Quantitative trait loci analysis in animals:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Cambridge, Mass. [u.a.]
CABI
2009
|
| Edition: | 2. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | XIII, 272 S. graph. Darst. |
| ISBN: | 9781845934675 |
Staff View
MARC
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| 100 | 1 | |a Weller, Joel Ira |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Quantitative trait loci analysis in animals |c Joel Ira Weller |
| 250 | |a 2. ed. | ||
| 264 | 1 | |a Cambridge, Mass. [u.a.] |b CABI |c 2009 | |
| 300 | |a XIII, 272 S. |b graph. Darst. | ||
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| 500 | |a Includes bibliographical references and index | ||
| 650 | 4 | |a Livestock - Breeding | |
| 650 | 4 | |a Livestock - Genetics | |
| 650 | 4 | |a Quantitative genetics | |
| 650 | 4 | |a Livestock |x Breeding | |
| 650 | 4 | |a Livestock |x Genetics | |
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Record in the Search Index
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|---|---|
| adam_text | Titel: Quantitative trait loci analysis in animals
Autor: Weller, Joel Ira
Jahr: 2009
Contents
Preface: Theory Versus Results xi
Preface to the Second Edition xiii
1 Historical Overview 1
1.1 Introduction 1
1.2 From Mendel to Sax 1
1.3 Quantitative Genetics 1920-1980, or Who Needs Mendel ? 3
1.4 QTL Detection 1930-1980, Theory and Experiments 4
1.5 From Biochemistry to Biotechnology, or More Markers Than
We Will Ever Need 4
1.6 Genetic Mapping Functions 6
1.7 Physical and Genetic Mapping, Questions of Scale 9
1.8 Summary 10
2 Principles of Parameter Estimation 11
2.1 Introduction 11
2.2 Desired Properties of QTL Parameter Estimates 12
2.3 Moments Method of Estimation 13
2.4 Least-squares Parameter Estimation 13
2.5 Least-squares Solutions for a Single Parameter 14
2.6 Least-squares Solutions for the General Linear Model 15
2.7 Maximum Likelihood Estimation for a Single Parameter 15
2.8 Maximum Likelihood Multi-parameter Estimation 17
2.9 Confidence Intervals and Hypothesis Testing for MLE 18
2.10 Methods to Maximize Likelihood Functions 19
2.11 Derivative-free Methods 19
2.12 Second Derivative-based Methods 20
2.13 First Derivative-based Methods (Expectation-maximization) 20
2.14 Bayesian Estimation 21
2.15 Minimum Difference Estimation 22
2.16 Summary 22
3 Random and Fixed Effects, the Mixed Model 24
3.1 Introduction 24
3.2 The Mixed Linear Model 24
3.3 The Mixed Model Equations 25
3.4 Solving the Mixed Model Equations 26
3.5 Some Important Properties of Mixed Model Solutions 27
3.6 Equation Absorption 28
3.7 Mukivariate Mixed Model Analysis 28
3.8 The Repeatability Model 29
3.9 The Individual Animal Model 30
3.10 Grouping Individuals with Unknown Ancestors 31
Contents
3.11 The Reduced Animal Model 32
3.12 Maximum Likelihood Estimation with Mixed Models 33
3.13 Estimation of Variance Components, Analysis of Variance-type
Methods 33
3.14 Maximum Likelihood Estimation of Variance Components 34
3.15 Restricted Maximum Likelihood Estimation of Variance
Components 36
3.16 The Problem of Variance Components Outside the Parameter Space 37
3.17 Summary 38
Experimental Designs to Detect QTL: Generation of Linkage Disequilibrium 39
4.1 Introduction 39
4.2 Assumptions, Problems and Types of Effects Postulated 39
4.3 Experimental Designs for Detection of QTL in Crosses Between
Inbred Lines 42
4.4 Linear Model Analysis of Crosses Between Inbred Lines 43
4.5 Experimental Designs for Detection of QTL in Segregating
Populations: General Considerations 47
4.6 Experimental Designs for Detection of QTL in Segregating
Populations: Large Families 48
4.7 Experimental Designs for Detection of QTL in Segregating
Populations: Small Families 51
4.8 Experimental Designs Based on Additional Generations:
Inbred Lines 54
4.9 Experimental Designs Based on Additional Generations:
Segregating Populations 55
4.10 Comparison of the Expected Contrasts for Different Experimental
Designs 58
4.11 Gametic Effect Models for Complete Population Analyses 59
4.12 Summary 60
QTL Parameter Estimation for Crosses between Inbred Lines 63
5.1 Introduction 63
5.2 Moments Method of Estimation ^
5.3 Least-squares Estimation of QTL Parameters 65
5.4 Least-squares Estimation of QTL Location for Sib-pair Analysis with
Flanking Markers 68
5.5 Linear Regression Mapping of QTL with Flanking Markers 69
5.6 Marker Information Content for Interval Mapping, Uninformative
and Missing Marker Genotypes 71
5.7 Maximum Likelihood QTL Parameter Estimation for Crosses
Between Inbred Lines and a Single Marker 73
5.8 Maximum Likelihood Tests of Significance for a Segregating QTL 74
5.9 Maximum Likelihood QTL Parameter Estimation for Crosses
between Inbred Lines and Two Flanking Markers 74
5.10 Estimation of QTL Parameters by the Expectation-maximization
Algorithm 75
5.11 Biases in Estimation of QTL Parameters with Interval Mapping 77
5.12 The Likelihood Ratio Test with Interval Mapping 78
5.13 Summary 79
Contents
6 Advanced Statistical Methods for QTL Detection and Parameter Estimation 80
6.1 Introduction 80
6.2 Higher-order QTL Effects 80
6.3 QTL Interaction Effects 81
6.4 Simultaneous Analysis of Multiple Marker Brackets 83
6.5 Principles of Composite Interval Mapping 84
6.6 Properties of Composite Interval Mapping 85
6.7 Derivation of Maximum Likelihood Parameter Estimates by
Composite Interval Mapping 85
6.8 Hypothesis Testing with Composite Interval Mapping 86
6.9 Multi-marker and QTL Analysis by Regression of Phenotype on
Marker Genotypes 87
6.10 Estimation of QTL Parameters in Outbred Populations 88
6.11 Analysis of Field Data, Daughter and Granddaughter Designs 89
6.12 Maximum Likelihood Analysis of QTL Parameters for the Daughter
Design with Linkage to a Single Marker 91
6.13 Non-linear and Linear Regression Estimation for Complex Pedigrees 93
6.14 Estimation of QTL Allelic Frequencies in Segregating Populations 94
6.15 Maximum Likelihood Estimation with Random Effects Included in
the Model 96
6.16 Incorporation of Genotype Effects into Animal Model Evaluations
When Only a Small Fraction of the Population Has Been Genotyped 97
6.17 Maximum Likelihood Estimation of QTL Effects on Categorical
Traits 98
6.18 Estimation of QTL Effects with the Threshold Model 100
6.19 Estimation of QTL Effects on Disease Traits by the Allele-sharing
Method 101
6.20 Summary 101
7 Analysis of QTL as Random Effects 103
7.1 Introduction 103
7.2 ML Estimation of Variance Components for the Haseman-Elston
Sib-pair Model 104
7.3 The Random Gametic Model of Fernando and Grossman,
Computing Gv 106
7.4 Computing the Inverse of Gv 107
7.5 Analysis of the Random Gametic Model by a Reduced Animal Model 108
7.6 Analysis of the Random Gametic QTL Model with Multiple QTL and
Marker Brackets 110
7.7 Computation of the Gametic Effects Variance Matrix 110
7.8 The Gametic Effect Model for Crosses Between Inbred Lines 111
7.9 REML Estimation of the QTL Variance and Recombination for the
Model of Fernando and Grossman 112
7.10 REML Estimation of the QTL Variance and Location with
Marker Brackets 113
7.11 Bayesian Estimation of QTL Effects, Determining the Prior
Distribution 114
7.12 Formula for Bayesian Estimation and Tests of Significance of a
Segregating QTL in a Simulated Granddaughter Design 117
7.13 Comparison of ML and Bayesian Analyses of a Simulated
Granddaughter Design 119
Contents vii
7.14 Markov Chain Monte Carlo Algorithms, Gibbs Sampling 119
7.15 Summary 120
8 Statistical Power to Detect QTL, and Parameter Confidence Intervals 122
8.1 Introduction 122
8.2 Estimation of Power in Crosses Between Inbred Lines 123
8.3 Replicate Progeny in Crosses Between Inbred Lines 124
8.4 Estimation of Power for Segregating Populations 126
8.5 Power Estimates for Likelihood Ratio Tests: General Considerations 128
8.6 The Effect of Statistical Methodology on the Power of QTL Detection 129
8.7 Estimation of Power with Random QTL Models 130
8.8 Confidence Intervals for QTL Parameters, Analytical Methods 130
8.9 Simulation Studies of Confidence Intervals 132
8.10 Empirical Methods to Estimate Confidence Intervals, Parametric and
Nonparametric Bootstrap and Jackknife Methods 132
8.11 Summary 133
9 Optimization of Experimental Designs 135
9.1 Introduction 135
9.2 Economic Optimization of Marker Spacing When the Number of
Individuals Genotyped Is Non-limiting 135
9.3 Economic Optimization with Replicate Progeny 136
9.4 Selective Genotyping 137
9.5 Sample Pooling: General Considerations 140
9.6 Estimation of Power with Sample Pooling 140
9.7 Comparison of Power and Sample Sizes with Random Genotyping,
Selective Genotyping and Sample Pooling 142
9.8 Sequential Sampling 143
9.9 Summary 144
10 Fine Mapping of QTL 145
10.1 Introduction 145
10.2 Determination of the Genetic Map Critical Interval for a Marker
Locus with a Saturated Genetic Marker Map 145
10.3 Confidence Interval for QTL Location with a Saturated Genetic
Marker Map 146
10.4 Fine Mapping of QTL via Advanced Intercross Lines 150
10.5 Selective Phenotyping 151
10.6 Recombinant Progeny Testing 151
10.7 Interval-specific Congenic Strains 152
10.8 Recombinant Inbred Segregation Test 152
10.9 Fine Mapping of QTL in Outcrossing Populations by Identity
by Descent 153
10.10 Estimation and Evaluation of Linkage Disequilibrium in
Animal Populations 154
10.11 Linkage Disequilibrium QTL Mapping, Basic Principles 155
10.12 Linkage Disequilibrium Mapping, Advanced Topics 15
10.13 Summary 157
11 Complete Genome QTL Scans: The Problem of Multiple Comparisons 159
11.1 Introduction 159
11.2 Multiple Markers and Whole-genome Scans 159
Contents
11.3 QTL Detection by Permutation Tests 161
11.4 QTL Detection Based on the False Discovery Rate 162
11.5 A Priori Determination of the Proportion of False Positives 165
11.6 Analysis of Multiple Pedigrees 166
11.7 Biases with Estimation of Multiple QTL 167
11.8 Bayesian Estimation of QTL from Whole-genome Scans, Theory 168
11.9 Bayesian Estimation of QTL from Whole-genome Scans, Simulation
Results 171
11.10 Summary 172
12 Multitrait QTL Analysis 173
12.1 Introduction 173
12.2 Problems and Solutions for Multitrait QTL Analyses 173
12.3 Multivariate Estimation of QTL Parameters for Correlated Traits 174
12.4 Comparison of Power for Single and Multitrait QTL Analyses 175
12.5 Pleiotropy Versus Linkage 178
12.6 Estimation of QTL Parameters for Correlated Traits by Canonical
Transformation 179
12.7 Determination of Statistical Significance for Multitrait Analyses 180
12.8 Selective Genotyping with Multiple Traits 182
12.9 Multitrait LD Mapping 184
12.10 Summary 184
13 From the QTL to the Gene 186
13.1 Introduction 186
13.2 The Molecular Basis of QTL Discovered So Far 187
13.3 Determination of QTL Candidate Genes 188
13.4 Determination of Concordance 189
13.5 QTN Validation by Other Statistical Methods 190
13.6 QTN Validation by Functional Studies 192
13.7 Summary 193
14 Principles of Selection Index and Traditional Breeding Programmes 194
14.1 Introduction 194
14.2 Selection Index for a Single Trait 194
14.3 Changes in QTL Allelic Frequencies Due to Selection 196
14.4 Multitrait Selection Index 197
14.5 The Value of Genetic Gain 198
14.6 Dairy Cattle Breeding Programmes, Half-sib and Progeny Tests 199
14.7 Nucleus Breeding Schemes 202
14.8 Summary 203
15 Marker-assisted Selection: Theory 204
15.1 Introduction 204
15.2 Situations in which Selection Index Is Inefficient 204
15.3 Potential Contribution of MAS for Selection Within a Breed: General
Considerations 205
15.4 Phenotypic Selection Versus MAS for Individual Selection 206
15.5 MAS for Sex-limited Traits 207
15.6 Two-stage Selection: MAS on Juveniles, and Phenotypic Selection
of Adults 207
15.7 MAS Including Marker and Phenotypic Information on Relatives 208
Contents
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 209
15.9 Marker Information in Segregating Populations 210
15.10 Inclusion of Marker Information in Animal Model Genetic
Evaluations 210
15.11 Genetic Evaluation Based on Dense Whole-genome Scans 212
15.12 Velogenetics: the Synergistic Use of MAS and Germ-line
Manipulation 214
15.13 Summary 215
16 Marker-assisted Selection: Current Status and Results of Simulation Studies 216
16.1 Introduction 216
16.2 Modelling the Polygenic Variance 216
16.3 The Effective Number of QTL 217
16.4 Proposed Dairy Cattle Breeding Schemes with MAS: Overview 218
16.5 Inclusion of Marker Information into Standard Progeny Test and
MOET Nucleus Breeding Schemes 219
16.6 Progeny Test Schemes, in Which Information on Genetic Markers is
Used to Preselect Young Sires 220
16.7 The Current Status of MAS in Dairy Cattle 222
16.8 Selection of Sires Based on Marker Information Without a
Progeny Test 223
16.9 Computation of Reliabilities of Genetic Evaluations Based on
Complete Genome Scans 224
16.10 Long-term Considerations, MAS Versus Selection Index 225
16.11 MAS for a Multitrait Breeding Objective with a Single
Identified QTL 228
16.12 MAS for a Multitrait Breeding Objective with Multiple
Identified QTL 230
16.13 Summary 231
17 Marker-assisted Introgression 232
17.1 Introduction 232
17.2 Marker-assisted Introgression: General Considerations 233
17.3 Marker-assisted Introgression of a Major Gene into an Inbred Line 234
17.4 Marker-assisted Introgression of a QTL into a Donor Population
Under Selection 235
17.5 Marker-assisted Introgression for Multiple Genes 237
17.6 Summary 237
Glossary of Symbols 238
Latin Symbols 238
Greek Symbols 242
Other Symbols 243
References 244
Author Index 258
Subject Index 261
Contents
|
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| id | DE-604.BV035781195 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:04:24Z |
| institution | BVB |
| isbn | 9781845934675 |
| language | English |
| lccn | 2008037115 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-018640707 |
| oclc_num | 488473558 |
| open_access_boolean | |
| owner | DE-M49 DE-BY-TUM |
| owner_facet | DE-M49 DE-BY-TUM |
| physical | XIII, 272 S. graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | CABI |
| record_format | marc |
| spelling | Weller, Joel Ira Verfasser aut Quantitative trait loci analysis in animals Joel Ira Weller 2. ed. Cambridge, Mass. [u.a.] CABI 2009 XIII, 272 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Livestock - Breeding Livestock - Genetics Quantitative genetics Livestock Breeding Livestock Genetics QTL (DE-588)4411159-9 gnd rswk-swf Tierzucht (DE-588)4060143-2 gnd rswk-swf Tierzucht (DE-588)4060143-2 s QTL (DE-588)4411159-9 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018640707&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Weller, Joel Ira Quantitative trait loci analysis in animals Livestock - Breeding Livestock - Genetics Quantitative genetics Livestock Breeding Livestock Genetics QTL (DE-588)4411159-9 gnd Tierzucht (DE-588)4060143-2 gnd |
| subject_GND | (DE-588)4411159-9 (DE-588)4060143-2 |
| title | Quantitative trait loci analysis in animals |
| title_auth | Quantitative trait loci analysis in animals |
| title_exact_search | Quantitative trait loci analysis in animals |
| title_full | Quantitative trait loci analysis in animals Joel Ira Weller |
| title_fullStr | Quantitative trait loci analysis in animals Joel Ira Weller |
| title_full_unstemmed | Quantitative trait loci analysis in animals Joel Ira Weller |
| title_short | Quantitative trait loci analysis in animals |
| title_sort | quantitative trait loci analysis in animals |
| topic | Livestock - Breeding Livestock - Genetics Quantitative genetics Livestock Breeding Livestock Genetics QTL (DE-588)4411159-9 gnd Tierzucht (DE-588)4060143-2 gnd |
| topic_facet | Livestock - Breeding Livestock - Genetics Quantitative genetics Livestock Breeding Livestock Genetics QTL Tierzucht |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018640707&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT wellerjoelira quantitativetraitlocianalysisinanimals |