Statistical Genomics: Linkage, Mapping, and QTL Analysis

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ISBN 9780849331664
Cat# 3166

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Features

  • Covers background information, such as basic genetics, mating design, and genetic markers
  • Includes statistical theory for genomics and statistical principles and methods
  • Presents the theory and methods for searching genes controlling complex traits, known as Quantitative Trait Loci (QTL) mapping
  • Provides computer tools for genomic map construction and QTL analysis, as well as resampling techniques and information on computer simulation
  • Enhanced by useful statistical software, available on the Internet, that helps you implement many of the techniques presented in the book
  • Contains many different types of applications emphasizing the use of computers, and includes all of the latest statistical methods used today
  • Covers both the theory and the implementation of that theory, both of which are important in interpreting results
  • Details the recent concepts in statistical genomics, such as gene ordering, synteny detection and genetic map merging, mapping using natural populations, high resolution QTL mapping, and computer simulation
  • Summary

    Genomics, the mapping of the entire genetic complement of an organism, is the new frontier in biology. This handbook on the statistical issues of genomics covers current methods and the tried-and-true classical approaches.

    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

    Editorial Reviews

    "The book deals with one of the most active areas of genomic science… It is a very comprehensive treatment of the subject from a practical and theoretical perspective. This book is significantly ahead of what is currently published."
    Ronald Sederoff
    North Carolina State University

    "First, this book is extremely timely as genomics and gene mapping is an area undergoing exponential growth. Second, the coverage is indeed excellent. Third, Dr. Liu is extremely well qualified to write this book… he knows both the underlying theory as well as problems in applying it in real settings."
    Bruce Walsh
    University of Arizona