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Chapter 1 A Framework for Genetic Optimization

Chapter 2 Describing Genetics in a Production System Context

Genetic and Biological Components of Production Systems: Genetic populations; Genetic differences in animals and alleles; Biological components; Mating systems/strategies; Genetic program structure

Economic and Environmental Components of Production Systems: Market place and product: revenue; Pricing considerations; Production environment: costs and limitations

Chapter 3 Building Genotypes into Production Models

Expressing Revenues and Costs In Equation Format: Profit equation general forms; Planning horizon

Single Equation Profit Function: Linear additive profit functions; Non-additive and non-linear profit functions

Multiple-Equation Descriptions of Profit

Population Dynamics and Trait Expression: Incorporation of population dynamics; Mathematical theory, population age structures Maternal Effects

Modelling Mating Strategies

Alternate Perspectives on Profit Functions

Chapter 4 Optimizing Management in Genotype Comparisons

Introduction to Linear Programming

Optimizing Choices of Genotypes Using Simple Revenues and Expenses

Optimizing Choices of Genotypes Including Replacements

Optimizing Choices of Genotypes Including Replacements and Accounting for Population Age Distribution

Optimizing Management to Evaluate Genotypes

Bio-Economic Modelling and Optimizing Management

Chapter 5 Economic Evaluation and Ranking of Genotypes

Ranking and Evaluation of Genotypes: Single Equation Approach

Ranking and Evaluation of Parents of Production Animals

Ranking and Evaluation of Genotypes: Multiple Equation Approach

Ranking Genotypes and Breeding Systems with Simultaneous Optimization of Management

Comparison of Ranking Genotypes on Profit Functions Relative to Selection Indexes

Chapter 6 Defining and Using Aggregate Genotypes

Definition of Aggregate Genotype

Constructing an Aggregate Genotype from a Profit Function: Economic values calculated from linear profit functions; from non-linear profit functions; for traits in quadratic profit functions; for traits in multiplicative profit functions; for traits measured on a categorical scale; for traits with categorical pricing

Aggregate Genotypes for Transformed Traits

Optimizing Management and Breeding Objectives Simultaneously

Defining an Aggregate Genotype for Alternative Endpoints

Constructing an Aggregate Genotype from a Bio-Economic Model

Re-Parameterization of Aggregate Genotypes

Perspective Equivalences in Defining Aggregate Genotypes

Robustness of Economic Values and Risk Analysis

Alternative Definitions of Aggregate Genotype

Chapter 7 Predicting Selection Response in Multiple Traits

Predicting Selection Responses with Alternate Information Sources

Suboptimal Selection Indexes

Probability Statements about True Total Merit for Individuals

Alternative Selection Indexes

Chapter 8 Allele Flow and Long-Term Prediction

Tracking Allele Flow Through a Population Over Time

Predicting Long-Term Economic Effects of Allele Flow and Expression

Predicting Polyallelic Selection Response Using Allele Flow: Selection response and economic returns over time; General prediction of response and economic returns from selection

Allele Flow and Discounting Methods in Multiple-Trait Selection: Value of an ongoing multiple-trait selection program in a structured population; Discounted trait expressions; Allele flow and bio-economic modelling

Chapter 9 Limits and Costs of Genetic Improvement Strategies

Economic Costs and Benefits of Implementing Genetic Change: Cost-benefit analysis for comparing genotypes; Cost-benefit analysis for comparing selection strategies

Practical Limits to Implementing Genetic Improvement Programs

Genetic Costs of Selection and Inbreeding

Chapter 10 Opportunities and Challenges for Future Genetic Improvement

Changing Markets and Environments

Changing Knowledge and Technology

Acting on the Opportunities

Case Study: Development of terminal and maternal indexes for intensive lamb production considering survival and reproductive traits

Introduction and Objectives; Description of Production System; Models of Production System (Profit Functions); Aggregate Genotype (Breeding Objective); Predictions of Selection Response

R Script for Modelling Herd Dynamics

R Scripts for Optimization with Linear Programming

R Scripts for Calculating Economic Values

Traits measured on a categorical scale; Traits with categorical or grid pricing; Parents with offspring priced according to a grid; Pricing determined by weight category only

Theoretical Basis and R Script for Prediction with Selection Index Methods

Theoretical basis for deriving selection indices; Predicting genetic progress in total merit; Trait changes and change in total merit as a result of selection; Equivalence of selection index to substitution of genetic evaluation into the aggregate genotype

R script for selection index calculations

R Scripts for Modelling Allele Flow and Predicting Selection Response and Economic Returns

Tracking allele flow through a herd and predicting effects of breeding strategies; Allele flow, selection response and economic returns in a herd; In a closed population with a terminal crossbreeding structure