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