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• Genetic Improvement of Farmed Animals
• Copyright
• Contents
• Foreword
• Preface
• Acknowledgements
• 1 The Origins and Rôles of Today’s Livestock Breeds
• Natural Selection and Evolution
• Domestication
• Livestock Breeds and Their Origins
• The Rôles of Livestock
• Summary
• References
• Recommended Reading
• 2 Genes, Genetic Codes and Genetic Variation
• Introduction
• Chromosomes and Genes
• The Structure and Function of Genes
• DNA and genetic codes
• Loci and alleles
• Transfer of genetic codes during cell division
• Mitosis
• Meiosis
• Mutation
• Tracking genes across generations
• Genes, Genotypes and Phenotypes
• Predicting the outcome of matings among different genotypes
• Genotype and gene (or allele) frequencies
• Sources of genetic variation between animals
• Types of Gene Action
• Additive and non-additive gene action
• Co-dominance, no dominance or additive gene action
• Complete dominance
• Partial dominance
• Overdominance
• Other types of gene action and inheritance
• Sex-linked genes
• Sex-limited gene action
• Sex-influenced gene action
• Genomic imprinting
• Pleiotropy
• Epistasis
• Incomplete penetrance and variable expressivity
• Cytoplasmic or mitochondrial inheritance
• Names and abbreviations of genes
• The Nature of Traits of Interest in Farmed Animals
• Qualitative and quantitative traits
• Genetic and environmental influences
• Traits affected by single genes
• Traits affected by many genes
• Measuring Variation in Performance
• Measuring Associations Between Traits and Between Animals
• Phenotypic, Genetic and Environmental Associations
• Summary
• References
• Recommended Reading
• 3 Strategies for Genetic Improvement
• Introduction
• The Structure of Livestock Breeding Industries
• Selection Between Breeds or Breed Types
• Selection Within Breeds or Breed Types
• Requirements for within-breed selection
• Factors affecting rates of improvement
• Selection for more than one trait
• Crossbreeding
• Reasons for crossing
• Types of heterosis
• Systems of crossing
• Conservation of Genetic Resources
• Why conserve rare breeds?
• Which breeds should be conserved?
• Methods of conservation
• Summary
• References
• Recommended Reading
• 4 What Affects Response to Selection Within Breeds?
• Introduction
• Factors Affecting Rates of Genetic Gain
• Selection differential
• Heritability
• Generation interval
• A more useful formula for predicting response
• The link between selection intensity and generation interval
• Using information from relatives
• Accuracy of selection
• Additive genetic standard deviation
• A practical example
• Using repeated records of performance
• Predicting correlated responses to selection
• Limitations of these predictions
• Reduction in variation following selection
• Selection limits
• Variation in response
• Controlling Inbreeding
• Summary
• Appendix: The Connection Between the Two Formulae Presented to Predict Response to Selection
• References
• Recommended Reading
• 5 Tools and Technologies in Animal Breeding
• Introduction
• Reproductive Technologies
• Artificial insemination
• Multiple ovulation and embryo transfer
• In vitro production of embryos
• Semen and embryo sexing
• Embryo cloning
• Surrogate sire technology
• The value of reproductive technologies in genetic improvement
• Molecular Genetic Tools
• Linkage disequilibrium and haplotypes
• Laboratory methodology
• Genome mapping
• Whole-genome sequencing methods
• Sequence databases
• Current status of livestock genomes
• Genome annotation
• Current status of livestock genomes
• Genome-wide association studies
• Signatures of selection
• Genomic selection
• Genotype imputation
• Genetic engineering
• Genome editing
• Modern Data Capture Tools
• Milk mid-infrared spectral data
• Sensors for health, reproduction and live weight traits
• Automated systems for measuring feed intake
• In vivo prediction of carcass traits
• Video image analysis/computer vision to measure weight, conformation and carcass traits
• Greenhouse gas emissions
• Use of mobile apps to capture phenotypic data
• Summary
• References
• 6 Analysing Genetic Variation in Farm Animals
• Introduction
• Estimating Heritability
• Additive variance
• Observational and causal variances
• Sire-based methods
• Animal model
• Alternative models
• Additional causal components of variance
• Estimating Non-Additive Parameters, Correlations and Genotype- by-Environment Interactions
• Non-additive components of variance
• Genetic correlations
• Genotype-by-environment interactions
• Random regression
• Software solutions
• Molecular Genetics and Trait Variation
• Calculating inbreeding using SNP markers
• Summary
• References
• Recommended Reading
• 7 Predicting Breeding Values
• Introduction
• Performance Data and Pedigrees
• Management of Candidates for Selection
• Adjusting Records of Performance
• Additive correction factors
• Multiplicative correction factors
• Standardizing to adjust records
• Principles of Breeding Values and Indexes
• Clues to an animal’s breeding value
• Calculating PBVs
• Using the animal’s own performance
• Using information from relatives
• Selection indexes
• Combining information from relatives on a single trait
• Combining information on different traits
• A practical example
• Predicting Breeding Values Using Best Linear Unbiased Prediction
• How BLUP works
• BLUP models
• Direct and maternal genetic effects
• Single and multi-trait BLUP
• Random regression models
• Social interaction model
• Estimates of Heritabilities and Correlations for PBV Calculations
• Genomic Prediction of Breeding Values
• Models for genomic prediction and selection
• GBLUP
• SNP-BLUP
• Single-step procedure
• Benefits of BLUP
• Using Economic Values with BLUP
• Scale of Presentation of Genetic Merit
• Accuracies and Reliabilities
• Publishing Results
• Genetic bases
• International Evaluations and Conversions
• International evaluations
• International conversions
• Summary
• References
• Recommended Reading
• 8 Dairy Cattle Breeding
• Introduction
• Breeding Goals
• Breeds and Crosses Used in Dairying
• Selection Within Breeds
• Systems of testing
• Progeny testing schemes
• Genomic selection
• Nucleus breeding schemes
• Traits recorded
• Milk recording
• Type traits
• Claw disease traits
• Reproduction, health and workability
• Feed intake, feed efficiency, live weightand body condition
• Climate change mitigation and adaptation traits
• Methods and results of genetic evaluation
• Milk production traits
• Other traits
• Indexes of overall economic merit
• Evidence of genetic improvement and its value
• Genotype-by-environment interactions
• Practical Guidelines on Selection
• Summary
• References
• Recommended Reading
• 9 Beef Cattle Breeding
• Introduction
• Breeding Goals
• Beef breeding goals in dairy and dual-purpose breeds
• Terminal sires for use in dairy herds and specialized beef herds
• Breeding replacement females for specialized beef herds
• Smallholder and pastoral systems in lower income countries
• Breeds and Crosses Used in Beef Production
• Selection within breeds
• Systems of testing
• Performance testing
• Progeny testing
• Other breeding schemes
• Traits recorded
• Methods and results of genetic evaluation
• Overview
• Evaluations across herds, breeds and countries
• Indexes of overall economic merit
• Evidence of genetic improvementand its value
• Evidence of genetic improvement and its value
• Evidence of genetic improvement and its value
• Genotype × Environment Interactions
• Practical Guidelines on Selection
• Selection between breeds or crosses
• Selection of bulls (or semen) for use in a purebred herd
• Selection of replacement females in a purebred herd
• Selection of replacement bulls and cows for a commercial herd
• Summary
• References
• Recommended Reading
• 10 Sheep and Goat Breeding
• Introduction
• Breeding goals
• Meat production
• Wool production
• Milk production
• Additional breeding goals
• Multi-purpose breeding goals
• Breeds and Crosses Used in Sheep Production
• Meat production
• Wool production
• Dual-purpose meat and wool production
• Milk production
• Goat Breeds
• Selection Within Breeds
• Meat production
• Systems of testing
• Traits recorded
• Methods and results of genetic evaluation
• Use of indexes of overall economic merit
• Evidence of genetic improvement and its value
• Wool production
• Systems of testing
• Traits recorded
• Methods of genetic evaluation
• Use of indexes of overall economic merit
• Evidence of genetic improvement and its value
• Milk production
• Use of genomics in sheep and goat breeding
• Genotype × Environment Interactions
• Practical Guidelines on Selection
• Selection between breeds or crosses
• Selection of rams, bucks or semen for use in a purebred flock or herd
• Selection of replacement females in a purebred flock or herd
• Selection of replacement males and females for commercial flocks or herds
• Summary
• References
• Recommended Reading
• 11 Poultry Breeding
• Introduction
• The Global Poultry Sector
• Breeding Goals
• Meat production
• Selection for early growth, feed conversion and carcass composition
• Selection for health and welfare traits
• Selection for adult traits
• Egg production
• Legislative framework
• Consumer preferences
• Housing systems
• Layer breeding objectives and criteria
• Selection for egg traits
• Selection for health traits
• Selection for social and behavioural traits
• Future selection goals
• Breeds, Crosses and Hybrid Lines Used in Poultry Production
• Genetic Improvement Strategies in Large-Scale Chicken Production Systems
• Overview
• Meat production
• Health traits in broilers
• Male and female traits in broilers
• Methods and results of genetic evaluation in broilers
• Use of indexes of overall economic merit in broilers
• Using genomics in broiler production
• Evidence of genetic change in broilers
• Egg production
• Welfare of layers
• Layer breeding structures
• Methods and results of genetic evaluation in layers
• Use of indexes of overall economic merit in layers
• Using genomics in layers
• Using genomics in layers
• Evidence of genetic improvement in layers
• Practical Guidelines on Selection
• Summary
• References
• Recommended Reading
• 12 Pig Breeding
• Introduction
• The Global Pig Sector
• Pig-meat Value Chains
• Breeding Objectives
• Drivers of profitability
• Historical and modern breeding objectives
• Breeds and Lines Used in Pig Production
• Genetic Improvement Strategies within Large-scale Pig-production Systems Typical of Developed Count
• Overview
• Systems of testing
• Breeding companies
• National genetic improvement programmes
• Breed societies
• Traits recorded
• Methods of Genetic Evaluation
• Use of Indexes
• Evidence of Genetic Improvement and its Value
• Genetic Improvement Strategies Within the Smallholder Pig Sectors
• Use of reproductive technologies in dissemination of improved genetics
• Practical Guidelines on Selection
• Summary
• References
• Recommended Reading
• 13 Aquaculture Breeding
• Introduction
• Aquaculture: Global Status and Trends
• Aquaculture Versus Terrestrial Livestock
• The Potential of Selective Breeding
• History of Selective Breeding in Aquaculture
• Atlantic salmon breeding programmes
• Breeding programmes for other aquaculture species
• Disease resistance as a primary target trait
• Genotype × Environment Interactions
• Reproductive Technologies in Aquaculture Production
• Use of Genomic Technology in Aquaculture Breeding
• Molecular markers
• Genomic selection
• Possibilities for genome editing
• Practical Guidelines on Selection
• Summary
• References
• Recommended Reading
• 14 Future Directions
• Introduction
• Towards Sustainable Livestock Production
• Economic dimension
• Environmental dimension
• Societal dimension
• Ethical implications of livestock breeding
• Tailpiece
• Summary
• References
• Recommended Reading
• Appendix
• Appendix
• Glossary of Technical Terms
• Index
• Back Cover