Joel Weller
Genomic Selection in Animals
Joel Weller
Genomic Selection in Animals
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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…mehr
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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. A concise, useful summary of the field by one of the world's leading researchers, Genomic Selection in Animals fills an important gap in the literature of animal breeding and genomics.
Produktdetails
- Produktdetails
- Verlag: John Wiley & Sons / Turner Publishing Company
- Seitenzahl: 192
- Erscheinungstermin: 7. März 2016
- Englisch
- Abmessung: 250mm x 175mm x 15mm
- Gewicht: 519g
- ISBN-13: 9780470960073
- ISBN-10: 0470960078
- Artikelnr.: 43542531
- Verlag: John Wiley & Sons / Turner Publishing Company
- Seitenzahl: 192
- Erscheinungstermin: 7. März 2016
- Englisch
- Abmessung: 250mm x 175mm x 15mm
- Gewicht: 519g
- ISBN-13: 9780470960073
- ISBN-10: 0470960078
- Artikelnr.: 43542531
Joel Ira Weller is a Research Scientist at the Institute of Animal Sciences, ARO, The Volcani Center in Bet Dagan, Israel.
Preface: Welcome to the "Promised Land" xiii Chapter 1 Historical Overview
1 Introduction 1 The Mendelian Theory of Genetics 1 The Mendelian Basis of
Quantitative Variation 2 Detection of QTL with Morphological and
Biochemical Markers 2 DNA?-Level Markers, 1974-1994 3 DNA?-Level Markers
Since 1995: SNPs and CNV 4 QTL Detection Prior to Genomic Selection 4 MAS
Prior to Genomic Selection 5 Summary 6 Chapter 2 Types of Current Genetic
Markers and Genotyping Methodologies 7 Introduction 7 From Biochemical
Markers to DNA?]Level Markers 7 DNA Microsatellites 8 Single Nucleotide
Polymorphisms 8 Copy Number Variation 9 Complete Genome Sequencing 9
Summary 10 Chapter 3 Advanced Animal Breeding Programs Prior to Genomic
Selection 11 Introduction 11 Within a Breed Selection: Basic Principles and
Equations 11 Traditional Selection Schemes for Dairy Cattle 12
Crossbreeding Schemes: Advantages and Disadvantages 14 Summary 15 Chapter 4
Economic Evaluation of Genetic Breeding Programs 17 Introduction 17
National Economy versus Competition among Breeders 17 Criteria for Economic
Evaluation: Profit Horizon, Interest Rate, and Return on Investment 18
Summary 20 Chapter 5 Least Squares, Maximum Likelihood, and Bayesian
Parameter Estimation 21 Introduction 21 Least Squares Parameter Estimation
21 ML Estimation for a Single Parameter 22 ML Multiparameter Estimation 24
Methods to Maximize Likelihood Functions 26 Confidence Intervals and
Hypothesis Testing for MLE 26 Bayesian Estimation 27 Parameter Estimation
via the Gibbs Sampler 28 Summary 29 Chapter 6 Trait-Based Genetic
Evaluation: The Mixed Model 31 Introduction 31 Principles of Selection
Index 31 The Mixed Linear Model 34 The Mixed Model Equations 34 Solving the
Mixed Model Equations 35 Important Properties of Mixed Model Solutions 36
Multivariate Mixed Model Analysis 37 The Individual Animal Model 38 Yield
Deviations and Daughter Yield Deviations 39 Analysis of DYD as the
Dependent Variable 40 Summary 41 Chapter 7 Maximum Likelihood and Bayesian
Estimation of QTL Parameters with Random Effects Included in the Model 43
Introduction 43 Maximum Likelihood Estimation of QTL Effects with Random
Effects Included in the Model, the Daughter Design 43 The Granddaughter
Design 45 Determination of Prior Distributions of the QTL Parameters for
the Granddaughter Design 46 Formula for Bayesian Estimation and Tests of
Significance of a Segregating QTL in a Granddaughter Design 49 Summary 50
Chapter 8 Maximum Likelihood, Restricted Maximum Likelihood, and Bayesian
Estimation for Mixed Models 51 Introduction 51 Derivation of Solutions to
the Mixed Model Equations by Maximum Likelihood 51 Estimation of the Mixed
Model Variance Components 52 Maximum Likelihood Estimation of Variance
Components 52 Restricted Maximum Likelihood Estimation of Variance
Components 54 Estimation of Variance Components via the Gibbs Sampler 55
Summary 58 Chapter 9 Distribution of Genetic Effects, Theory, and Results
59 Introduction 59 Modeling the Polygenic Variance 59 The Effective Number
of QTL 61 The Case of the Missing Heritability 61 Methods for Determination
of Causative Mutations for QTL in Animals and Humans 62 Determination of
QTN in Dairy Cattle 63 Estimating the Number of Segregating QTL Based on
Linkage Mapping Studies 64 Results of Genome Scans of Dairy Cattle by
Granddaughter Designs 65 Results of Genome?]Wide Association Studies in
Dairy Cattle by SNP Chips 66 Summary 66 Chapter 10 The Multiple Comparison
Problem 69 Introduction 69 Multiple Markers and Whole Genome Scans 69 QTL
Detection by Permutation Tests 71 QTL Detection Based on the False
Discovery Rate 71 A Priori Determination of the Proportion of False
Positives 74 Biases with Estimation of Multiple QTL 75 Bayesian Estimation
of QTL from Whole Genome Scans: Theory 76 Bayes A and Bayes B Models 77
Bayesian Estimation of QTL from Whole Genome Scans: Simulation Results 79
Summary 80 Chapter 11 Linkage Mapping of QTL 81 Introduction 81 Interval
Mapping by Nonlinear Regression: The Backcross Design 81 Interval Mapping
for Daughter and Granddaughter Designs 83 Computation of Confidence
Intervals 84 Simulation Studies of CIs 85 Empirical Methods to Estimate
CIs, Parametric and Nonparametric Bootstrap, and Jackknife Methods 86
Summary 87 Chapter 12 Linkage Disequilibrium Mapping of QTL 89 Introduction
89 Estimation of Linkage Disequilibrium in Animal Populations 89 Linkage
Disequilibrium QTL Mapping: Basic Principles 90 Joint Linkage and Linkage
Disequilibrium Mapping 92 Multitrait and Multiple QTL LD Mapping 93 Summary
93 Chapter 13 Marker-Assisted Selection: Basic Strategies 95 Introduction
95 Situations in Which Selection Index is Inefficient 95 Potential
Contribution of MAS for Selection within a Breed: General Considerations 96
Phenotypic Selection versus MAS for Individual Selection 97 MAS for
Sex?-Limited Traits 98 MAS Including Marker and Phenotypic Information on
Relatives 99 Maximum Selection Efficiency of MAS with All QTL Known,
Relative to Trait?-Based Selection, and the Reduction in RSE Due to
Sampling Variance 99 Marker Information in Segregating Populations 100
Inclusion of Marker Information in "Animal Model" Genetic Evaluations 100
Predicted Genetic Gains with Genomic Estimated Breeding Values: Results of
Simulation Studies 101 Summary 102 Chapter 14 Genetic Evaluation Based on
Dense Marker Maps: Basic Strategies 103 Introduction 103 The Basic Steps in
Genomic Evaluation 103 Evaluation of Genomic Estimated Breeding Values 104
Sources of Bias in Genomic Evaluation 104 Marker Effects Fixed or Random?
105 Individual Markers versus Haplotypes 106 Total Markers versus Usable
Markers 106 Deviation of Genotype Frequencies from Their Expectations 107
Inclusion of All Markers versus Selection of Markers with Significant
Effects 107 The Genomic Relationship Matrix 108 Summary 109 Chapter 15
Genetic Evaluation Based on Analysis of Genetic Evaluations or
Daughter-Yield Evaluations 111 Introduction 111 Comparison of Single?]Step
and Multistep Models 111 Derivation and Properties of Daughter Yields and
DYD 112 Computation of "Deregressed" Genetic Evaluations 113 Analysis of
DYD as the Dependent Variable with All Markers Included as Random Effects
114 Computation of Reliabilities for Genomic Estimated Breeding Values 116
Bayesian Weighting of Marker Effects 116 Additional Bayesian Methods for
Genomic Evaluation 117 Summary 117 Chapter 16 Genomic Evaluation Based on
Analysis of Production Records 119 Introduction 119 Single?-Step
Methodologies: The Basic Strategy 119 Computation of the Modified
Relationship Matrix when only a Fraction of the Animals are Genotyped: The
Problem 120 Criteria for Valid Genetic Relationship Matrices 120
Computation of the Modified Relationship Matrix when only a Fraction of the
Animals are Genotyped, the Solution 121 Solving the Mixed Model Equations
without Inverting H 121 Inverting the Genomic Relationship Matrix 122
Estimation of Reliabilities for Genomic Breeding Values Derived by
Single?]Step Methodologies 122 Single?-Step Computation of Genomic
Evaluations with Unequally Weighted Marker Effects 123 Summary 124 Chapter
17 Validation of Methods for Genomic Estimated Breeding Values 125
Introduction 125 Criteria for Evaluation of Estimated Genetic Values 125
Methods Used to Validate Genomic Genetic Evaluations 126 Evaluation of
Two?-Step Methodology Based on Simulated Dairy Cattle Data 127 Evaluation
of Multistep Methodology Based on Actual Dairy Cattle Data 127 Evaluation
of Single-Step Methodologies Based on Actual Dairy Cattle Data 128
Evaluation of Single?- and Multistep Methodologies Based on Actual Poultry
Data 129 Evaluation of Single?- and Multistep Methodologies Based on Actual
Swine Data 130 Evaluation of GEBV for Plants Based on Actual Data 130
Summary 131 Chapter 18 By?-Products of Genomic Analysis: Pedigree
Validation and Determination 133 Introduction 133 The Effects of Incorrect
Parentage Identification on Breeding Programs 133 Principles of Parentage
Verification and Identification with Genetic Markers 134 Paternity
Validation Prior to High?]Density SNP Chips 135 Paternity Validation and
Determination with SNP Chips 135 Validation of More Distant Relationships
136 Pedigree Reconstruction with High?]Density Genetic Markers 137 Summary
137 Chapter 19 Imputation of Missing Genotypes: Methodologies, Accuracies,
and Effects on Genomic Evaluations 139 Introduction 139 Determination of
Haplotypes for Imputation 139 Imputation in Humans versus Imputation in
Farm Animals 140 Algorithms Proposed for Imputation in Human and Animal
Populations 141 Comparisons of Accuracy and Speed of Imputation Methods 142
Effect of Imputation on Genomic Genetic Evaluations 143 Summary 144 Chapter
20 Detection and Validation of Quantitative Trait Nucleotides 145
Introduction 145 GWAS for Economic Traits in Commercial Animals 146
Detection of QTN: Is It Worth the Effort? 146 QTN Determination in Farm
Animals: What Constitutes Proof? 147 Concordance between DNA?-Level
Genotypes and QTL Status 148 Determination of Concordance by the "APGD" 148
Determination of Phase for Grandsires Heterozygous for the QTL 149
Determination of Recessive Lethal Genes by GWAS and Effects Associated with
Heterozygotes 150 Verification of QTN by Statistical and Biological Methods
150 Summary 151 Chapter 21 Future Directions and Conclusions 153
Introduction 153 More Markers versus More Individuals with Genotypes 153
Computation of Genomic Evaluations for Cow and Female Calves 154
Improvement of Genomic Evaluation Methods 154 Long?-Term Considerations 155
Weighting Evaluations of Old versus Young Bulls 156 Direct Genetic
Manipulation in Farm Animals 156 Velogenetics: The Synergistic Use of MAS
and Germ?-Line Manipulation 157 Summary 157 References 159 Index 171
1 Introduction 1 The Mendelian Theory of Genetics 1 The Mendelian Basis of
Quantitative Variation 2 Detection of QTL with Morphological and
Biochemical Markers 2 DNA?-Level Markers, 1974-1994 3 DNA?-Level Markers
Since 1995: SNPs and CNV 4 QTL Detection Prior to Genomic Selection 4 MAS
Prior to Genomic Selection 5 Summary 6 Chapter 2 Types of Current Genetic
Markers and Genotyping Methodologies 7 Introduction 7 From Biochemical
Markers to DNA?]Level Markers 7 DNA Microsatellites 8 Single Nucleotide
Polymorphisms 8 Copy Number Variation 9 Complete Genome Sequencing 9
Summary 10 Chapter 3 Advanced Animal Breeding Programs Prior to Genomic
Selection 11 Introduction 11 Within a Breed Selection: Basic Principles and
Equations 11 Traditional Selection Schemes for Dairy Cattle 12
Crossbreeding Schemes: Advantages and Disadvantages 14 Summary 15 Chapter 4
Economic Evaluation of Genetic Breeding Programs 17 Introduction 17
National Economy versus Competition among Breeders 17 Criteria for Economic
Evaluation: Profit Horizon, Interest Rate, and Return on Investment 18
Summary 20 Chapter 5 Least Squares, Maximum Likelihood, and Bayesian
Parameter Estimation 21 Introduction 21 Least Squares Parameter Estimation
21 ML Estimation for a Single Parameter 22 ML Multiparameter Estimation 24
Methods to Maximize Likelihood Functions 26 Confidence Intervals and
Hypothesis Testing for MLE 26 Bayesian Estimation 27 Parameter Estimation
via the Gibbs Sampler 28 Summary 29 Chapter 6 Trait-Based Genetic
Evaluation: The Mixed Model 31 Introduction 31 Principles of Selection
Index 31 The Mixed Linear Model 34 The Mixed Model Equations 34 Solving the
Mixed Model Equations 35 Important Properties of Mixed Model Solutions 36
Multivariate Mixed Model Analysis 37 The Individual Animal Model 38 Yield
Deviations and Daughter Yield Deviations 39 Analysis of DYD as the
Dependent Variable 40 Summary 41 Chapter 7 Maximum Likelihood and Bayesian
Estimation of QTL Parameters with Random Effects Included in the Model 43
Introduction 43 Maximum Likelihood Estimation of QTL Effects with Random
Effects Included in the Model, the Daughter Design 43 The Granddaughter
Design 45 Determination of Prior Distributions of the QTL Parameters for
the Granddaughter Design 46 Formula for Bayesian Estimation and Tests of
Significance of a Segregating QTL in a Granddaughter Design 49 Summary 50
Chapter 8 Maximum Likelihood, Restricted Maximum Likelihood, and Bayesian
Estimation for Mixed Models 51 Introduction 51 Derivation of Solutions to
the Mixed Model Equations by Maximum Likelihood 51 Estimation of the Mixed
Model Variance Components 52 Maximum Likelihood Estimation of Variance
Components 52 Restricted Maximum Likelihood Estimation of Variance
Components 54 Estimation of Variance Components via the Gibbs Sampler 55
Summary 58 Chapter 9 Distribution of Genetic Effects, Theory, and Results
59 Introduction 59 Modeling the Polygenic Variance 59 The Effective Number
of QTL 61 The Case of the Missing Heritability 61 Methods for Determination
of Causative Mutations for QTL in Animals and Humans 62 Determination of
QTN in Dairy Cattle 63 Estimating the Number of Segregating QTL Based on
Linkage Mapping Studies 64 Results of Genome Scans of Dairy Cattle by
Granddaughter Designs 65 Results of Genome?]Wide Association Studies in
Dairy Cattle by SNP Chips 66 Summary 66 Chapter 10 The Multiple Comparison
Problem 69 Introduction 69 Multiple Markers and Whole Genome Scans 69 QTL
Detection by Permutation Tests 71 QTL Detection Based on the False
Discovery Rate 71 A Priori Determination of the Proportion of False
Positives 74 Biases with Estimation of Multiple QTL 75 Bayesian Estimation
of QTL from Whole Genome Scans: Theory 76 Bayes A and Bayes B Models 77
Bayesian Estimation of QTL from Whole Genome Scans: Simulation Results 79
Summary 80 Chapter 11 Linkage Mapping of QTL 81 Introduction 81 Interval
Mapping by Nonlinear Regression: The Backcross Design 81 Interval Mapping
for Daughter and Granddaughter Designs 83 Computation of Confidence
Intervals 84 Simulation Studies of CIs 85 Empirical Methods to Estimate
CIs, Parametric and Nonparametric Bootstrap, and Jackknife Methods 86
Summary 87 Chapter 12 Linkage Disequilibrium Mapping of QTL 89 Introduction
89 Estimation of Linkage Disequilibrium in Animal Populations 89 Linkage
Disequilibrium QTL Mapping: Basic Principles 90 Joint Linkage and Linkage
Disequilibrium Mapping 92 Multitrait and Multiple QTL LD Mapping 93 Summary
93 Chapter 13 Marker-Assisted Selection: Basic Strategies 95 Introduction
95 Situations in Which Selection Index is Inefficient 95 Potential
Contribution of MAS for Selection within a Breed: General Considerations 96
Phenotypic Selection versus MAS for Individual Selection 97 MAS for
Sex?-Limited Traits 98 MAS Including Marker and Phenotypic Information on
Relatives 99 Maximum Selection Efficiency of MAS with All QTL Known,
Relative to Trait?-Based Selection, and the Reduction in RSE Due to
Sampling Variance 99 Marker Information in Segregating Populations 100
Inclusion of Marker Information in "Animal Model" Genetic Evaluations 100
Predicted Genetic Gains with Genomic Estimated Breeding Values: Results of
Simulation Studies 101 Summary 102 Chapter 14 Genetic Evaluation Based on
Dense Marker Maps: Basic Strategies 103 Introduction 103 The Basic Steps in
Genomic Evaluation 103 Evaluation of Genomic Estimated Breeding Values 104
Sources of Bias in Genomic Evaluation 104 Marker Effects Fixed or Random?
105 Individual Markers versus Haplotypes 106 Total Markers versus Usable
Markers 106 Deviation of Genotype Frequencies from Their Expectations 107
Inclusion of All Markers versus Selection of Markers with Significant
Effects 107 The Genomic Relationship Matrix 108 Summary 109 Chapter 15
Genetic Evaluation Based on Analysis of Genetic Evaluations or
Daughter-Yield Evaluations 111 Introduction 111 Comparison of Single?]Step
and Multistep Models 111 Derivation and Properties of Daughter Yields and
DYD 112 Computation of "Deregressed" Genetic Evaluations 113 Analysis of
DYD as the Dependent Variable with All Markers Included as Random Effects
114 Computation of Reliabilities for Genomic Estimated Breeding Values 116
Bayesian Weighting of Marker Effects 116 Additional Bayesian Methods for
Genomic Evaluation 117 Summary 117 Chapter 16 Genomic Evaluation Based on
Analysis of Production Records 119 Introduction 119 Single?-Step
Methodologies: The Basic Strategy 119 Computation of the Modified
Relationship Matrix when only a Fraction of the Animals are Genotyped: The
Problem 120 Criteria for Valid Genetic Relationship Matrices 120
Computation of the Modified Relationship Matrix when only a Fraction of the
Animals are Genotyped, the Solution 121 Solving the Mixed Model Equations
without Inverting H 121 Inverting the Genomic Relationship Matrix 122
Estimation of Reliabilities for Genomic Breeding Values Derived by
Single?]Step Methodologies 122 Single?-Step Computation of Genomic
Evaluations with Unequally Weighted Marker Effects 123 Summary 124 Chapter
17 Validation of Methods for Genomic Estimated Breeding Values 125
Introduction 125 Criteria for Evaluation of Estimated Genetic Values 125
Methods Used to Validate Genomic Genetic Evaluations 126 Evaluation of
Two?-Step Methodology Based on Simulated Dairy Cattle Data 127 Evaluation
of Multistep Methodology Based on Actual Dairy Cattle Data 127 Evaluation
of Single-Step Methodologies Based on Actual Dairy Cattle Data 128
Evaluation of Single?- and Multistep Methodologies Based on Actual Poultry
Data 129 Evaluation of Single?- and Multistep Methodologies Based on Actual
Swine Data 130 Evaluation of GEBV for Plants Based on Actual Data 130
Summary 131 Chapter 18 By?-Products of Genomic Analysis: Pedigree
Validation and Determination 133 Introduction 133 The Effects of Incorrect
Parentage Identification on Breeding Programs 133 Principles of Parentage
Verification and Identification with Genetic Markers 134 Paternity
Validation Prior to High?]Density SNP Chips 135 Paternity Validation and
Determination with SNP Chips 135 Validation of More Distant Relationships
136 Pedigree Reconstruction with High?]Density Genetic Markers 137 Summary
137 Chapter 19 Imputation of Missing Genotypes: Methodologies, Accuracies,
and Effects on Genomic Evaluations 139 Introduction 139 Determination of
Haplotypes for Imputation 139 Imputation in Humans versus Imputation in
Farm Animals 140 Algorithms Proposed for Imputation in Human and Animal
Populations 141 Comparisons of Accuracy and Speed of Imputation Methods 142
Effect of Imputation on Genomic Genetic Evaluations 143 Summary 144 Chapter
20 Detection and Validation of Quantitative Trait Nucleotides 145
Introduction 145 GWAS for Economic Traits in Commercial Animals 146
Detection of QTN: Is It Worth the Effort? 146 QTN Determination in Farm
Animals: What Constitutes Proof? 147 Concordance between DNA?-Level
Genotypes and QTL Status 148 Determination of Concordance by the "APGD" 148
Determination of Phase for Grandsires Heterozygous for the QTL 149
Determination of Recessive Lethal Genes by GWAS and Effects Associated with
Heterozygotes 150 Verification of QTN by Statistical and Biological Methods
150 Summary 151 Chapter 21 Future Directions and Conclusions 153
Introduction 153 More Markers versus More Individuals with Genotypes 153
Computation of Genomic Evaluations for Cow and Female Calves 154
Improvement of Genomic Evaluation Methods 154 Long?-Term Considerations 155
Weighting Evaluations of Old versus Young Bulls 156 Direct Genetic
Manipulation in Farm Animals 156 Velogenetics: The Synergistic Use of MAS
and Germ?-Line Manipulation 157 Summary 157 References 159 Index 171
Preface: Welcome to the "Promised Land" xiii Chapter 1 Historical Overview
1 Introduction 1 The Mendelian Theory of Genetics 1 The Mendelian Basis of
Quantitative Variation 2 Detection of QTL with Morphological and
Biochemical Markers 2 DNA?-Level Markers, 1974-1994 3 DNA?-Level Markers
Since 1995: SNPs and CNV 4 QTL Detection Prior to Genomic Selection 4 MAS
Prior to Genomic Selection 5 Summary 6 Chapter 2 Types of Current Genetic
Markers and Genotyping Methodologies 7 Introduction 7 From Biochemical
Markers to DNA?]Level Markers 7 DNA Microsatellites 8 Single Nucleotide
Polymorphisms 8 Copy Number Variation 9 Complete Genome Sequencing 9
Summary 10 Chapter 3 Advanced Animal Breeding Programs Prior to Genomic
Selection 11 Introduction 11 Within a Breed Selection: Basic Principles and
Equations 11 Traditional Selection Schemes for Dairy Cattle 12
Crossbreeding Schemes: Advantages and Disadvantages 14 Summary 15 Chapter 4
Economic Evaluation of Genetic Breeding Programs 17 Introduction 17
National Economy versus Competition among Breeders 17 Criteria for Economic
Evaluation: Profit Horizon, Interest Rate, and Return on Investment 18
Summary 20 Chapter 5 Least Squares, Maximum Likelihood, and Bayesian
Parameter Estimation 21 Introduction 21 Least Squares Parameter Estimation
21 ML Estimation for a Single Parameter 22 ML Multiparameter Estimation 24
Methods to Maximize Likelihood Functions 26 Confidence Intervals and
Hypothesis Testing for MLE 26 Bayesian Estimation 27 Parameter Estimation
via the Gibbs Sampler 28 Summary 29 Chapter 6 Trait-Based Genetic
Evaluation: The Mixed Model 31 Introduction 31 Principles of Selection
Index 31 The Mixed Linear Model 34 The Mixed Model Equations 34 Solving the
Mixed Model Equations 35 Important Properties of Mixed Model Solutions 36
Multivariate Mixed Model Analysis 37 The Individual Animal Model 38 Yield
Deviations and Daughter Yield Deviations 39 Analysis of DYD as the
Dependent Variable 40 Summary 41 Chapter 7 Maximum Likelihood and Bayesian
Estimation of QTL Parameters with Random Effects Included in the Model 43
Introduction 43 Maximum Likelihood Estimation of QTL Effects with Random
Effects Included in the Model, the Daughter Design 43 The Granddaughter
Design 45 Determination of Prior Distributions of the QTL Parameters for
the Granddaughter Design 46 Formula for Bayesian Estimation and Tests of
Significance of a Segregating QTL in a Granddaughter Design 49 Summary 50
Chapter 8 Maximum Likelihood, Restricted Maximum Likelihood, and Bayesian
Estimation for Mixed Models 51 Introduction 51 Derivation of Solutions to
the Mixed Model Equations by Maximum Likelihood 51 Estimation of the Mixed
Model Variance Components 52 Maximum Likelihood Estimation of Variance
Components 52 Restricted Maximum Likelihood Estimation of Variance
Components 54 Estimation of Variance Components via the Gibbs Sampler 55
Summary 58 Chapter 9 Distribution of Genetic Effects, Theory, and Results
59 Introduction 59 Modeling the Polygenic Variance 59 The Effective Number
of QTL 61 The Case of the Missing Heritability 61 Methods for Determination
of Causative Mutations for QTL in Animals and Humans 62 Determination of
QTN in Dairy Cattle 63 Estimating the Number of Segregating QTL Based on
Linkage Mapping Studies 64 Results of Genome Scans of Dairy Cattle by
Granddaughter Designs 65 Results of Genome?]Wide Association Studies in
Dairy Cattle by SNP Chips 66 Summary 66 Chapter 10 The Multiple Comparison
Problem 69 Introduction 69 Multiple Markers and Whole Genome Scans 69 QTL
Detection by Permutation Tests 71 QTL Detection Based on the False
Discovery Rate 71 A Priori Determination of the Proportion of False
Positives 74 Biases with Estimation of Multiple QTL 75 Bayesian Estimation
of QTL from Whole Genome Scans: Theory 76 Bayes A and Bayes B Models 77
Bayesian Estimation of QTL from Whole Genome Scans: Simulation Results 79
Summary 80 Chapter 11 Linkage Mapping of QTL 81 Introduction 81 Interval
Mapping by Nonlinear Regression: The Backcross Design 81 Interval Mapping
for Daughter and Granddaughter Designs 83 Computation of Confidence
Intervals 84 Simulation Studies of CIs 85 Empirical Methods to Estimate
CIs, Parametric and Nonparametric Bootstrap, and Jackknife Methods 86
Summary 87 Chapter 12 Linkage Disequilibrium Mapping of QTL 89 Introduction
89 Estimation of Linkage Disequilibrium in Animal Populations 89 Linkage
Disequilibrium QTL Mapping: Basic Principles 90 Joint Linkage and Linkage
Disequilibrium Mapping 92 Multitrait and Multiple QTL LD Mapping 93 Summary
93 Chapter 13 Marker-Assisted Selection: Basic Strategies 95 Introduction
95 Situations in Which Selection Index is Inefficient 95 Potential
Contribution of MAS for Selection within a Breed: General Considerations 96
Phenotypic Selection versus MAS for Individual Selection 97 MAS for
Sex?-Limited Traits 98 MAS Including Marker and Phenotypic Information on
Relatives 99 Maximum Selection Efficiency of MAS with All QTL Known,
Relative to Trait?-Based Selection, and the Reduction in RSE Due to
Sampling Variance 99 Marker Information in Segregating Populations 100
Inclusion of Marker Information in "Animal Model" Genetic Evaluations 100
Predicted Genetic Gains with Genomic Estimated Breeding Values: Results of
Simulation Studies 101 Summary 102 Chapter 14 Genetic Evaluation Based on
Dense Marker Maps: Basic Strategies 103 Introduction 103 The Basic Steps in
Genomic Evaluation 103 Evaluation of Genomic Estimated Breeding Values 104
Sources of Bias in Genomic Evaluation 104 Marker Effects Fixed or Random?
105 Individual Markers versus Haplotypes 106 Total Markers versus Usable
Markers 106 Deviation of Genotype Frequencies from Their Expectations 107
Inclusion of All Markers versus Selection of Markers with Significant
Effects 107 The Genomic Relationship Matrix 108 Summary 109 Chapter 15
Genetic Evaluation Based on Analysis of Genetic Evaluations or
Daughter-Yield Evaluations 111 Introduction 111 Comparison of Single?]Step
and Multistep Models 111 Derivation and Properties of Daughter Yields and
DYD 112 Computation of "Deregressed" Genetic Evaluations 113 Analysis of
DYD as the Dependent Variable with All Markers Included as Random Effects
114 Computation of Reliabilities for Genomic Estimated Breeding Values 116
Bayesian Weighting of Marker Effects 116 Additional Bayesian Methods for
Genomic Evaluation 117 Summary 117 Chapter 16 Genomic Evaluation Based on
Analysis of Production Records 119 Introduction 119 Single?-Step
Methodologies: The Basic Strategy 119 Computation of the Modified
Relationship Matrix when only a Fraction of the Animals are Genotyped: The
Problem 120 Criteria for Valid Genetic Relationship Matrices 120
Computation of the Modified Relationship Matrix when only a Fraction of the
Animals are Genotyped, the Solution 121 Solving the Mixed Model Equations
without Inverting H 121 Inverting the Genomic Relationship Matrix 122
Estimation of Reliabilities for Genomic Breeding Values Derived by
Single?]Step Methodologies 122 Single?-Step Computation of Genomic
Evaluations with Unequally Weighted Marker Effects 123 Summary 124 Chapter
17 Validation of Methods for Genomic Estimated Breeding Values 125
Introduction 125 Criteria for Evaluation of Estimated Genetic Values 125
Methods Used to Validate Genomic Genetic Evaluations 126 Evaluation of
Two?-Step Methodology Based on Simulated Dairy Cattle Data 127 Evaluation
of Multistep Methodology Based on Actual Dairy Cattle Data 127 Evaluation
of Single-Step Methodologies Based on Actual Dairy Cattle Data 128
Evaluation of Single?- and Multistep Methodologies Based on Actual Poultry
Data 129 Evaluation of Single?- and Multistep Methodologies Based on Actual
Swine Data 130 Evaluation of GEBV for Plants Based on Actual Data 130
Summary 131 Chapter 18 By?-Products of Genomic Analysis: Pedigree
Validation and Determination 133 Introduction 133 The Effects of Incorrect
Parentage Identification on Breeding Programs 133 Principles of Parentage
Verification and Identification with Genetic Markers 134 Paternity
Validation Prior to High?]Density SNP Chips 135 Paternity Validation and
Determination with SNP Chips 135 Validation of More Distant Relationships
136 Pedigree Reconstruction with High?]Density Genetic Markers 137 Summary
137 Chapter 19 Imputation of Missing Genotypes: Methodologies, Accuracies,
and Effects on Genomic Evaluations 139 Introduction 139 Determination of
Haplotypes for Imputation 139 Imputation in Humans versus Imputation in
Farm Animals 140 Algorithms Proposed for Imputation in Human and Animal
Populations 141 Comparisons of Accuracy and Speed of Imputation Methods 142
Effect of Imputation on Genomic Genetic Evaluations 143 Summary 144 Chapter
20 Detection and Validation of Quantitative Trait Nucleotides 145
Introduction 145 GWAS for Economic Traits in Commercial Animals 146
Detection of QTN: Is It Worth the Effort? 146 QTN Determination in Farm
Animals: What Constitutes Proof? 147 Concordance between DNA?-Level
Genotypes and QTL Status 148 Determination of Concordance by the "APGD" 148
Determination of Phase for Grandsires Heterozygous for the QTL 149
Determination of Recessive Lethal Genes by GWAS and Effects Associated with
Heterozygotes 150 Verification of QTN by Statistical and Biological Methods
150 Summary 151 Chapter 21 Future Directions and Conclusions 153
Introduction 153 More Markers versus More Individuals with Genotypes 153
Computation of Genomic Evaluations for Cow and Female Calves 154
Improvement of Genomic Evaluation Methods 154 Long?-Term Considerations 155
Weighting Evaluations of Old versus Young Bulls 156 Direct Genetic
Manipulation in Farm Animals 156 Velogenetics: The Synergistic Use of MAS
and Germ?-Line Manipulation 157 Summary 157 References 159 Index 171
1 Introduction 1 The Mendelian Theory of Genetics 1 The Mendelian Basis of
Quantitative Variation 2 Detection of QTL with Morphological and
Biochemical Markers 2 DNA?-Level Markers, 1974-1994 3 DNA?-Level Markers
Since 1995: SNPs and CNV 4 QTL Detection Prior to Genomic Selection 4 MAS
Prior to Genomic Selection 5 Summary 6 Chapter 2 Types of Current Genetic
Markers and Genotyping Methodologies 7 Introduction 7 From Biochemical
Markers to DNA?]Level Markers 7 DNA Microsatellites 8 Single Nucleotide
Polymorphisms 8 Copy Number Variation 9 Complete Genome Sequencing 9
Summary 10 Chapter 3 Advanced Animal Breeding Programs Prior to Genomic
Selection 11 Introduction 11 Within a Breed Selection: Basic Principles and
Equations 11 Traditional Selection Schemes for Dairy Cattle 12
Crossbreeding Schemes: Advantages and Disadvantages 14 Summary 15 Chapter 4
Economic Evaluation of Genetic Breeding Programs 17 Introduction 17
National Economy versus Competition among Breeders 17 Criteria for Economic
Evaluation: Profit Horizon, Interest Rate, and Return on Investment 18
Summary 20 Chapter 5 Least Squares, Maximum Likelihood, and Bayesian
Parameter Estimation 21 Introduction 21 Least Squares Parameter Estimation
21 ML Estimation for a Single Parameter 22 ML Multiparameter Estimation 24
Methods to Maximize Likelihood Functions 26 Confidence Intervals and
Hypothesis Testing for MLE 26 Bayesian Estimation 27 Parameter Estimation
via the Gibbs Sampler 28 Summary 29 Chapter 6 Trait-Based Genetic
Evaluation: The Mixed Model 31 Introduction 31 Principles of Selection
Index 31 The Mixed Linear Model 34 The Mixed Model Equations 34 Solving the
Mixed Model Equations 35 Important Properties of Mixed Model Solutions 36
Multivariate Mixed Model Analysis 37 The Individual Animal Model 38 Yield
Deviations and Daughter Yield Deviations 39 Analysis of DYD as the
Dependent Variable 40 Summary 41 Chapter 7 Maximum Likelihood and Bayesian
Estimation of QTL Parameters with Random Effects Included in the Model 43
Introduction 43 Maximum Likelihood Estimation of QTL Effects with Random
Effects Included in the Model, the Daughter Design 43 The Granddaughter
Design 45 Determination of Prior Distributions of the QTL Parameters for
the Granddaughter Design 46 Formula for Bayesian Estimation and Tests of
Significance of a Segregating QTL in a Granddaughter Design 49 Summary 50
Chapter 8 Maximum Likelihood, Restricted Maximum Likelihood, and Bayesian
Estimation for Mixed Models 51 Introduction 51 Derivation of Solutions to
the Mixed Model Equations by Maximum Likelihood 51 Estimation of the Mixed
Model Variance Components 52 Maximum Likelihood Estimation of Variance
Components 52 Restricted Maximum Likelihood Estimation of Variance
Components 54 Estimation of Variance Components via the Gibbs Sampler 55
Summary 58 Chapter 9 Distribution of Genetic Effects, Theory, and Results
59 Introduction 59 Modeling the Polygenic Variance 59 The Effective Number
of QTL 61 The Case of the Missing Heritability 61 Methods for Determination
of Causative Mutations for QTL in Animals and Humans 62 Determination of
QTN in Dairy Cattle 63 Estimating the Number of Segregating QTL Based on
Linkage Mapping Studies 64 Results of Genome Scans of Dairy Cattle by
Granddaughter Designs 65 Results of Genome?]Wide Association Studies in
Dairy Cattle by SNP Chips 66 Summary 66 Chapter 10 The Multiple Comparison
Problem 69 Introduction 69 Multiple Markers and Whole Genome Scans 69 QTL
Detection by Permutation Tests 71 QTL Detection Based on the False
Discovery Rate 71 A Priori Determination of the Proportion of False
Positives 74 Biases with Estimation of Multiple QTL 75 Bayesian Estimation
of QTL from Whole Genome Scans: Theory 76 Bayes A and Bayes B Models 77
Bayesian Estimation of QTL from Whole Genome Scans: Simulation Results 79
Summary 80 Chapter 11 Linkage Mapping of QTL 81 Introduction 81 Interval
Mapping by Nonlinear Regression: The Backcross Design 81 Interval Mapping
for Daughter and Granddaughter Designs 83 Computation of Confidence
Intervals 84 Simulation Studies of CIs 85 Empirical Methods to Estimate
CIs, Parametric and Nonparametric Bootstrap, and Jackknife Methods 86
Summary 87 Chapter 12 Linkage Disequilibrium Mapping of QTL 89 Introduction
89 Estimation of Linkage Disequilibrium in Animal Populations 89 Linkage
Disequilibrium QTL Mapping: Basic Principles 90 Joint Linkage and Linkage
Disequilibrium Mapping 92 Multitrait and Multiple QTL LD Mapping 93 Summary
93 Chapter 13 Marker-Assisted Selection: Basic Strategies 95 Introduction
95 Situations in Which Selection Index is Inefficient 95 Potential
Contribution of MAS for Selection within a Breed: General Considerations 96
Phenotypic Selection versus MAS for Individual Selection 97 MAS for
Sex?-Limited Traits 98 MAS Including Marker and Phenotypic Information on
Relatives 99 Maximum Selection Efficiency of MAS with All QTL Known,
Relative to Trait?-Based Selection, and the Reduction in RSE Due to
Sampling Variance 99 Marker Information in Segregating Populations 100
Inclusion of Marker Information in "Animal Model" Genetic Evaluations 100
Predicted Genetic Gains with Genomic Estimated Breeding Values: Results of
Simulation Studies 101 Summary 102 Chapter 14 Genetic Evaluation Based on
Dense Marker Maps: Basic Strategies 103 Introduction 103 The Basic Steps in
Genomic Evaluation 103 Evaluation of Genomic Estimated Breeding Values 104
Sources of Bias in Genomic Evaluation 104 Marker Effects Fixed or Random?
105 Individual Markers versus Haplotypes 106 Total Markers versus Usable
Markers 106 Deviation of Genotype Frequencies from Their Expectations 107
Inclusion of All Markers versus Selection of Markers with Significant
Effects 107 The Genomic Relationship Matrix 108 Summary 109 Chapter 15
Genetic Evaluation Based on Analysis of Genetic Evaluations or
Daughter-Yield Evaluations 111 Introduction 111 Comparison of Single?]Step
and Multistep Models 111 Derivation and Properties of Daughter Yields and
DYD 112 Computation of "Deregressed" Genetic Evaluations 113 Analysis of
DYD as the Dependent Variable with All Markers Included as Random Effects
114 Computation of Reliabilities for Genomic Estimated Breeding Values 116
Bayesian Weighting of Marker Effects 116 Additional Bayesian Methods for
Genomic Evaluation 117 Summary 117 Chapter 16 Genomic Evaluation Based on
Analysis of Production Records 119 Introduction 119 Single?-Step
Methodologies: The Basic Strategy 119 Computation of the Modified
Relationship Matrix when only a Fraction of the Animals are Genotyped: The
Problem 120 Criteria for Valid Genetic Relationship Matrices 120
Computation of the Modified Relationship Matrix when only a Fraction of the
Animals are Genotyped, the Solution 121 Solving the Mixed Model Equations
without Inverting H 121 Inverting the Genomic Relationship Matrix 122
Estimation of Reliabilities for Genomic Breeding Values Derived by
Single?]Step Methodologies 122 Single?-Step Computation of Genomic
Evaluations with Unequally Weighted Marker Effects 123 Summary 124 Chapter
17 Validation of Methods for Genomic Estimated Breeding Values 125
Introduction 125 Criteria for Evaluation of Estimated Genetic Values 125
Methods Used to Validate Genomic Genetic Evaluations 126 Evaluation of
Two?-Step Methodology Based on Simulated Dairy Cattle Data 127 Evaluation
of Multistep Methodology Based on Actual Dairy Cattle Data 127 Evaluation
of Single-Step Methodologies Based on Actual Dairy Cattle Data 128
Evaluation of Single?- and Multistep Methodologies Based on Actual Poultry
Data 129 Evaluation of Single?- and Multistep Methodologies Based on Actual
Swine Data 130 Evaluation of GEBV for Plants Based on Actual Data 130
Summary 131 Chapter 18 By?-Products of Genomic Analysis: Pedigree
Validation and Determination 133 Introduction 133 The Effects of Incorrect
Parentage Identification on Breeding Programs 133 Principles of Parentage
Verification and Identification with Genetic Markers 134 Paternity
Validation Prior to High?]Density SNP Chips 135 Paternity Validation and
Determination with SNP Chips 135 Validation of More Distant Relationships
136 Pedigree Reconstruction with High?]Density Genetic Markers 137 Summary
137 Chapter 19 Imputation of Missing Genotypes: Methodologies, Accuracies,
and Effects on Genomic Evaluations 139 Introduction 139 Determination of
Haplotypes for Imputation 139 Imputation in Humans versus Imputation in
Farm Animals 140 Algorithms Proposed for Imputation in Human and Animal
Populations 141 Comparisons of Accuracy and Speed of Imputation Methods 142
Effect of Imputation on Genomic Genetic Evaluations 143 Summary 144 Chapter
20 Detection and Validation of Quantitative Trait Nucleotides 145
Introduction 145 GWAS for Economic Traits in Commercial Animals 146
Detection of QTN: Is It Worth the Effort? 146 QTN Determination in Farm
Animals: What Constitutes Proof? 147 Concordance between DNA?-Level
Genotypes and QTL Status 148 Determination of Concordance by the "APGD" 148
Determination of Phase for Grandsires Heterozygous for the QTL 149
Determination of Recessive Lethal Genes by GWAS and Effects Associated with
Heterozygotes 150 Verification of QTN by Statistical and Biological Methods
150 Summary 151 Chapter 21 Future Directions and Conclusions 153
Introduction 153 More Markers versus More Individuals with Genotypes 153
Computation of Genomic Evaluations for Cow and Female Calves 154
Improvement of Genomic Evaluation Methods 154 Long?-Term Considerations 155
Weighting Evaluations of Old versus Young Bulls 156 Direct Genetic
Manipulation in Farm Animals 156 Velogenetics: The Synergistic Use of MAS
and Germ?-Line Manipulation 157 Summary 157 References 159 Index 171