*T*he book introduces the basic concepts and methods that are useful in the statistical analysis and modeling of DNA-based marker and phenotypic data that arise in agriculture, forrestry, experimental biology, and other fields. It concentrates on the linkage analysis of markers, map construction and quantitative trait locus (QTL) mapping and assumes a background in regression analysis and maximum likelihood approaches. The strengths of this book lie in the construction of general models and algorithms for linkage analysis and QTL mapping in any kind of crossed pedigrees initiated with inbred lines of crops and plant and animal model systems or outbred lines in forest trees and wildlife species.

*T*he book includes a detailed description of each approach and the step-by-step demonstration of live-example analyses designed to explain the utilization and usefulness of statistical methods. The book also includes exercise sets and computer codes for all the analyses used.

*T*his book can serve as a textbook for graduates and senior undergraduates in genetics, agronomy, forest biology, plant breeding and animal sciences. It will also be useful to researchers and other professionals in the areas of statistics, biology and agriculture.

*R*ongling Wu is Associate Professor of Statistics at the University of Florida, Gainesville. He currently serves as Associate Editor for six genetics and bioinformatics journals. Chang-Xing Ma is Assistant Professor of Biostatistics at the State University of New York at Buffalo. George Casella is Distinguished Professor of Statistics and Distinguished Member of the Genetics Institute at the Univesity of Florida, Gainesville. He is a fellow of the American Statistical Association and the Institute of Mathematical Sciences, and the author of four other statistics books.

*T*his book can serve as a textbook for graduates and senior undergraduates in genetics, agronomy, forest biology, plant breeding and animal sciences. It will also be useful to researchers and other professionals in the areas of statistics, biology and agriculture.

"**I**t is a big help and guidance in the field of statistical developments for genetic mapping, synthesised all in one volume helping to build a bridge between genetics and statistics."

"...**T**his is an ideal book for a young researcher looking for an exciting and developing field to get into."

Most traits in nature and of importance to agriculture are quantitatively inherited.These traits are difficult to study due to the complex nature of their inheritance.However, recent developments of genomic technologies provide a revolutionary means for unraveling the secrets of genetic variation in ...

Now that we have seen the basics of genetics, we turn to an introduction to the statistical methodologies that we will use throughout this book. Most of the statistical inferences that we will make will be based on likelihood analysis, and we will be concerned not only with constructing the appropriate ...

- 01
- Basic Genetics.

1.1 Introduction

1.2 Genes and Chromosomes

1.3 Meiosis

1.4 Mendelfs Laws

1.5 Linkage and Mapping

1.6 Interference

1.7 Quantitative Genetics

1.8 Molecular Genetics

1.9 SNP

1.10 Exercises

1.11 Note

- 02
- Basic Statistics.

2.1 Introduction

2.2 Likelihood Estimation

2.3 Hypothesis Testing

2.4 Exercises

- 03
- Linkage Analysis and Map Construction.

3.1 Introduction

3.2 Experimental Design

3.3 Mendelian Segregation

3.4 Segregation Patterns in a Full-Sib Family

3.5 Two-Point Analysis

3.6 Three-Point Analysis

3.7 Multilocus Likelihood and Locus Ordering

3.8 Estimation with Many Loci

3.9 Mixture Likelihoods and Order Probabilities

3.10 Map Functions

3.11 Exercises

3.12 Notes: Algorithms and Software for Map Construction

- 04
- A General Model for Linkage Analysis in Controlled Crosses.

4.1 Introduction

4.2 Fully Informative Markers: A Diplotype Model

4.3 Fully Informative Markers: A Genotype Model

4.4 Joint modeling of the Linkage, Parental Diplotype, and Gene Order

4.5 Partially Informative Markers

4.6 Exercises

4.7 Notes

- 05
- Linkage Analysis with Recombinant Inbred Lines.

5.1 Introduction

5.2 RILs by Selfing

5.3 RILs by Sibling Mating

5.4 Bias Reduction

5.5 Multiway RILs

5.6 Exercises

5.7 Note

- 06
- Linkage Analysis for Distorted and Misclassified Markers

6.1 Introduction

6.2 Gametic Differential Viability

6.3 Zygotic Differential Viability

6.4 Misclassification

6.5 Simulation

6.6 Exercises

- 07
- Special Considerations in Linkage Analysis

7.1 Introduction

7.2 Linkage Analysis with a Complicated Pedigree

7.3 Information Analysis of Dominant Markers

7.4 Exercises

- 08
- Marker Analysis of Phenotypes.

8.1 Introduction

8.2 QTL Regression Model

8.3 Analysis at the Marker

8.4 Moving Away from the Marker

8.5 Power Calculation

8.6 Marker Interaction Analysis

8.7 Whole-Genome Marker Analysis

8.8 Exercises

- 09
- The Structure of QTL Mapping.

9.1 Introduction

9.2 The Mixture Model

9.3 Population Genetic Structure of the Mixture Model

9.4 Quantitative Genetic Structure of the Mixture Model

9.5 Experimental Setting of the Mixture Model

9.6 Estimation in the Mixture Model

9.7 Computational Algorithms for the Mixture Model

9.8 Exercises

- 10
- Interval Mapping with Regression Analysis.

10.1 Introduction

10.2 Linear Regression Model

10.3 Interval Mapping in the Backcross

10.4 Interval Mapping in an F2

10.5 Remarks

10.6 Exercises

- 11
- Interval Mapping by Maximum Likelihood Approach.

11.1 Introduction

11.2 QTL Interval Mapping in a Backcross

11.3 Hypothesis Testing

11.4 QTL Interval Mapping in an F2

11.5 Factors That Affect QTL Detection

11.6 Procedures for QTL Mapping

11.7 Exercises

- 12
- Threshold and Precision Analysis.

12.1 Introduction

12.2 Threshold Determination

12.3 Precision of Parameter Estimation

12.4 Confidence Intervals for the QTL Location

12.5 Exercises

- 13
- Composite QTL Mapping.

13.1 Introduction

13.2 Composite Interval Mapping for a Backcross

13.3 Composite Interval Mapping for an F2

13.4 A Statistical Justification of Composite Interval Mapping

13.5 Comparisons Between Composite Interval Mapping and Interval Mapping

13.6 Multiple Interval Mapping

13.7 Exercises

- 14
- QTL Mapping in Outbred Pedigrees .

14.1 Introduction

14.2 A Fixed-Effect Model for a Full-Sib Family

14.3 Random-Effect Mapping Model for a Complicated Pedigree

14.4 Exercises

- A
- General Statistical Results and Algorithms.

- B
- R Programs.

- C
- References .