Table of Contents

Introduction Forward Introducing Genomics Statistical Genomics Related Books Biology in Genomics Introduction Mendelian Genetics and Cytogenetics Population Genetics Quantitative Genetics Molecular Genetics Exercises Introduction to Genomics Genome Genomics Genetic Markers Exercises Statistics in Genomics Introduction Distribution Likelihood Hypothesis Test Estimation Sample Size Determination Summary Exercises Single-Locus Models Introduction Expected Segregation Ratio Marker Screening Natural Population Exercises Two-Locus Models I: Controlled Cross Introduction Linkage Detection Recombination Frequency Estimation Statistical Properties Sample Size Consideration Dominant Markers in F2 Progeny Violation of Assumptions Summary Exercises Two-Locus Model II: Natural Population Introduction Linkage Phase Problem Mixture of Self and Random Mating Exercises Two-Locus Model III: Using Disequilibrium Introduction Linkage Disequilibrium Transmission Disequilibrium Test Other Disequilibrium Based Analysis Estimation of Recombination Frequency Exercises Linkage Grouping and Locus Ordering Introduction Linkage Grouping Three-Locus Ordering Multiple-Locus Ordering Probability of Estimated Locus Orders Exercise Multi-Locus Model Introduction Three-Locus Model Map Function Multi-Locus Map Distance Marker Coverage and Map Density Exercises Linkage Map Merging Introduction Factors Related to Linkage Map Merging Hypothesis on Gene Orders Linkage Map Pooling Exercises QTL Mapping I: Introduction History Quantitative Genetics Models Example Data Exercise QTL Mapping II: Single-Marker Analysis Rationale Single-Marker Analysis in Backcross Progeny Single Marker Analysis Using F2 Progeny Summary Exercises QTL Mapping III: Interval Mapping Introduction Interval Mapping Using Backcross Progeny Interval Mapping Using F2 Progeny Composite Interval Mapping Summary Exercises QTL Mapping IV: Natural Population Introduction Open-Pollinated Populations Sib-Pair Method Exercises QTL Mapping V: Power Introduction Single QTL Detection Power Multiple QTL Exercises QTL Mapping VI: Future Considerations Problems with QTL Mapping QTL Resolution Mapping Strategies What are QTL Future QTL Mapping Exercises Computer Tools Computer Tools for Genomic Data Analysis Future Considerations PGRI (Plant Genome Research Initiative Resampling and Simulation in Genomics Introduction Resampling Computer Simulation Mapping Population Simulation Exercises Bibliography Author Index Subject Index