Analysis | p. 269 |
| Introduction | p. 269 |
| Threshold Determination | p. 270 |
| Background | p. 270 |
| Analytical Approximations | p. 271 |
| Simulation Studies | p. 275 |
| Permutation Tests | p. 275 |
| A Quick Approach | p. 276 |
| A Score Statistic | p. 277 |
| Precision of Parameter Estimation | p. 279 |
| Asymptotic Variance-Covariance Matrix | p. 279 |
| Simulation Studies | p. 282 |
| Confidence Intervals for the QTL Location | p. 283 |
| Exercises | p. 285 |
| Composite QTL Mapping | p. 287 |
| Introduction | p. 287 |
| Composite Interval Mapping for a Backcross | p. 288 |
| The Likelihood | p. 288 |
| Maximizing the Likelihood | p. 289 |
| Hypothesis Testing | p. 290 |
| Composite Interval Mapping for an F2 | p. 291 |
| A Statistical Justification of Composite Interval Mapping | p. 293 |
| Conditional Marker (Co)variances | p. 293 |
| Conditional QTL Variance | p. 295 |
| Marker Selection | p. 298 |
| Comparisons Between Composite Interval Mapping and Interval Mapping | p. 298 |
| Multiple Interval Mapping | p. 301 |
| Exercises | p. 302 |
| QTL Mapping in Outbred Pedigrees | p. 303 |
| Introduction | p. 303 |
| A Fixed-Effect Model for a Full-Sib Family | p. 304 |
| Introduction | p. 304 |
| A Mixture Model for a Parental Diplotype | p. 304 |
| Quantitative Genetic Model | p. 308 |
| Likelihood Analysis | p. 309 |
| Fitting Marker Phenotypes | p. 312 |
| Hypothesis Tests | p. 313 |
| The Influence of Linkage Phases | p. 316 |
| Random-Effect Mapping Model for a Complicated Pedigree | p. 317 |
| Introduction | p. 317 |
| Statistical Model | p. 319 |
| IBD at a QTL | p. 320 |
| The Likelihood | p. 321 |
| Hypothesis Testing | p. 323 |
| Exercises | p. 325 |
| General Statistical Results and Algorithms | p. 331 |
| Likelihood Asymptotics | p. 331 |
| General Form of the EM Algorithm | p. 332 |
| R Programs | p. 335 |
| Chapter 2 | p. 335 |
| Chapter 8 | p. 337 |
| References | p. 343 |
| Author Index | p. 355 |
| Subject Index | p. 361 |
| Table of Contents provided by Publisher. All Rights Reserved. |
