Chapter
Large Taurines during Classical Antiquity
Small Cattle in Medieval Europe
Modernization of Cattle Husbandry
Industrial Cattle, Crossbreds and Local Breeds
Bos taurus and Bos indicus
Categorization According to Utility and Mode of Origin
Classification and Phylogeny of Breeds
Description of Cattle Breeds
4. Molecular Genetics of Coat Colour Variation
The Basis of Pigmentation
Genes Causing Spatial and Temporal Pigment-type Switching
The Extension locus (MC1R)
Extension –Agouti interactions
Genes Diluting Pigmentation
The Dilution locus (PMEL17)
Genes Affecting Migration and Survival of Pigment Cells
The Belted locus (BTA3, possibly HES6)
The Colour-sided locus (KIT; BTA6→BTA29→BTA6 translocations)
The White-spotting locus (KIT )
Other Genes Influencing Coat Colour
Pleiotropic Effects Caused by Coat Colour Mutations
5. Genetics of Morphological Traits and Inherited Disorders
Current Sources of Information
6. Cytogenetics and Chromosome Maps
The Cattle Chromosome Nomenclature
Numerical chromosome aberrations
Structural chromosome aberrations
Overview of chromosome mapping
Future of Cattle Genome Mapping
University of Maryland (UMD) assembly
Differences in the Current Baylor and UMD Assemblies
Gene Expression Sub-networks
The Major Histocompatibility Complex
Molecular structure and function of MHC molecules
Genomic organization of the bovine MHC
Bovine class I gene products and polymorphisms
Classical bovine class I molecules
Non-classical bovine class I molecules
Bovine MHC class I-like molecules
Bovine class II gene products and polymorphisms
The bovine class IIa region
T cells are defined as αβ vs γδ based ontheir TCR gene usage
TCR gamma chain immunogenetics
TCR delta chain immunogenetics
TCR alpha chain immunogenetics
TCR beta chain immunogenetics
Multigene Families of Germline Encoded Receptors
Pattern recognition receptors
Immunoglobulin heavy chain immunogenetics
Variable-region heavy chain genes
Immunoglobulin light chain immunogenetics
Development of B cells and antibody repertoires
Mechanisms of antibodydiversification
9. Genetics of Disease Resistance
Genetics of Disease Resistance in Cattle: Relevant Notes
Genetic Aspects of Resistance Traits for the Most Significant Cattle Diseases
Keratoconjunctivitis (IBK)
Paratuberculosis (Johne’s disease)
10. Molecular Biology and Genetics of Bovine Spongiform Encephalopathy
Clinical Signs and Pathology
The Importance of PrP Protein
Pathogenesis of BSE in Cattle
Experimental BSE in cattle
Experimental atypical BSE in cattle
Preclinical Diagnosis of BSE in Cattle
BSE Transmission Characteristics
Genetics of TSEs in Sheep and Humans
Cattle PRNP Gene Polymorphisms and Susceptibility to BSE
IS BSE not subject to host genetic control by the PRNP gene?
11. Genetics of Behaviour in Cattle
Breeding for docility in Limousins
Associations with production traits
Group structure and dominance
12. Genetics of Reproduction in Cattle
Genetics of Ovulation Rate and Related Traits
Genetics of Puberty and Related Traits
Genetics of Conception or Pregnancy Rate
Genetics of Gestation Length
Genetics of Dystocia and Related Traits
Genetics of Male Reproductive Traits
13. Modern Reproductive Technologies and Breed improvement
The Paternal Contribution
Breeding soundness evaluation (BSE) and estimation of sire fertility
Adding ‘new’ parameters to sperm quality evaluation
Marker-based sorting of fertile sperm
Improving male fertility through integration of the ‘omics’
Artificial insemination (AI)
The Maternal Contribution
Oestrus/ovulation synchronization
Fixed-timed artificial insemination (FTAI)
Fixed-time embryo transfer (FTET)
Occurrence of embryonic death and strategies to improve embryo survival
Multiple ovulation and embryo transfer (MOET)
In vitro production of embryos
Oocyte/embryo cryopreservation
Integrating genomic selection and reproductive technologies
Studying the (epi)-genome
14. Developmental Genetics
Developmental Stages of the Cattle Embryo
Fertilization and embryonic development within the zona pellucida
Post-hatching development
Genetic Control of Pre-implantation Development
Expression of maternal genes
Activation of the embryonic genome
Reprogramming, methylation patterns and genomic imprinting
Gene expression during blastocyst formation, expansion and elongation
Genetic control of gastrulation
Establishment of axial identity
The three germ layers and theirderivates
Genetic Regulation of Implantation and Placentation
Endometrial and trophoblast gene expression
Maternal recognition of pregnancy
Implantation and placental development
Molecular signals affecting implantation and placentation
Genes Involved in Post-implantation Development
Development of segment identity and HOX genes
Muscle development and gene regulation
Organogenesis: T-box and PAX genes
The major steps in gonad differentiation
The genes involved in sex differentiation
Cycle of the X chromosome
Anomalies of sex development
Specific features of the bovine placenta and chimerism
Diagnosis of freemartins and practical aspect
15. Genetic Improvement of Dairy Cattle
Derivation of a breeding objective
Recent evolutions in breeding objectives
Correlation between trait groups
Inbreeding, genetic variability and heterosis
QTLs and individual genes affecting traits of economic importance
Genotype by environment interaction
National vs international evaluations
Consequences on the international scene
Perspectives and challenges
Design of Breeding Programmes
Breeding programmes with genomic selection
16. Molecular Genetics of Milk Protein Production
The caseins and their genes
The major whey proteins and their genes
Multi-level Regulation of Milk Protein Genes Expression in the Mammary Gland: Endocrine, Autocrine and Paracrine Regulation
Local control of milk composition and milk production
Regulation by the extracellular matrix
Transcriptional Regulation of Milk Protein Production
Prolactin-mediated activation of transcription
The glucocorticoid receptor
The progesterone receptor – a negative regulator of milk protein gene expression
The extracellular matrix and transcriptional regulation
Transgenic Studies Utilizing Bovine Milk Protein Gene Promoters
The alteration of milk composition via transgenesis
17. Genetics of Fatty Acid Composition in Bovine Milk and Beef
Fatty Acid Composition of Bovine Milk and Beef
Environmental Factors Influencing Fatty Acid Composition
Fatty Acid Heritabilities and Genetic Correlations
Breed Effects on Fatty Acid Composition in Bovine Milk and Beef
Genetic Polymorphisms and Fatty Acid Composition
Diacylglycerol O-acyltransferase 1
Sterol regulatory element binding factor 1
Fatty acid transport genes
18. Genetic Improvement of Beef Cattle
The economically rational approach
The desired gains approach
Breeding objectives for beef production systems
Beef breeding objectives in dairy and dual-purpose breeds
Terminal sires for use in dairy herds and specialized beef herds
Breeding replacement females for specialized beef herds
Breed Resources and Crossbreeding
Evaluating breed resources
An overview of crossbreeding theory
The value of crossbreeding
The genetic basis of heterosis
Choice of crossing system
Breeds and crosses used in beef production
The use of genomics to target increases in heterosis
Use of genomic information
Cooperative breeding schemes
Evaluations across herds, breeds and countries
Indices of overall economic merit
Evidence of genetic improvement and its value
Estimates of genetic change achievable
The economic value of genetic improvement
19. Genomic Prediction and Genome-wide Association Studies in Beef and Dairy Cattle
Conventional Pedigree-based Prediction
Generalized least squares and best linear unbiased prediction
Identity by descent and the numerator relationship matrix
Prediction of breeding values and associated reliabilities
Limitations of conventional prediction
Prediction using Genomic Information
Practical models based on mixed model equations (SNP effects or genomic relationships)
Bayesian regression methods
Validation of Predictive Ability
Prediction using admixed breeds
Understanding Predictive Ability
Haplotypes and their distribution
Models including the QTL as one of the markers
Equivalent models with fewer markers
Multi marker-QTL LD versus single marker-QTL LD
Models with inadequate markers
Models with haplotype covariates
Blending Genomic and Pedigree Information
Single-step Bayesian regression
Genome-wide Association Studies
Incorporation of Sequence Information
Immediate and Future Challenges
20. Genetics of Feed Intake and Efficiency
Advantages and disadvantages of the different measures of feed efficiency
Genetics of Feed Intake and Efficiency
Heritability estimates and genetic correlations between measures
Genetic correlations between feed intake and efficiency with other performance measures
Male and female reproduction
Breeding Programmes for Feed Intake and Efficiency
Breeding programmes including feed intake and efficiency
Genotype by environment interactions for feed intake and efficiency
Genomics of Feed Intake and Efficiency
Future Research Priorities
21. Genetics of Growth and Body Composition
Growth Traits and Growth Curves
22. Genetics of Meat Quality
Fat composition and qualities
Meat physico-chemical qualities
Heritability of Meat Quality Traits
Fat composition and qualities
Meat physico-chemical qualities
Genetic Correlations with Meat Traits
Meat sensory and physico-chemical qualities
Fat composition and qualities
Major Genes and Gene Markers Associated with Meat Quality Traits
23. Genetic Aspects of Cattle Adaptation in the Tropics
Measuring Adaptation of Cattle to Tropical Environments
Breed Differences in Adaptive Traits
Breed groupings and comparative performance of the breeds
Impact of heterosis on adaptive traits
Exploiting breed differences and heterosis for adaptive traits to improve performance of cattle in the tropics
Within-breed Selection to Improve Adaptive Traits
Role of Molecular Information in Improving Adaptive Traits
Resistance to trypanosomiasis
Resistance to Bovine Respiratory Disease
Resistance to heat stress
Resistance to gastrointestinal nematodes (worms)
Heritabilities of adaptive traits
Genetic correlations between adaptive and productive traits
Adaptive Traits in Breeding Programmes
24. Standard Genetic Nomenclature
Locus and Gene Names and Symbols
Gene annotations and the gene ontology (GO)
Trait and Phenotype Terminology
Trait hierarchy and ontology
Trait and phenotype nomenclature
The Genetics of Cattle
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