Muutke küpsiste eelistusi

Quantitative Trait Loci Analysis in Animals 2nd edition [Pehme köide]

(Agricultural Research Organization (ARO), Israel)
  • Formaat: Paperback / softback, 288 pages, kõrgus x laius x paksus: 246x189x16 mm, kaal: 700 g
  • Ilmumisaeg: 25-Mar-2009
  • Kirjastus: CABI Publishing
  • ISBN-10: 1845934679
  • ISBN-13: 9781845934675
Teised raamatud teemal:
Quantitative Trait Loci Analysis in Animals 2nd editionSuurem pilt
  • Formaat: Paperback / softback, 288 pages, kõrgus x laius x paksus: 246x189x16 mm, kaal: 700 g
  • Ilmumisaeg: 25-Mar-2009
  • Kirjastus: CABI Publishing
  • ISBN-10: 1845934679
  • ISBN-13: 9781845934675
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9781845934675.html
Märksõnad:
Quantitative Trait Loci (QTL) is a topic of major agricultural significance for efficient livestock production. This advanced-level textbook covers all the statistical methods that have been used or proposed for detection and analysis of QTL and marker- and gene- assisted selection in animal genetics and breeding, as well as new advances that have revolutionized the field since the first edition.

Arvustused

"...the book is certainly a must-have for anyone involved in the statistical analysis of QTL studies in livestock... and (is) a useful textbook for advanced undergraduate and postgraduate students" - Chris Haley, Roslin Institute, on the first edition."

Preface: Theory Versus Results xi
Preface to the Second Edition xiii
Historical Overview
1(10)
Introduction
1(1)
From Mendel to Sax
1(2)
Quantitative Genetics 1920-1980, or Who Needs Mendel?
3(1)
QTL Detection 1930-1980, Theory and Experiments
4(1)
From Biochemistry to Biotechnology, or More Markers Than We Will Ever Need
4(2)
Genetic Mapping Functions
6(3)
Physical and Genetic Mapping, Questions of Scale
9(1)
Summary
10(1)
Principles of Parameter Estimation
11(13)
Introduction
11(1)
Desired Properties of QTL Parameter Estimates
12(1)
Moments Method of Estimation
13(1)
Least-squares Parameter Estimation
13(1)
Least-squares Solutions for a Single Parameter
14(1)
Least-squares Solutions for the General Linear Model
15(1)
Maximum Likelihood Estimation for a Single Parameter
15(2)
Maximum Likelihood Multi-parameter Estimation
17(1)
Confidence Intervals and Hypothesis Testing for MLE
18(1)
Methods to Maximize Likelihood Functions
19(1)
Derivative-free Methods
19(1)
Second Derivative-based Methods
20(1)
First Derivative-based Methods (Expectation-maximization)
20(1)
Bayesian Estimation
21(1)
Minimum Difference Estimation
22(1)
Summary
22(2)
Random and Fixed Effects, the Mixed Model
24(15)
Introduction
24(1)
The Mixed Linear Model
24(1)
The Mixed Model Equations
25(1)
Solving the Mixed Model Equations
26(1)
Some Important Properties of Mixed Model Solutions
27(1)
Equation Absorption
28(1)
Multivariate Mixed Model Analysis
28(1)
The Repeatability Model
29(1)
The Individual Animal Model
30(1)
Grouping Individuals with Unknown Ancestors
31(1)
The Reduced Animal Model
32(1)
Maximum Likelihood Estimation with Mixed Models
33(1)
Estimation of Variance Components, Analysis of Variance-type Methods
33(1)
Maximum Likelihood Estimation of Variance Components
34(2)
Restricted Maximum Likelihood Estimation of Variance Components
36(1)
The Problem of Variance Components Outside the Parameter Space
37(1)
Summary
38(1)
Experimental Designs to Detect QTL: Generation of Linkage Disequilibrium
39(24)
Introduction
39(1)
Assumptions, Problems and Types of Effects Postulated
39(3)
Experimental Designs for Detection of QTL in Crosses Between Inbred Lines
42(1)
Linear Model Analysis of Crosses Between Inbred Lines
43(4)
Experimental Designs for Detection of QTL in Segregating Populations: General Considerations
47(1)
Experimental Designs for Detection of QTL in Segregating Populations: Large Families
48(3)
Experimental Designs for Detection of QTL in Segregating Populations: Small Families
51(3)
Experimental Designs Based on Additional Generations: Inbred Lines
54(1)
Experimental Designs Based on Additional Generations: Segregating Populations
55(3)
Comparison of the Expected Contrasts for Different Experimental Designs
58(1)
Gametic Effect Models for Complete Population Analyses
59(1)
Summary
60(3)
QTL Parameter Estimation for Crosses between Inbred Lines
63(17)
Introduction
63(1)
Moments Method of Estimation
63(2)
Least-squares Estimation of QTL Parameters
65(3)
Least-squares Estimation of QTL Location for Sib-pair Analysis with Flanking Markers
68(1)
Linear Regression Mapping of QTL with Flanking Markers
69(2)
Marker Information Content for Interval Mapping, Uninformative and Missing Marker Genotypes
71(2)
Maximum Likelihood QTL Parameter Estimation for Crosses Between Inbred Lines and a Single Marker
73(1)
Maximum Likelihood Tests of Significance for a Segregating QTL
74(1)
Maximum Likelihood QTL Parameter Estimation for Crosses between Inbred Lines and Two Flanking Markers
74(1)
Estimation of QTL Parameters by the Expectation-maximization Algorithm
75(2)
Biases in Estimation of QTL Parameters with Interval Mapping
77(1)
The Likelihood Ratio Test with Interval Mapping
78(1)
Summary
79(1)
Advanced Statistical Methods for QTL Detection and Parameter Estimation
80(23)
Introduction
80(1)
Higher-order QTL Effects
80(1)
QTL Interaction Effects
81(2)
Simultaneous Analysis of Multiple Marker Brackets
83(1)
Principles of Composite Interval Mapping
84(1)
Properties of Composite Interval Mapping
85(1)
Derivation of Maximum Likelihood Parameter Estimates by Composite Interval Mapping
85(1)
Hypothesis Testing with Composite Interval Mapping
86(1)
Multi-marker and QTL Analysis by Regression of Phenotype on Marker Genotypes
87(1)
Estimation of QTL Parameters in Outbred Populations
88(1)
Analysis of Field Data, Daughter and Granddaughter Designs
89(2)
Maximum Likelihood Analysis of QTL Parameters for the Daughter Design with Linkage to a Single Marker
91(2)
Non-linear and Linear Regression Estimation for Complex Pedigrees
93(1)
Estimation of QTL Allelic Frequencies in Segregating Populations
94(2)
Maximum Likelihood Estimation with Random Effects Included in the Model
96(1)
Incorporation of Genotype Effects into Animal Model Evaluations When Only a Small Fraction of the Population Has Been Genotyped
97(1)
Maximum Likelihood Estimation of QTL Effects on Categorical Traits
98(2)
Estimation of QTL Effects with the Threshold Model
100(1)
Estimation of QTL Effects on Disease Traits by the Allele-sharing Method
101(1)
Summary
101(2)
Analysis of QTL as Random Effects
103(19)
Introduction
103(1)
ML Estimation of Variance Components for the Haseman-Elston Sib-pair Model
104(2)
The Random Gametic Model of Fernando and Grossman, Computing Gv
106(1)
Computing the Inverse of Gv
107(1)
Analysis of the Random Gametic Model by a Reduced Animal Model
108(2)
Analysis of the Random Gametic QTL Model with Multiple QTL and Marker Brackets
110(1)
Computation of the Gametic Effects Variance Matrix
110(1)
The Gametic Effect Model for Crosses Between Inbred Lines
111(1)
REML Estimation of the QTL Variance and Recombination for the Model of Fernando and Grossman
112(1)
REML Estimation of the QTL Variance and Location with Marker Brackets
113(1)
Bayesian Estimation of QTL Effects, Determining the Prior Distribution
114(3)
Formula for Bayesian Estimation and Tests of Significance of a Segregating QTL in a Simulated Granddaughter Design
117(2)
Comparison of ML and Bayesian Analyses of a Simulated Granddaughter Design
119(1)
Markov Chain Monte Carlo Algorithms, Gibbs Sampling
119(1)
Summary
120(2)
Statistical Power to Detect QTL, and Parameter Confidence Intervals
122(13)
Introduction
122(1)
Estimation of Power in Crosses Between Inbred Lines
123(1)
Replicate Progeny in Crosses Between Inbred Lines
124(2)
Estimation of Power for Segregating Populations
126(2)
Power Estimates for Likelihood Ratio Tests: General Considerations
128(1)
The Effect of Statistical Methodology on the Power of QTL Detection
129(1)
Estimation of Power with Random QTL Models
130(1)
Confidence Intervals for QTL Parameters, Analytical Methods
130(2)
Simulation Studies of Confidence Intervals
132(1)
Empirical Methods to Estimate Confidence Intervals, Parametric and Nonparametric Bootstrap and Jackknife Methods
132(1)
Summary
133(2)
Optimization of Experimental Designs
135(10)
Introduction
135(1)
Economic Optimization of Marker Spacing When the Number of Individuals Genotyped Is Non-limiting
135(1)
Economic Optimization with Replicate Progeny
136(1)
Selective Genotyping
137(3)
Sample Pooling: General Considerations
140(1)
Estimation of Power with Sample Pooling
140(2)
Comparison of Power and Sample Sizes with Random Genotyping, Selective Genotyping and Sample Pooling
142(1)
Sequential Sampling
143(1)
Summary
144(1)
Fine Mapping of QTL
145(14)
Introduction
145(1)
Determination of the Genetic Map Critical Interval for a Marker Locus with a Saturated Genetic Marker Map
145(1)
Confidence Interval for QTL Location with a Saturated Genetic Marker Map
146(4)
Fine Mapping of QTL via Advanced Intercross Lines
150(1)
Selective Phenotyping
151(1)
Recombinant Progeny Testing
151(1)
Interval-specific Congenic Strains
152(1)
Recombinant Inbred Segregation Test
152(1)
Fine Mapping of QTL in Outcrossing Populations by Identity by Descent
153(1)
Estimation and Evaluation of Linkage Disequilibrium in Animal Populations
154(1)
Linkage Disequilibrium QTL Mapping, Basic Principles
155(1)
Linkage Disequilibrium Mapping, Advanced Topics
156(1)
Summary
157(2)
Complete Genome QTL Scans: The Problem of Multiple Comparisons
159(14)
Introduction
159(1)
Multiple Markers and Whole-genome Scans
159(2)
QTL Detection by Permutation Tests
161(1)
QTL Detection Based on the False Discovery Rate
162(3)
A Priori Determination of the Proportion of False Positives
165(1)
Analysis of Multiple Pedigrees
166(1)
Biases with Estimation of Multiple QTL
167(1)
Bayesian Estimation of QTL from Whole-genome Scans, Theory
168(3)
Bayesian Estimation of QTL from Whole-genome Scans, Simulation Results
171(1)
Summary
172(1)
Multitrait QTL Analysis
173(13)
Introduction
173(1)
Problems and Solutions for Multitrait QTL Analyses
173(1)
Multivariate Estimation of QTL Parameters for Correlated Traits
174(1)
Comparison of Power for Single and Multitrait QTL Analyses
175(3)
Pleiotropy Versus Linkage
178(1)
Estimation of QTL Parameters for Correlated Traits by Canonical Transformation
179(1)
Determination of Statistical Significance for Multitrait Analyses
180(2)
Selective Genotyping with Multiple Traits
182(2)
Multitrait LD Mapping
184(1)
Summary
184(2)
From the QTL to the Gene
186(8)
Introduction
186(1)
The Molecular Basis of QTL Discovered So Far
187(1)
Determination of QTL Candidate Genes
188(1)
Determination of Concordance
189(1)
QTN Validation by Other Statistical Methods
190(2)
QTN Validation by Functional Studies
192(1)
Summary
193(1)
Principles of Selection Index and Traditional Breeding Programmes
194(10)
Introduction
194(1)
Selection Index for a Single Trait
194(2)
Changes in QTL Allelic Frequencies Due to Selection
196(1)
Multitrait Selection Index
197(1)
The Value of Genetic Gain
198(1)
Dairy Cattle Breeding Programmes, Half-sib and Progeny Tests
199(3)
Nucleus Breeding Schemes
202(1)
Summary
203(1)
Marker-assisted Selection: Theory
204(12)
Introduction
204(1)
Situations in which Selection Index Is Inefficient
204(1)
Potential Contribution of MAS for Selection Within a Breed: General Considerations
205(1)
Phenotypic Selection Versus MAS for Individual Selection
206(1)
MAS for Sex-limited Traits
207(1)
Two-stage Selection: MAS on Juveniles, and Phenotypic Selection of Adults
207(1)
MAS Including Marker and Phenotypic Information on Relatives
208(1)
Maximum Selection Efficiency of MAS with All QTL Known, Relative to Trait-based Selection, and the Reduction in RSE Due to Sampling Variance
209(1)
Marker Information in Segregating Populations
210(1)
Inclusion of Marker Information in `Animal Model' Genetic Evaluations
210(2)
Genetic Evaluation Based on Dense Whole-genome Scans
212(2)
Velogenetics: the Synergistic Use of MAS and Germ-line Manipulation
214(1)
Summary
215(1)
Marker-assisted Selection: Current Status and Results of Simulation Studies
216(16)
Introduction
216(1)
Modelling the Polygenic Variance
216(1)
The Effective Number of QTL
217(1)
Proposed Dairy Cattle Breeding Schemes with MAS: Overview
218(1)
Inclusion of Marker Information into Standard Progeny Test and MOET Nucleus Breeding Schemes
219(1)
Progeny Test Schemes, in Which Information on Genetic Markers is Used to Preselect Young Sires
220(2)
The Current Status of MAS in Dairy Cattle
222(1)
Selection of Sires Based on Marker Information Without a Progeny Test
223(1)
Computation of Reliabilities of Genetic Evaluations Based on Complete Genome Scans
224(1)
Long-term Considerations, MAS Versus Selection Index
225(3)
MAS for a Multitrait Breeding Objective with a Single Identified QTL
228(2)
MAS for a Multitrait Breeding Objective with Multiple Identified QTL
230(1)
Summary
231(1)
Marker-assisted Introgression
232(6)
Introduction
232(1)
Marker-assisted Introgression: General Considerations
233(1)
Marker-assisted Introgression of a Major Gene into an Inbred Line
234(1)
Marker-assisted Introgression of a QTL into a Donor Population Under Selection
235(2)
Marker-assisted Introgression for Multiple Genes
237(1)
Summary
237(1)
Glossary of Symbols
238(6)
Latin Symbols
238(4)
Greek Symbols
242(1)
Other Symbols
243(1)
References 244(14)
Author Index 258(3)
Subject Index 261