Notebook for QG
1
Preface
2
Genetic Constitution of A Population
2.1
Frequencies of genes(alleles) and genotypes
2.1.1
Mendelian variation in natural populations
2.1.2
Causes of change
2.2
Hardy-Weinberg equilibrium
2.2.1
The Hardy-Weinberg law
2.2.2
Applications of the Hardy-Weinberg law
2.2.3
Mating frequencies and another proof of the Hardy-Weinberg law
2.2.4
Multiple alleles
2.2.5
Sex-linked genes
2.2.6
More than one locus
2.3
Non-random mating
2.3.1
Assortative mating
3
Changes of Gene Frequency
3.1
Migration
3.2
Mutation
3.2.1
Non-recurrent mutation
3.2.2
Recurrent mutation
3.3
Selection
3.3.1
Change of gene frequency under selection
3.3.2
Effectiveness of selection
3.3.3
Number of generations required
3.3.4
Average fitness and load
3.4
Equilibria
3.4.1
Balance between mutation and selection
3.4.2
Changes of equilibrium
3.4.3
Selection favouring heterozygotes
3.5
Polymorphism
4
Small populations: I. Changes of Gene Frequency Under Simplfied Conditions
4.1
The idealized population
4.2
Sampling
4.2.1
Variance of gene frequency
4.2.2
Fixation
4.2.3
Genotype frequencies
4.3
Inbreeding
4.3.1
Inbreeding in the idealized population
4.3.2
Variance of gene frequency
4.3.3
Genotype frequencies
5
Small Populations: II. Less Simplified Conditions
5.1
Effective population size
5.1.1
exclusion of closely related matings
5.1.2
Different numbers of males and females
5.1.3
Unequal numbers in successive generations
5.1.4
Non-random distribution of family size
5.1.5
Minimal inbreeding
5.1.6
Overlapping generations
5.2
Mutation, migration, and selection
5.2.1
Non-recurrent neutral mutation
5.2.2
Recureent mutation and migration
5.2.3
Selection
5.3
Random drift in natural populations
5.4
Polymorphism
5.4.1
Neutral theory
6
Small Populations: III. Pedigreed Populations and Close Inbreeding
6.1
Pedigreed populations
6.1.1
The inbreeding coefficient of an individual
6.1.2
Coancestry or kinship
6.2
Regular systems of inbreeding
6.2.1
Close inbreeding
6.2.2
Fixation
6.2.3
Repeated backcrosses
6.2.4
Crosses and subsequent generations
6.2.5
Mixed inbreeding and crossing
6.2.6
Change of base: strutured population
6.2.7
Mutation
6.2.8
Selection favouring heterozygotes
7
Continuous Variation
7.1
Metric characters
7.2
Properties of metric characters
8
Values and Means
8.1
Population mean
8.2
Average effect
8.3
Breeding value
8.4
Dominance deviation
8.5
Interaction deviation
8.6
Note: Proof of the slope of regression line
9
Variance
9.1
Components of variance
9.1.1
Components as proportions of the total
9.1.2
Estimation of the degree of genetic determination,
\(V_G/V_P\)
9.2
Genetic components of variance
9.2.1
Additive and dominance variance
9.2.2
Total genetic variance
9.2.3
Interaction variance
9.2.4
Variance due to disequilibrium
9.3
Correlation and interaction between genotype and environment
9.3.1
Correlation
9.3.2
Interaction
9.4
Environmental variance
9.4.1
Multiple measurements: repeatability
9.5
Summary of variance partitioning
10
Resemblance between relatives
10.1
Genetic covariance
10.1.1
Offspring and one parent
10.1.2
Offspring and mid-parent
10.1.3
Half sibs
10.1.4
Full sibs
10.1.5
Twins
10.1.6
General
10.1.7
Epistatic interaction
10.2
Environmental covariance
10.3
Phenotypic resemblance
11
Heritability
11.1
Estimation of heritability
11.1.1
Offspring-parent regression
11.1.2
Sib analysis
11.1.3
Intra-sire regression of offspring on dam
11.1.4
Combined estimates
11.2
Twins and human data
11.3
Assortative mating
11.4
Precision of estimates and design of experiments
11.4.1
Offspring-parent regression
11.4.2
Sib analysis
11.4.3
Selection of parents
12
Selection: 1. The response and its prediction
12.1
Response to selection
12.1.1
Prediction of response
12.1.2
Selection differential and intensity of selection
12.1.3
Improvement of response
12.2
Measurenment of response
12.2.1
Variability of generation means
12.2.2
Weighting the selection differential
12.2.3
Realized heritability
12.2.4
Maternal effects
12.3
Change of gene frequency under artificial selection
12.4
Effects of selection on variance
13
Selection: II The results of experiments
13.1
Short-term results
13.1.1
Repeatability of response
13.1.2
Sampling variance
13.1.3
Asymmetry of response
13.2
Long-term results
13.2.1
Selection limits
13.2.2
Mutation
13.2.3
Causes of selection limits
13.2.4
Number of loci (effective factors) and standardized effects
14
Selection: III Information from relatives
14.1
Criteria for selection
14.1.1
Simple methods
14.1.2
Prediction of response
14.1.3
Combined selection
14.1.4
Relative merits of the methods
14.2
Index selection
14.2.1
Construction of an index
14.2.2
Accuracy
14.2.3
Response to selection
14.2.4
Actual achievements
15
Inbreeding and crossbreeding: I Changes of mean value
15.1
Inbreeding depression
15.1.1
The effect of selection
15.2
Heterosis
15.2.1
Single crosses
16
Inbreeding and crossbreeding: II changes of variance
16.1
Inbreeding
16.1.1
Redistribution of genetic variance
16.1.2
Environmental variance
16.1.3
Uniformity of inbred strains
16.2
Mutation
16.2.1
Subline divergence
16.3
Crossing
16.3.1
Variance between crosses
16.3.2
Combining ability
17
Inbreeding and crossbreeding: III Applications
17.0.1
Selection for combining ability
17.0.2
Three-way and four-way crosses; backcrosses
17.0.3
Reciprocal recurrent selection
17.0.4
Overdominance
17.0.5
Naturally self-fertilizing plants
18
Scale
18.0.1
Distribution and variance
18.0.2
Interactions
18.0.3
Conclusions
19
Threshold characters
19.0.1
Liability and threshold
19.0.2
Two clases, one threshold
19.0.3
Adequacy of the liability model
19.0.4
Scale relationships
19.0.5
Three classes, two thresholds
19.0.6
Selection for threshold characters
20
Correlated characters
20.1
Genetic and environmental correlations
20.1.1
Estimation of the genetic correlation
20.2
Correlated response to selection
20.2.1
Indirect selection
20.3
Genotype-environment interaction
20.4
Index selection
20.4.1
Construction of the index
20.4.2
Response
20.4.3
Effect of selection on genetic correlations
21
Metric characters under natural selction
21.1
Natural selection
21.1.1
Fitness and its components
21.2
Relationships between metric characters and fitness
21.2.1
Fitness profiles
21.3
Responses to natural selection
21.3.1
Fitness
21.3.2
Correlated responses
21.3.3
Strength of selection
21.4
Equilibrium populations
21.4.1
Fitness
21.4.2
Major components
21.4.3
Characters with intermediate optima
21.4.4
Characters with minimum fitness of intermediates
21.4.5
Neutral characters
21.5
Origin of variation by mutation
21.5.1
Mutational variance
21.6
Maintenance of genetic variation
21.6.1
Balance between neutral mutation and random drift
21.6.2
Mutation-selection balance
22
Quantitative trait loci
22.1
Major genes
22.1.1
Methods of detecton
22.2
Methods for mapping QTLs
22.2.1
Marker loci
22.2.2
QTL genotypes
22.2.3
Single marker analysis
22.2.4
Interval mapping analysis
22.3
Genetical and statistical considerations
22.3.1
Experimental design
22.3.2
Multiple test
22.3.3
Maximum likelihood estimation
22.3.4
Multiple QTLs
22.4
Experimental results
22.4.1
Number of loci
22.4.2
Gene effects
22.4.3
Consistency
22.5
From QTL to gene
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4
Small populations: I. Changes of Gene Frequency Under Simplfied Conditions
4.1
The idealized population
4.2
Sampling
4.2.1
Variance of gene frequency
4.2.2
Fixation
4.2.3
Genotype frequencies
4.3
Inbreeding
4.3.1
Inbreeding in the idealized population
4.3.2
Variance of gene frequency
4.3.3
Genotype frequencies