Quantitative Trait Loci Analysis in Animals, 2nd Edition (Modular Texts)

Contents......Page 6
Preface: Theory Versus Results......Page 12
Preface to the Second Edition......Page 14
1.2 From Mendel to Sax......Page 16
1.3 Quantitative Genetics 1920–1980, or Who Needs Mendel?......Page 18
1.5 From Biochemistry to Biotechnology, or More Markers Than We Will Ever Need......Page 19
1.6 Genetic Mapping Functions......Page 21
1.7 Physical and Genetic Mapping, Questions of Scale......Page 24
1.8 Summary......Page 25
2.1 Introduction......Page 26
2.2 Desired Properties of QTL Parameter Estimates......Page 27
2.4 Least-squares Parameter Estimation......Page 28
2.5 Least-squares Solutions for a Single Parameter......Page 29
2.7 Maximum Likelihood Estimation for a Single Parameter......Page 30
2.8 Maximum Likelihood Multi-parameter Estimation......Page 32
2.9 Confidence Intervals and Hypothesis Testing for MLE......Page 33
2.11 Derivative-free Methods......Page 34
2.13 First Derivative-based Methods (Expectation-maximization)......Page 35
2.14 Bayesian Estimation......Page 36
2.16 Summary......Page 37
3.2 The Mixed Linear Model......Page 39
3.3 The Mixed Model Equations......Page 40
3.4 Solving the Mixed Model Equations......Page 41
3.5 Some Important Properties of Mixed Model Solutions......Page 42
3.7 Multivariate Mixed Model Analysis......Page 43
3.8 The Repeatability Model......Page 44
3.9 The Individual Animal Model......Page 45
3.10 Grouping Individuals with Unknown Ancestors......Page 46
3.11 The Reduced Animal Model......Page 47
3.13 Estimation of Variance Components, Analysis of Variance-type Methods......Page 48
3.14 Maximum Likelihood Estimation of Variance Components......Page 49
3.15 Restricted Maximum Likelihood Estimation of Variance Components......Page 51
3.16 The Problem of Variance Components Outside the Parameter Space......Page 52
3.17 Summary......Page 53
4.2 Assumptions, Problems and Types of Effects Postulated......Page 54
4.3 Experimental Designs for Detection of QTL in Crosses Between Inbred Lines......Page 57
4.4 Linear Model Analysis of Crosses Between Inbred Lines......Page 58
4.5 Experimental Designs for Detection of QTL in Segregating Populations: General Considerations......Page 62
4.6 Experimental Designs for Detection of QTL in Segregating Populations: Large Families......Page 63
4.7 Experimental Designs for Detection of QTL in Segregating Populations: Small Families......Page 66
4.8 Experimental Designs Based on Additional Generations: Inbred Lines......Page 69
4.9 Experimental Designs Based on Additional Generations: Segregating Populations......Page 70
4.10 Comparison of the Expected Contrasts for Different Experimental Designs......Page 73
4.11 Gametic Effect Models for Complete Population Analyses......Page 74
4.12 Summary......Page 75
5.2 Moments Method of Estimation......Page 78
5.3 Least-squares Estimation of QTL Parameters......Page 80
5.4 Least-squares Estimation of QTL Location for Sib-pair Analysis with Flanking Markers......Page 83
5.5 Linear Regression Mapping of QTL with Flanking Markers......Page 84
5.6 Marker Information Content for Interval Mapping, Uninformative and Missing Marker Genotypes......Page 86
5.7 Maximum Likelihood QTL Parameter Estimation for Crosses Between Inbred Lines and a Single Marker......Page 88
5.9 Maximum Likelihood QTL Parameter Estimation for Crosses between Inbred Lines and Two Flanking Markers......Page 89
5.10 Estimation of QTL Parameters by the Expectation-maximization Algorithm......Page 90
5.11 Biases in Estimation of QTL Parameters with Interval Mapping......Page 92
5.12 The Likelihood Ratio Test with Interval Mapping......Page 93
5.13 Summary......Page 94
6.2 Higher-order QTL Effects......Page 95
6.3 QTL Interaction Effects......Page 96
6.4 Simultaneous Analysis of Multiple Marker Brackets......Page 98
6.5 Principles of Composite Interval Mapping......Page 99
6.7 Derivation of Maximum Likelihood Parameter Estimates by Composite Interval Mapping......Page 100
6.8 Hypothesis Testing with Composite Interval Mapping......Page 101
6.9 Multi-marker and QTL Analysis by Regression of Phenotype on Marker Genotypes......Page 102
6.10 Estimation of QTL Parameters in Outbred Populations......Page 103
6.11 Analysis of Field Data, Daughter and Granddaughter Designs......Page 104
6.12 Maximum Likelihood Analysis of QTL Parameters for the Daughter Design with Linkage to a Single Marker......Page 106
6.13 Non-linear and Linear Regression Estimation for Complex Pedigrees......Page 108
6.14 Estimation of QTL Allelic Frequencies in Segregating Populations......Page 109
6.15 Maximum Likelihood Estimation with Random Effects Included in the Model......Page 111
6.16 Incorporation of Genotype Effects into Animal Model Evaluations When Only a Small Fraction of the Population Has Been Genotyped......Page 112
6.17 Maximum Likelihood Estimation of QTL Effects on Categorical Traits......Page 113
6.18 Estimation of QTL Effects with the Threshold Model......Page 115
6.20 Summary......Page 116
7.1 Introduction......Page 118
7.2 ML Estimation of Variance Components for the Haseman–Elston Sib-pair Model......Page 119
7.3 The Random Gametic Model of Fernando and Grossman, Computing G[sub(v)]......Page 121
7.4 Computing the Inverse of G[sub(v)]......Page 122
7.5 Analysis of the Random Gametic Model by a Reduced Animal Model......Page 123
7.7 Computation of the Gametic Effects Variance Matrix......Page 125
7.8 The Gametic Effect Model for Crosses Between Inbred Lines......Page 126
7.9 REML Estimation of the QTL Variance and Recombination for the Model of Fernando and Grossman......Page 127
7.10 REML Estimation of the QTL Variance and Location with Marker Brackets......Page 128
7.11 Bayesian Estimation of QTL Effects, Determining the Prior Distribution......Page 129
7.12 Formula for Bayesian Estimation and Tests of Significance of a Segregating QTL in a Simulated Granddaughter Design......Page 132
7.14 Markov Chain Monte Carlo Algorithms, Gibbs Sampling......Page 134
7.15 Summary......Page 135
8.1 Introduction......Page 137
8.2 Estimation of Power in Crosses Between Inbred Lines......Page 138
8.3 Replicate Progeny in Crosses Between Inbred Lines......Page 139
8.4 Estimation of Power for Segregating Populations......Page 141
8.5 Power Estimates for Likelihood Ratio Tests: General Considerations......Page 143
8.6 The Effect of Statistical Methodology on the Power of QTL Detection......Page 144
8.8 Confidence Intervals for QTL Parameters, Analytical Methods......Page 145
8.10 Empirical Methods to Estimate Confidence Intervals, Parametric and Nonparametric Bootstrap and Jackknife Methods......Page 147
8.11 Summary......Page 148
9.2 Economic Optimization of Marker Spacing When the Number of Individuals Genotyped Is Non-limiting......Page 150
9.3 Economic Optimization with Replicate Progeny......Page 151
9.4 Selective Genotyping......Page 152
9.6 Estimation of Power with Sample Pooling......Page 155
9.7 Comparison of Power and Sample Sizes with Random Genotyping, Selective Genotyping and Sample Pooling......Page 157
9.8 Sequential Sampling......Page 158
9.9 Summary......Page 159
10.2 Determination of the Genetic Map Critical Interval for a Marker Locus with a Saturated Genetic Marker Map......Page 160
10.3 Confidence Interval for QTL Location with a Saturated Genetic Marker Map......Page 161
10.4 Fine Mapping of QTL via Advanced Intercross Lines......Page 165
10.6 Recombinant Progeny Testing......Page 166
10.8 Recombinant Inbred Segregation Test......Page 167
10.9 Fine Mapping of QTL in Outcrossing Populations by Identity by Descent......Page 168
10.10 Estimation and Evaluation of Linkage Disequilibrium in Animal Populations......Page 169
10.11 Linkage Disequilibrium QTL Mapping, Basic Principles......Page 170
10.12 Linkage Disequilibrium Mapping, Advanced Topics......Page 171
10.13 Summary......Page 172
11.2 Multiple Markers and Whole-genome Scans......Page 174
11.3 QTL Detection by Permutation Tests......Page 176
11.4 QTL Detection Based on the False Discovery Rate......Page 177
11.5 A Priori Determination of the Proportion of False Positives......Page 180
11.6 Analysis of Multiple Pedigrees......Page 181
11.7 Biases with Estimation of Multiple QTL......Page 182
11.8 Bayesian Estimation of QTL from Whole-genome Scans, Theory......Page 183
11.9 Bayesian Estimation of QTL from Whole-genome Scans, Simulation Results......Page 186
11.10 Summary......Page 187
12.2 Problems and Solutions for Multitrait QTL Analyses......Page 188
12.3 Multivariate Estimation of QTL Parameters for Correlated Traits......Page 189
12.4 Comparison of Power for Single and Multitrait QTL Analyses......Page 190
12.5 Pleiotropy Versus Linkage......Page 193
12.6 Estimation of QTL Parameters for Correlated Traits by Canonical Transformation......Page 194
12.7 Determination of Statistical Significance for Multitrait Analyses......Page 195
12.8 Selective Genotyping with Multiple Traits......Page 197
12.10 Summary......Page 199
13.1 Introduction......Page 201
13.2 The Molecular Basis of QTL Discovered So Far......Page 202
13.3 Determination of QTL Candidate Genes......Page 203
13.4 Determination of Concordance......Page 204
13.5 QTN Validation by Other Statistical Methods......Page 205
13.6 QTN Validation by Functional Studies......Page 207
13.7 Summary......Page 208
14.2 Selection Index for a Single Trait......Page 209
14.3 Changes in QTL Allelic Frequencies Due to Selection......Page 211
14.4 Multitrait Selection Index......Page 212
14.5 The Value of Genetic Gain......Page 213
14.6 Dairy Cattle Breeding Programmes, Half-sib and Progeny Tests......Page 214
14.7 Nucleus Breeding Schemes......Page 217
14.8 Summary......Page 218
15.2 Situations in which Selection Index Is Inefficient......Page 219
15.3 Potential Contribution of MAS for Selection Within a Breed: General Considerations......Page 220
15.4 Phenotypic Selection Versus MAS for Individual Selection......Page 221
15.6 Two-stage Selection: MAS on Juveniles, and Phenotypic Selection of Adults......Page 222
15.7 MAS Including Marker and Phenotypic Information on Relatives......Page 223
15.8 Maximum Selection Efficiency of MAS with All QTL Known, Relative to Trait-based Selection, and the Reduction in RSE Due to Sampling Variance......Page 224
15.10 Inclusion of Marker Information in ‘Animal Model’ Genetic Evaluations......Page 225
15.11 Genetic Evaluation Based on Dense Whole-genome Scans......Page 227
15.12 Velogenetics: the Synergistic Use of MAS and Germ-line Manipulation......Page 229
15.13 Summary......Page 230
16.2 Modelling the Polygenic Variance......Page 231
16.3 The Effective Number of QTL......Page 232
16.4 Proposed Dairy Cattle Breeding Schemes with MAS: Overview......Page 233
16.5 Inclusion of Marker Information into Standard Progeny Test and MOET Nucleus Breeding Schemes......Page 234
16.6 Progeny Test Schemes, in Which Information on Genetic Markers is Used to Preselect Young Sires......Page 235
16.7 The Current Status of MAS in Dairy Cattle......Page 237
16.8 Selection of Sires Based on Marker Information Without a Progeny Test......Page 238
16.9 Computation of Reliabilities of Genetic Evaluations Based on Complete Genome Scans......Page 239
16.10 Long-term Considerations, MAS Versus Selection Index......Page 240
16.11 MAS for a Multitrait Breeding Objective with a Single Identified QTL......Page 243
16.12 MAS for a Multitrait Breeding Objective with Multiple Identified QTL......Page 245
16.13 Summary......Page 246
17.1 Introduction......Page 247
17.2 Marker-assisted Introgression: General Considerations......Page 248
17.3 Marker-assisted Introgression of a Major Gene into an Inbred Line......Page 249
17.4 Marker-assisted Introgression of a QTL into a Donor Population Under Selection......Page 250
17.6 Summary......Page 252
Latin Symbols......Page 253
Greek Symbols......Page 257
Other Symbols......Page 258
References......Page 259
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