Animal Breeding and Genetics

Series Preface
Volume Preface
Contents
About the Editor-in-Chief
About the Editor
Contributors
Animal Breeding and Genetics: Introduction
Animal Breeding Methods and Sustainability
Glossary
Definition of the Subject
Introduction
Animal Breeding and Sustainability
Definition of Breed
Breed Conservation
Breeds and Sustainable Systems
Animal Breeding Methods and Schemes
Breeding Companies. Organization and Diffusion of Genetic Progress
Statistical Methods of Selection
The Use of Molecular Genetics in Animal Breeding
Transgenesis
Genetic Markers and Genomic Selection
Future Directions
The Future Evolution of Methods and Schemes
The Limits to Genetic Progress
Bibliography
Primary Literature
Books and Reviews
Quantitative Methods Applied to Animal Breeding
Glossary
Definition of the Subject
Introduction
Principles of Selection
Basic Genetic Model for Quantitative Traits
Phenotypic Selection
Correlated Response and Indirect Selection
Selection Index
Multiple-Trait Selection
Mixed Model Methodology
Introduction
The Animal Model
Extensions and Variations of the Animal Model
Marker-Assisted Selection
Introduction
Classical Approaches with Few Markers
Genomic Selection
Future Directions
Bibliography
Primary Literature
Books and Reviews
Foundations of Molecular Genetics: From Major Genes to Genomics
Glossary
Definition of the Subject
Introduction
The Promise of Molecular Genetics
The Quest of Gene Mapping
Elusive Validation and Repeatability
The Challenges of Fine Mapping
Positional Cloning of QTN - Success Stories
New Genomic Approaches to Discover Causative Mutations
The Advent and Rise of Genomic Selection
Opportunities for Improved Sustainability
Conclusion
Bibliography
Building Genetic Models
Glossary
Definition of the Subject
Introduction
The Introductory Equation
Completing the Model
Adding a Constant to the Model
Parts of the Mixed Model
Fixed Factors
Covariates
Fixed Factors, Solutions, and Estimable Functions
Example with Constraints
Interactions Between Fixed Factors
Heterosis
Maternal Effects and Heterosis
Singularities with Fixed Effects and Random Effects
Is It Fixed or Random?
Genetic Values and Other Random Factors
Prediction of Genetic Values Depends on Variance Components
The Basic Animal Model
Animal Model with Repeated Records
Embedded Traits
Maternal and Paternal Effects Model
Maternal and Grandmaternal Model
Competition-Social Interaction-Pen Mate Effects
Dominance Genetic Values
Genotype by Environment Interactions
Sex Limited Traits
Usual Multiple Trait Models
Normality
Typical Fixed and Random Effects in Models for Yield of Dairy Cows, Weaning Weight of Beef Calves and Lambs, and Carcass Trait...
Future Directions
Bibliography
Primary Literature
Books and Reviews
Genotype by Environment Interactions in Livestock Farming
Glossary
Definition of the subject
Introduction
Expanding the Model
Example: Environment and Diet Composition (ExA)
Example: Environment and Sow Housing (ExB)
The Baseline Model
The Multiple-Trait Model
The Random-Regression Model
The Reproducing Kernel Hilbert Spaces Regression Model
How to Express and Report the Breeding Values
Caveats When Estimating Breeding Values for GxE
Macro-environmental Plasticity: Estimation of Variance Components
Macro-environmental Plasticity: Prediction of Breeding Values
Micro-environmental Plasticity and Its Covariance with Macro-environmental Plasticity
Future directions
References
Socially Affected Traits, Inheritance and Genetic Improvement
Glossary
Definition of the Subject
Introduction
Quantitative Genetics of Socially Affected Traits
Quantitative Genetic Model
Classical Model
Social Model
Breeding Value
Heritable Variance
The Effect of Group Size on Heritable Variance
Response to Selection
General Expression for Response to Selection
Accuracies of Selection
Individual Selection (IS)
Group Selection (GS)
Multilevel Selection
Optimum Index Selection
Selection Based in Information of Relatives
Selection on Estimated Breeding Values (EBVs)
BLUP Ignoring Associative Effects
BLUP Including Associative Effects
A Special Case: Maternal Genetic Effects
Results of Social Selection Experiments
Estimation of Genetic Parameters
Statistical Methodology
Empirical Estimates of the Associative Variance
Mixed Models
Non-Genetic Associative Effects
Accounting for Variation in Group Size
Identifiability of the Associative Genetic Variance
Statistical Power and Optimum Designs
Standard Errors of Estimated Variance Components
Future Directions
Bibliography
Pig Breeding for Increased Sustainability
Glossary
Definition of the Subject
Introduction
Biodiversity
Genetic Distinctiveness
Population Size and Structure
Relative Utility
Urgency, Importance, and Feasibility: Priority Level of the Breed
Target Traits for Genetic Improvement
Genetic Improvement Programs
Environmental Load and Climate Change
Technology
Strategies: Carbon Shadow Prices
Animal Welfare
Robustness
Selection for Robustness Traits
Reaction Norms
Deprivation
Neuroendocrinology
Selection Objectives
Dominance Aggression
Avoidance of Invasive Treatments
Boar Taint
Harmful Interactional Behavior
Ethical Aspects
Artificial Selection
Integrity
Future Directions
Acknowledgments
Bibliography
Primary Literature
Books and Reviews
Poultry Breeding
Glossary
Definition of the Subject
Introduction
Input Resources (Background)
Environmental Impact
Human and Animal Health
Practical Example of Sustainable Genetic Improvement
Balanced Breeding for Optimized Genetic Gain, Maintained Genetic Diversity, and Decreased Impact on Functional and Environment...
Future Directions
Bibliography
Beef Cattle Breeding
Definition of the Subject
Introduction
Beef breeds
Genetic Differences for Beef-Related Traits
Current Beef Breeding Objectives
Terminal indexes
Maternal Indexes
Dairy-Beef Index
Validation
Future Breeding Objectives
Improvements to the Current Selection of Traits
New traits
Estimation of Weighting Factors on Traits
Beef Breeding Schemes
Decision Support Tools
The Role of Breed Societies
Future Challenges
Conclusions
References
Books and Reviews
Novel Trait Selection to Enhance Sustainability of Beef Production Systems
Glossary
Definition of Subject
Introduction
Sustainability as a System Property
Characteristics of High-Leverage Actions
Trait Selection Impacts on Sustainability
Specific Examples of Novel Traits to Address Sustainability
Water Intake and Efficiency
Methane Emissions
Future Directions
References
Dairy Cattle Breeding
Glossary
Definition of the Subject
Introduction
Changing Breeding Programs
Traits Under Selection
Milk Production and Fertility
Longevity
Health and Disease Resistance
Mastitis
Lameness
General Disease Resistance
Novel Traits
Mid-Infrared Spectroscopy
Resilience
Heat Tolerance
Environmental Impact
Feed Efficiency
Animal Welfare
Inbreeding
Future Directions
Bibliography
References in the Text
Books and Reviews (Further Reading)
Sustainable Genetic Improvement in Dairy Goats
Glossary
Definition of the Subject
Introduction
Dairy Goat Production and Breeding Programs
Genetic Evaluation of Dairy Goats: The Canadian Example
Genomic Selection Methodologies
Benefits of Genomic Selection
Benefits and Challenges of Implementing Genomic Selection in Dairy Goats
Implementation of Genomic Selection in Dairy Goats
Development of Genotyping Panels
Genomic Selection in Worldwide Dairy Goat Populations
Genome-Wide Association Studies
Final Remarks
Future Directions
Bibliography
Horse Breeding
Glossary
Definition of the Subject
History of Modern Horse Breeds
Modern Horse Breeds
Breed Management
Breeding for Improvement
Breeding for Diversity
Future Directions
Bibliography
Primary Literature
Books and Reviews
Breeding in Developing Countries and Tropics
Glossary
Definition of the Subject and Its Importance
Introduction
Setting the Scene
World Population
Global Food Production
Products of an Animal Origin
Global Food Security
Animal Resources
Domestication
Distribution of Livestock
Biodiversity as Reflected by Breed
The Most Important Livestock Products for Ensuring Food Security
Poultry
Pigs
Cattle
Small Stock
Per Capita Meat Consumption
Dairy Products
Challenges
External Challenges
Production under Various Systems
Disease
Heat Stress and Water Requirements
Internal Challenges
Infrastructure and Capacity
Structured Programs
Tools and Strategies in Livestock Breeding
Research Expenditure
Intellectual Capacity
The Contribution of Developing Countries to Global Science
The Case for Conserving Animal Genetic Resources
Animal Breeding in the Developing World: Successes and Failures
The Technological Age
Data Capturing, Analysis, and Dissemination
Genomic Selection
Future Directions
Future of Livestock Breeding in the Developing Regions and Tropics
Breeding Objectives
How to Achieve the Objective of Improving Fitness and Adaptability
Broadening the Knowledge Base
``New´´ Issues
Climate Change
Animal Welfare
Conclusion and Recommendations
Bibliography
Sustainability of Wild Populations: A Conservation Genetics Perspective
Glossary
Definition of the Subject
Introduction
Genetic Concepts and Application in Wildlife Biology
Estimating Population Vitality Metrics
Evaluating Variation and Fitness in Wild Populations
Connectivity in Wild Populations
Using Genomics in Wildlife Epidemiology
Population Genomics and Wildlife Adaptation to Climate Change
Captive Breeding Programs
Concluding Remarks
Acknowledgments
References
Further Reading
Breeding in an Era of Genome Editing
Glossary
Definition of the Subject
Introduction
What Is Genome Editing?
Examples of Genome Editing in Farmed Animal Species
Genome Editing as an Alternative to Selective Breeding
Genome Editing as an Alternative to Crossbreeding
Genome Editing Research of Relevance to Application in Farmed Animal Breeding Programs
Detection and Utilization of Causative Variants at QTLs
Introgression-by-Editing of Desirable Alleles
Creation of De Novo Alleles with Favorable Effects on Target Traits
Applying Genome Editing in Breeding Programs
Promotion of Alleles by Genome Editing (PAGE)
New Reproductive Technologies
Using Surrogate Sires to Disseminate ``Elite´´ Genetics
Genomic Evaluation of Genome-Edited Animals
Considerations for Including Genome Editing in Breeding Programs
Ethical and Regulatory Considerations
Future Directions
References
Long-term Challenges for Animal Breeding
Glossary
Definition of the Subject
Introduction
A Basic Algorithm for Animal Breeding
The Effectiveness of Animal Breeding
Essential Criteria for Sustained Genetic Improvement
Anticipated Long-Term Challenges
Breeding Goals with the Long Future in Mind
Genetic Variation: The Essential Raw Material for Long-Term Genetic Improvement
Organizational Effectiveness: Investments and Decisions for Sustained Genetic Improvement
Choice of Breeding Goal
Investment in Data
Implications for Players in the ``Animal Breeding Game´´
Less Technically or Financially Developed Animal Breeding Program
Renovating Programs to Meet Long-Term Challenges
Conclusion
References
Index