Genomic Selection in Animals 1st Edition by Joel Weller 0470960078 9780470960073

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ISBN 10: 0470960078
ISBN 13: 9780470960073
Author: Joel Weller

The field of whole genome selection has quickly developed into the breeding methodology of the future. As efforts to map a wide variety of animal genomes have matured and full animal genomes are now available for many animal scientists and breeders are looking to apply these techniques to livestock production.

Providing a comprehensive, forward-looking review of animal genomics, Genomic Selection in Animals provides coverage of genomic selection in a variety of economically important species including cattle, swine, and poultry. The historical foundations of genomic selection are followed by chapters that review and assess current techniques. The final chapter looks toward the future and what lies ahead for field as application of genomic selection becomes more widespread.

Genomic Selection in Animals 1st Table of contents:

Chapter 1 Historical Overview

Introduction
The Mendelian Theory of Genetics
The Mendelian Basis of Quantitative Variation
Detection of QTL with Morphological and Biochemical Markers
DNA-Level Markers, 1974–1994
DNA-Level Markers Since 1995: SNPs and CNV
QTL Detection Prior to Genomic Selection
MAS Prior to Genomic Selection
Summary

Chapter 2 Types of Current Genetic Markers and Genotyping Methodologies

Introduction
From Biochemical Markers to DNA-Level Markers
DNA Microsatellites
Single Nucleotide Polymorphisms
Copy Number Variation
Complete Genome Sequencing
Summary

Chapter 3 Advanced Animal Breeding Programs Prior to Genomic Selection

Introduction
Within a Breed Selection: Basic Principles and Equations
Traditional Selection Schemes for Dairy Cattle
Crossbreeding Schemes: Advantages and Disadvantages
Summary

Chapter 4 Economic Evaluation of Genetic Breeding Programs

Introduction
National Economy versus Competition among Breeders
Criteria for Economic Evaluation: Profit Horizon, Interest Rate, and Return on Investment
Summary

Chapter 5 Least Squares, Maximum Likelihood, and Bayesian Parameter Estimation

Introduction
Least Squares Parameter Estimation
ML Estimation for a Single Parameter
ML Multiparameter Estimation
Methods to Maximize Likelihood Functions
Confidence Intervals and Hypothesis Testing for MLE
Bayesian Estimation
Parameter Estimation via the Gibbs Sampler
Summary

Chapter 6 Trait-Based Genetic Evaluation: The Mixed Model

Introduction
Principles of Selection Index
The Mixed Linear Model
The Mixed Model Equations
Solving the Mixed Model Equations
Important Properties of Mixed Model Solutions
Multivariate Mixed Model Analysis
The Individual Animal Model
Yield Deviations and Daughter Yield Deviations
Analysis of DYD as the Dependent Variable
Summary

Chapter 7 Maximum Likelihood and Bayesian Estimation of QTL Parameters with Random Effects Included in the Model

Introduction
Maximum Likelihood Estimation of QTL Effects with Random Effects Included in the Model, the Daughter Design
The Granddaughter Design
Determination of Prior Distributions of the QTL Parameters for the Granddaughter Design
Formula for Bayesian Estimation and Tests of Significance of a Segregating QTL in a Granddaughter Design
Summary

Chapter 8 Maximum Likelihood, Restricted Maximum Likelihood, and Bayesian Estimation for Mixed Models

Introduction
Derivation of Solutions to the Mixed Model Equations by Maximum Likelihood
Estimation of the Mixed Model Variance Components
Maximum Likelihood Estimation of Variance Components
Restricted Maximum Likelihood Estimation of Variance Components
Estimation of Variance Components via the Gibbs Sampler
Summary

Chapter 9 Distribution of Genetic Effects, Theory, and Results

Introduction
Modeling the Polygenic Variance
The Effective Number of QTL
The Case of the Missing Heritability
Methods for Determination of Causative Mutations for QTL in Animals and Humans
Determination of QTN in Dairy Cattle
Estimating the Number of Segregating QTL Based on Linkage Mapping Studies
Results of Genome Scans of Dairy Cattle by Granddaughter Designs
Results of Genome-Wide Association Studies in Dairy Cattle by SNP Chips
Summary

Chapter 10 The Multiple Comparison Problem

Introduction
Multiple Markers and Whole Genome Scans
QTL Detection by Permutation Tests
QTL Detection Based on the False Discovery Rate
A Priori Determination of the Proportion of False Positives
Biases with Estimation of Multiple QTL
Bayesian Estimation of QTL from Whole Genome Scans: Theory
Bayes A and Bayes B Models
Bayesian Estimation of QTL from Whole Genome Scans: Simulation Results
Summary

Chapter 11 Linkage Mapping of QTL

Introduction
Interval Mapping by Nonlinear Regression: The Backcross Design
Interval Mapping for Daughter and Granddaughter Designs
Computation of Confidence Intervals
Simulation Studies of CIs
Empirical Methods to Estimate CIs, Parametric and Nonparametric Bootstrap, and Jackknife Methods
Summary

Chapter 12 Linkage Disequilibrium Mapping of QTL

Introduction
Estimation of Linkage Disequilibrium in Animal Populations
Linkage Disequilibrium QTL Mapping: Basic Principles
Joint Linkage and Linkage Disequilibrium Mapping
Multitrait and Multiple QTL LD Mapping
Summary

Chapter 13 Marker-Assisted Selection: Basic Strategies

Introduction
Situations in Which Selection Index is Inefficient
Potential Contribution of MAS for Selection within a Breed: General Considerations
Phenotypic Selection versus MAS for Individual Selection
MAS for Sex-Limited Traits
MAS Including Marker and Phenotypic Information on Relatives
Maximum Selection Efficiency of MAS with All QTL Known, Relative to Trait-Based Selection, and the Reduction in RSE Due to Sampling Variance
Marker Information in Segregating Populations
Inclusion of Marker Information in “Animal Model” Genetic Evaluations
Predicted Genetic Gains with Genomic Estimated Breeding Values: Results of Simulation Studies
Summary

Chapter 14 Genetic Evaluation Based on Dense Marker Maps: Basic Strategies

Introduction
The Basic Steps in Genomic Evaluation
Evaluation of Genomic Estimated Breeding Values
Sources of Bias in Genomic Evaluation
Marker Effects Fixed or Random?
Individual Markers versus Haplotypes
Total Markers versus Usable Markers
Deviation of Genotype Frequencies from Their Expectations
Inclusion of All Markers versus Selection of Markers with Significant Effects
The Genomic Relationship Matrix
Summary

Chapter 15 Genetic Evaluation Based on Analysis of Genetic Evaluations or Daughter-Yield Evaluations

Introduction
Comparison of Single-Step and Multistep Models
Derivation and Properties of Daughter Yields and DYD
Computation of “Deregressed” Genetic Evaluations
Analysis of DYD as the Dependent Variable with All Markers Included as Random Effects
Computation of Reliabilities for Genomic Estimated Breeding Values
Bayesian Weighting of Marker Effects
Additional Bayesian Methods for Genomic Evaluation
Summary

Chapter 16 Genomic Evaluation Based on Analysis of Production Records

Introduction
Single-Step Methodologies: The Basic Strategy
Computation of the Modified Relationship Matrix when only a Fraction of the Animals are Genotyped: The Problem
Criteria for Valid Genetic Relationship Matrices
Computation of the Modified Relationship Matrix when only a Fraction of the Animals are Genotyped, the Solution
Solving the Mixed Model Equations without Inverting H
Inverting the Genomic Relationship Matrix
Estimation of Reliabilities for Genomic Breeding Values Derived by Single-Step Methodologies
Single-Step Computation of Genomic Evaluations with Unequally Weighted Marker Effects
Summary

Chapter 17 Validation of Methods for Genomic Estimated Breeding Values

Introduction
Criteria for Evaluation of Estimated Genetic Values
Methods Used to Validate Genomic Genetic Evaluations
Evaluation of Two-Step Methodology Based on Simulated Dairy Cattle Data
Evaluation of Multistep Methodology Based on Actual Dairy Cattle Data
Evaluation of Single-Step Methodologies Based on Actual Dairy Cattle Data
Evaluation of Single- and Multistep Methodologies Based on Actual Poultry Data
Evaluation of Single- and Multistep Methodologies Based on Actual Swine Data
Evaluation of GEBV for Plants Based on Actual Data
Summary

Chapter 18 By-Products of Genomic Analysis: Pedigree Validation and Determination

Introduction
The Effects of Incorrect Parentage Identification on Breeding Programs
Principles of Parentage Verification and Identification with Genetic Markers
Paternity Validation Prior to High-Density SNP Chips
Paternity Validation and Determination with SNP Chips
Validation of More Distant Relationships
Pedigree Reconstruction with High-Density Genetic Markers
Summary

Chapter 19 Imputation of Missing Genotypes: Methodologies, Accuracies, and Effects on Genomic Evaluations

Introduction
Determination of Haplotypes for Imputation
Imputation in Humans versus Imputation in Farm Animals
Algorithms Proposed for Imputation in Human and Animal Populations
Comparisons of Accuracy and Speed of Imputation Methods
Effect of Imputation on Genomic Genetic Evaluations
Summary

Chapter 20 Detection and Validation of Quantitative Trait Nucleotides

Introduction
GWAS for Economic Traits in Commercial Animals
Detection of QTN: Is It Worth the Effort?
QTN Determination in Farm Animals: What Constitutes Proof?
Concordance between DNA-Level Genotypes and QTL Status
Determination of Concordance by the “APGD”
Determination of Phase for Grandsires Heterozygous for the QTL
Determination of Recessive Lethal Genes by GWAS and Effects Associated with Heterozygotes
Verification of QTN by Statistical and Biological Methods
Summary

 

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Tags: Genomic, Selection, Animals, Joel Weller