9780851994024

Quantitative Trait Loci Analysis in Animals

by
  • ISBN13:

    9780851994024

  • ISBN10:

    0851994024

  • Format: Paperback
  • Copyright: 2001-11-08
  • Publisher: Oxford University Press, USA

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Summary

Detection of Quantitative Trait Loci (QTL) has become a 'hot' topic in genetics in recent years and is of major agricultural significance. This advanced textbook describes the scientific literature and principles on methods for quantitative trait loci detection and analysis and marker assisted selection in animal breeding.No other similar textbook in this areaAuthor has excellent reputation in the fieldThis is a new and dynamically developing area of research, of worldwide interest

Table of Contents

Preface, theory vs. results 1(3)
Historical overview
3(12)
Introduction
3(1)
From Mendel to Sax
3(2)
Quantitative genetics 1920-1980, or who needs Mendel?
5(1)
QTL detection 1930-1980, theory and experiments
6(1)
From biochemistry to biotechnology, or more markers than we will ever need
7(2)
Genetic mapping functions
9(3)
Physical and genetic mapping, questions of scale
12(2)
Summary
14(1)
Principles of Parameter Estimation
15(15)
Introduction
15(1)
Desired properties of QTL parameter estimates
16(1)
Moments method of estimation
17(1)
Least-squares parameter estimation
17(1)
Least-squares solutions for a single parameter
18(1)
Least-squares solutions for the general linear model
19(1)
Maximum likelihood estimation for a single parameter
20(2)
Maximum likelihood multi-parameter estimation
22(1)
Confidence intervals and hypothesis testing for MLE
23(1)
Methods to maximize likelihood functions
24(1)
Derivative-free methods
25(1)
Second derivative-based methods
26(1)
First derivative-based methods (EM)
26(1)
Bayesian estimation
27(1)
Minimum difference estimation
28(1)
Summary
29(1)
Random and Fixed Effects, the Mixed Model
30(18)
Introduction
30(1)
The mixed linear model
30(2)
The mixed model equations
32(1)
Solving the mixed model equations
33(1)
Some important properties of mixed model solutions
34(1)
Equation absorption
34(1)
Multivariate mixed model analysis
35(2)
The repeatability model
37(1)
The individual animal model
38(1)
Grouping individuals with unknown ancestors
39(1)
The reduced animal model
40(1)
Maximum likelihood estimation with mixed models
41(1)
Estimation of variance components, analysis of variance type methods
41(1)
Maximum likelihood estimation of variance components
42(3)
Restricted maximum likelihood estimation of variance components
45(1)
The problem of variance components outside the parameter space
46(1)
Summary
47(1)
Experimental Designs to Detect QTL, Generation of Linkage Disequilibrium
48(27)
Introduction
48(1)
Assumptions, problems and types of effects postulated
48(4)
Experimental designs for detection of QTL in crosses between inbred lines
52(1)
Linear model analysis of crosses between inbred lines
53(4)
Experimental designs for detection of QTL in segregating populations - general considerations
57(3)
Experimental designs for detection of QTL in segregating populations - large families
60(3)
Experimental designs for detection of QTL in segregating populations - small families
63(4)
Experimental designs based on additional generations
67(3)
Comparison of the expected contrasts for different experimental designs
70(1)
Gametic effect models for complete population analyses
71(2)
Summary
73(2)
QTL Parameter Estimation for Crosses between Inbred Lines
75(21)
Introduction
75(1)
Moments method of estimation
76(1)
Least-squares estimation of QTL parameters
77(4)
Least-squares estimation of QTL location for sib-pair analysis with flanking markers
81(2)
Linear regression mapping of QTL with flanking markers
83(2)
Marker information content for interval mapping, uninformative and missing marker genotypes
85(2)
Maximum likelihood QTL parameter estimation for crosses between inbred lines and a single marker
87(1)
Maximum likelihood tests of significance for a segregating
88(1)
Maximum likelihood QTL parameter estimation for crosses between inbred lines and two flanking markers
89(1)
Estimation of QTL parameters by the expectation-maximization algorithm
90(2)
Biases in estimation of QTL parameters with interval mapping
92(1)
The likelihood ratio test with interval mapping
93(1)
Summary
94(2)
Advanced statistical methods for QTL detection and parameter estimation
96(24)
Introduction
96(1)
Higher order QTL effects
97(1)
QTL interaction effects
97(2)
Simultaneous analysis of multiple marker brackets
99(2)
Principles of composite interval mapping
101(1)
Properties of composite interval mapping
101(1)
Derivation of maximum likelihood parameter estimates by composite interval mapping
102(1)
Hypothesis testing with composite interval mapping
103(1)
Multi-marker and QTL analysis by regression of phenotype on marker genotypes
104(1)
Estimation of QTL parameters in outbred propulations
105(2)
Solutions for analysis of field data from segregating populations
107(2)
Maximum likelihood analysis of QTL parameters for the daughter design with linkage to a single marker
109(2)
Maximum likelihood estimation of QTL parameters from other complex pedigrees
111(1)
Non-linear regression estimation for complex pedigrees
112(2)
Maximum likelihood estimation with random effects included in the model
114(1)
Maximum likelihood estimation of QTL effects on categorical traits
115(2)
Estimation of QTL effects with the threshold model
117(1)
Estimation of QTL effects on disease traits by the allele-sharing method
118(1)
Summary
119(1)
Analysis of QTL as Random Effects
120(22)
Introduction
120(1)
ML estimation of variance components for the Haseman-Elston sib-pair model
121(2)
The random gametic model of Fernando and Grossman, computing Gv
123(2)
Computing the inverse of Gv
125(1)
Analysis of the random gametic model by a reduced animal model (RAM)
126(2)
Analysis of the random gametic QTL model with multiple QTL and marker brackets
128(1)
Computation of the gametic effects variance matrix
129(2)
The gametic effect model for crosses between inbred lines
131(1)
REML estimation of the QTL variance and recombination for the model of Fernando and Grossman
132(1)
REML estimation of the QTL variance and location with marker brackets
133(1)
Bayesian estimation of QTL effects, determining the prior distribution
134(4)
Formula for Bayesian estimation and tests of significance of a segregating QTL in a simulated grand-daughter design
138(1)
Comparison of ML and Bayesian analyses of a simulated grand-daughter design
139(1)
Markov Chain Monte Carlo algorithms, Gibbs' sampling
140(1)
Summary
141(1)
Statistical Power to Detect QTL, and Parameter Confidence Intervals
142(15)
Introduction
142(1)
Estimation of power in crosses between inbred lines
143(1)
Replicate progeny in crosses between inbred lines
144(2)
Estimation of power for segregating populations
146(4)
Power estimates for likelihood ratio tests - general considerations
150(1)
The effect of statistical methodology on the power of QTL detection
150(1)
Estimation of power with random QTL models
151(1)
Confidence intervals for QTL parameters - analytical methods
152(1)
Simulation studies of confidence intervals
153(1)
Empirical methods to estimate CI, parametric and non-parametric bootstrap and jackknife methods
154(2)
Summary
156(1)
Optimization of Experimental Designs
157(12)
Introduction
157(1)
Economic optimization of marker spacing when the number of individuals genotyped is non-limiting
157(1)
Economic optimization with replicate progeny
158(2)
Selective genotyping
160(3)
Sample pooling - general considerations
163(1)
Estimation of power with sample pooling
163(3)
Comparison of power and sample sizes with random genotyping, selective genotyping, and sample pooling
166(1)
Sequential sampling
167(1)
Summary
168(1)
Fine Mapping of QTL
169(9)
Introduction
169(1)
Determination of the genetic map critical interval for a marker locus with a saturated genetic marker map
169(2)
Confidence interval for QTL location with a saturated genetic marker map
171(1)
Fine mapping of QTL via advanced intercross lines
172(1)
Selective phenotyping
173(1)
Recombinant progeny testing
174(1)
Interval specific congenic strains
174(2)
Recombinant inbred segregation test
176(1)
Fine mapping of QTL in outcrossing populations by identity by descent
176(1)
Summary
177(1)
Complete Genome QTL Scans - the Problem of Multiple Comparisons
178(12)
Introduction
178(1)
Multiple markers and whole genome scans
179(2)
QTL detection by permutation tests
181(1)
QTL detection based on the false discovery rate
181(4)
A priori determination of the proportion of false positives
185(1)
Analysis of multiple pedigrees
186(2)
Biases with estimation of multiple QTL
188(1)
Summary
189(1)
Multiple Trait QTL analysis
190(15)
Introduction
190(1)
Problems and solutions for multiple trait QTL analyses
190(1)
Multivariate estimation of QTL parameters for correlated traits
191(2)
Comparison of power for single and multitrait QTL analyses
193(3)
Pleiotropy vs. linkage
196(1)
Estimation of QTL parameters for correlated traits by canonical transformation
197(2)
Determination of statistical significance for multitrait analyses
199(1)
Selective genotyping with multiple traits
200(3)
Summary
203(2)
Principles of Selection Index and Traditional Breeding Programmes
205(12)
Introduction
205(1)
Selection index for a single trait
205(2)
Changes in QTL allelic frequencies due to selection
207(1)
Multitrait selection index
208(1)
The value of genetic gain
209(2)
Dairy cattle breeding programmes, half sib and progeny tests
211(3)
Nucleus breeding schemes
214(1)
Summary
215(2)
Marker-assisted Selection - Theory
217(10)
Introduction
217(1)
Situations in which selection index is inefficient
217(1)
Potential contribution of MAS for selection within a breed - general considerations
218(1)
Phenotypic selection vs. MAS for individual selection
219(1)
MAS for sex-limited traits
220(1)
Two-stage selection: MAS on juveniles and phenotypic selection of adults
221(1)
MAS including marker and phenotypic information on relatives
222(1)
Maximum selection efficiency of MAS with all QTL known, relative to trait-based selection, and the reduction in RSE due to sampling variance
223(1)
Marker information in segregating populations
224(1)
Inclusion of marker information in ``animal model'' genetic evaluations
225(1)
Velogenetics - the synergistic use of MAS and germ-line manipulation
225(1)
Summary
226(1)
Marker-assisted Selection - Results of Simulation Studies
227(16)
Introduction
227(1)
Modeling the polygenic variance
227(2)
The effective number of QTL
229(1)
Proposed dairy cattle breeding schemes with MAS - overview
230(1)
Inclusion of marker information into standard progeny test and MOET nucleus breeding schemes
230(2)
Progeny test schemes, in which information on genetic markers is used to preselect young sires
232(2)
Selection of sires based on marker information without a progeny test
234(1)
Long-term considerations, MAS vs. selection index
235(3)
MAS for a multitrait breeding objective with a single identified QTL
238(3)
MAS for a multitrait breeding objective with multiple identified QTL
241(1)
Summary
241(2)
Marker-assisted Introgression
243(7)
Introduction
243(2)
Marker-assisted introgression - general considerations
245(1)
Marker-assisted introgression of a major gene into an inbred line
246(1)
Marker-assisted introgression of a QTL into a donor population under selection
247(1)
Marker-assisted introgression for multiple genes
248(1)
Summary
249(1)
Glossary of commonly used symbols 250(11)
Latin symbols
250(8)
Greek symbols
258(2)
Other symbols
260(1)
References 261(13)
Author index 274(3)
Subject index 277

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