The Genetics and Genomics of the Rabbit

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The Genetics and Genomics of the Rabbit
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Contents
To Giovanna, Davide and Sara
Contributors
Preface
1 The Evolution, Domestication and World Distribution of the European Rabbit (Oryctolagus cuniculus)
	1.1 The Order Lagomorpha
	1.2 The European Rabbit (Oryctolagus cuniculus)
		1.2.1 The evolutionary history of the European rabbit: fossil records
		1.2.2 The evolutionary history of the European rabbit: molecular data
		1.2.3 The domestication process of the European rabbit
			1.2.3.1 Molecular evidences
			1.2.3.2 The first waves of rabbit distribution in Europe: archaeological and historical sources
		1.2.4 World distribution of the European rabbit and genetic perspectives
	References
2 Rabbit Breeds and Lines and Genetic Resources
	2.1 What Does the Term ‘Race’ or Breed, as Applied to Rabbits, Mean Today?
	2.2 The Origin of Breeds
	2.3 Creation of Breeds
	2.4 Recognition of an Isolated Population as a Breed or a Line
	2.5 Rabbit Breeds on an International Level
	2.6 A Breed Has One or More Purposes
	2.7 Evolution of Breeds and Lines
	2.8 Synthetic Lines in Developing Countries
		2.8.1 Western Asia
		2.8.2 North Africa
		2.8.3 Sub-Saharan Africa
		2.8.4 Latin America
	References
3 The Genome of the European Rabbit and Genomic Tools
	3.1 Introduction
	3.2 The Genome of Oryctolagus cuniculus
	3.3 Genomic Tools and Applications
	References
4 Cytogenetics, Physical and Genetic Maps and QTL Mapping in the European Rabbit
	4.1 The Karyotype of Oryctolagus cuniculus
	4.2 Gene Mapping in the Domestic Rabbit: Physical Gene Maps
		4.2.1 Mapping using somatic cell hybrids
		4.2.2 Mapping by in situ hybridization
	4.3 Synteny Mapping
	4.4 Genetic Linkage Maps
		4.4.1 History of the rabbit linkage map
		4.4.2 Comparison of linkage maps in European rabbit populations
		4.4.3 Physical versus genetic maps
	4.5 QTL Studies in Rabbits
		4.5.1 QTL studies for carcass
		4.5.2 QTL studies for atherosclerosis and hypercholesterolemia
	4.6 Concluding Remarks
	References
5 Immunogenetics in the Rabbit
	5.1 Introduction
	5.2 Immunoglobulins (Igs)
		5.2.1 Genes encoding Igs
			5.2.1.1 Definitions
		5.2.2 Heavy-chain genes
		5.2.3 Light chain genes – Kappa and Lambda variable and constant regions
	5.3 Ig Protein Structure
		5.3.1 Genetic variants detectable with alloantisera (allotypes)
		5.3.2 Haplotypes and recombinants
	5.4 B Cell Development and Diversification of Sequence sEncodingIgs
		5.4.1 Early development of the B-cell repertoire
		5.4.2 Diversification by gene conversion and somatic hypermutation of rearranged rabbit heavy- and light-chain gene sequences
			5.4.2.1 Gene conversion
			5.4.2.2 Clonally related sequence diversification patterns in developing appendix differ from patterns during specific immune responses in secondary lymphoid organs
	5.5 T-Cell Receptors
		5.5.1 TCR Gamma (TRG)
		5.5.2 TCR beta (TRB)
		5.5.3 TCR alpha and delta
	5.6 The Rabbit Leukocyte Antigen (RLA) Complex
		5.6.1 Mapping and organization
		5.6.2 The MHC class I genes
		5.6.3 The MHC class II genes
		5.6.4 Genetic variability of the RLA complex
		5.6.5 Insights provided by the current assembly of the rabbit genome
	5.7 Cytokine Genes
	Acknowledgements
	References
6 Genetics and Molecular Genetics of Coat Colour in the European Rabbit
	6.1 Introduction
	6.2 The Albino Locus: Characterization of the Tyrosinase Gene
	6.3 The Extension Locus: Several Deletions in the Melanocortin 1 Receptor Gene
	6.4 The Agouti Locus: Mutations Affecting the Agouti Signalling Protein Gene
	6.5 The Dilute Locus: Polymorphisms in the Melanophilin Gene
	6.6 The Brown Locus: A Mutation in the Tyrosinase-related Protein 1 Gene
	6.7 The English Spotting Locus: Association with a KIT Gene Marker
	6.8 The Dutch Series
	6.9 The Viennese White Locus
	6.10 Silvering
	6.11 The Red Eye Locus
	6.12 The Wide Band Locus
	6.13 Conclusion
	References
7 Genetics of Fibre and Fur Production in Rabbits
	7.1 Introduction
	7.2 Biology of the Coat of the Rabbit
		7.2.1 Structure and composition of the coat
		7.2.2 Hair structure
		7.2.3 Hair growth and moulting periods
	7.3 Single Genes Affecting Hair and Coat Structure
		7.3.1 Angora
		7.3.2 Rex
		7.3.3 Satin
		7.3.4 Waved
		7.3.5 ‘Wuzzy’ (hair sticky and matted)
		7.3.6 Naked or furless
	7.4 Genetic Improvement of Fibre and Fur Production
		7.4.1 Genetic improvement of Angora rabbit for fibre production
			7.4.1.1 Relevant traits
			7.4.1.2 Non-genetic factors affecting fibre production in Angora rabbits
			7.4.1.3 Genetic parameters
			7.4.1.4 Response to selection
		7.4.2 Genetic improvement of rabbit for fur production
			7.4.2.1 Relevant traits in Rex rabbits
			7.4.2.2 Genetic parameters and response to selection for fur production in Rex rabbits
	7.5 Concluding Remarks
	References
8 Genetics and Molecular Genetics of Morphological and Physiological Traits and Inherited Disorders in the European Rabbit
	8.1 Introduction
	8.2 Sources of Information
	8.3 Sources of Genetic Variability
	8.4 Quantitative Inheritance
	8.5 Single-locus or Oligogenic Determined Traits and Defects
	8.6 Conclusion
	References
9 Genetics of Disease Resistance in the European Rabbit
	9.1 Introduction
	9.2 Pasteurellosis
		9.2.1 Disease description
		9.2.2 Selection for resistance to bacterial infection
		9.2.3 Genetic resistance to experimental Pasteurella multicoda infection
	9.3 Epizootic Rabbit Enterocolitis and Digestive Disorders
		9.3.1 Disease description
		9.3.2 Genetic variability of the resistance to digestive disorders of various origins
		9.3.3 Selection for the resistance to digestive disorders
		9.3.4 Resistance to an experimental Escherichia coli infection
		9.3.5 Candidate genes studied to identify markers associated with resistance to digestive disorders
	9.4 Multiple Disease Syndromes
		9.4.1 Unspecific disease resistance under two feeding systems
		9.4.2 Resistance to infectious syndromes
		9.4.3 Resistance to non-specific disease in a selection and challenged environment
	9.5 Myxomatosis
	9.6 Rabbit Haemorrhagic Disease (RHD)
	9.7 Concluding Remarks
	References
10 Genetics and Genomics of Growth, Carcass and Meat Production Traits in Rabbits
	10.1 Introduction
	10.2 Economic Importance of Growth and Carcass Traits in Genetic Programmes
	10.3 Genetics of Growth Traits
		10.3.1 Between-breed genetic variability
		10.3.2 Genetic parameters of growth traits
	10.4 Genetics of Carcass Traits
		10.4.1 Between-breed genetic variability
		10.4.2 Genetic parameters of carcass traits
	10.5 Genetics of Rabbit Meat Quality
		10.5.1 Genetic variability between rabbit lines
		10.5.2 Genetic parameters of meat-quality traits in rabbits
	10.6 Selection Experiments
		10.6.1 Selection for growth
		10.6.2 Selection for feed efficiency
		10.6.3 Consequences of selection for growth rate or feed efficiency
			10.6.3.1 Changes in adult weight
			10.6.3.2 Changes in feed conversion rate
			10.6.3.3 Changes in carcass quality
			10.6.3.4 Changes in meat quality
		10.6.4 Selection for increasing muscle volume
		10.6.5 Selection for intramuscular fat content
	10.7 Genomics in Rabbit Growth, Carcass and Meat Quality
		10.7.1 Genome-wide association studies for growth, carcass and meat quality in rabbits
		10.7.2 Rabbit metagenomics for growth, carcass and meat-quality traits
		10.7.3 Genomic selection for meat-quality traits
	References
11 Biology of Reproduction and Reproduction Technologies in the Rabbit
	11.1 Introduction
	11.2 Gonadogenesis
	11.3 Reproduction in the Male
		11.3.1 Sperm cell
		11.3.2 Sperm membrane
		11.3.3 Sperm capacitation and acrosome reaction
		11.3.4 Seminal granules (SGs), ejaculate and daily sperm production
		11.3.5 Buck and semen
			11.3.5.1 Factors influencing semen production
	11.4 Reproduction in the Female
		11.4.1 Estrous synchronization and ovulation
		11.4.2 Luteal function and pseudopregnancy
		11.4.3 Breeding strategies
			11.4.3.1 Induction of ovulation
			11.4.3.2 Sexual receptivity
	11.5 Modern ReproductiveTechnologies
		11.5.1 Cryopreservation of embryos
		11.5.2 Cryopreservation of rabbit spermatozoa
			11.5.2.1 Semen freezing in the straws (French method)
			15.5.2.2 Semen freezing in the PELLETS (Japanese method)
		11.5.3 Embryo development and losses
		11.5.4 Superovulation and collection of rabbit embryos and embryo transfer
	11.6 Feto-placental Development, Growth and Parturition
	11.7 The Rabbit Model in the ­Toxicology of Pregnancy and in the Developmental Origins of Health and Diseases
	References
12 Genetics of Reproduction in the Rabbit
	12.1 Genetics of Reproduction Traits
	12.2 Fertility
		12.2.1 Between-breed/line variation
		12.2.2 Within-line variation
		12.2.3 Relationship with other traits
	12.3 Semen Production and Quality
		12.3.1 Between-breed/line variation
		12.3.2 Within-line variation
		12.3.3 Relationship with other traits
	12.4 Prolificacy
		12.4.1 Between-breed/line variation
		12.4.2 Within-line variation
		12.4.3 Relationship with other traits
	12.5 Components of Prolificacy
		12.5.1 Within-line variation
			12.5.1.1 Relationship between litter size, ovulation rate and prenatal survival
	12.6 Selection Experiments
		12.6.1 Selection for uterine capacity
		12.6.2 Selection for ovulation rate
		12.6.3 Selection for ovulation rate and litter size
	12.7 Homogeneity and Residual Variance
		12.7.1 Residual variance of litter size
		12.7.2 Residual variance of birth weight
	12.8 Length of Productive Life
		12.8.1 Between-breed/line variation
		12.8.2 Within-line variation
		12.8.3 Selection experiments
		12.8.4 Relationships with other traits
	References
13 Genetic Improvement in the Meat Rabbit
	13.1 Introduction
	13.2 Rabbit Production Schemes
		13.2.1 Crossbreeding schemes
		13.2.2 Schemes based on multi-purpose lines
	13.3 Development of Lines
		13.3.1 Criteria for the development of new lines
		13.3.2 Criteria and methods of selection – paternal lines
			13.3.2.1 The current approaches
			13.3.2.2 Alternative approaches
		13.3.3 Criteria and methods of selection – maternal lines
			13.3.3.1 The current approaches
			13.3.3.2 Alternative approaches
		13.3.4 Responses to selection
			13.3.4.1 Within-line responses
			13.3.4.2 Crossbred responses
	13.4 Dissemination of the Genetic Improvement
	13.5 Perspectives of the Genomic Selection
	References
14 Rabbit Research in the Post-genomic Era: Transcriptome, Proteome and Metabolome Analyses
	14.1 Introduction
	14.2 Transcriptomics
		14.2.1 Microarrays: general principles, applications and case studies in the rabbit
			14.2.1.1 Performing a microarray experiment
			14.2.1.2 Arrays for rabbit analysis
			14.2.1.3 Target preparation
			14.2.1.4 Hybridization to the array
			14.2.1.5 Data analysis for a microarray experiment
		14.2.2 RNA sequencing application in rabbits
	14.3 Proteomics
		14.3.1 Principles and methodologies in proteomics: a brief introduction
		14.3.2 Proteomics in rabbit skeletal muscle research
	14.4 Metabolomics
	14.5 Conclusion
	Acknowledgements
	References
15 Methods to Create Transgenic and Genome-edited Rabbits
	15.1 Introduction
	15.2 Pronucleus Microinjection
	15.3 Artificial Chromosome-type Transgenesis
	15.4 Lentiviral Transgenesis
	15.5 Transposon-mediated Transgenesis
	15.6 The Role of Somatic Nuclear Transfer in Rabbit Transgenesis
	15.7 Adenoviral Transduction into Rabbit Somatic Cells for Local In Vivo Gene Transfer
	15.8 Genome Editor/Designer Nucleases
	15.9 The Influence of Transgene Expression on Productivity Traits
		15.9.1 Effect of transgene expression on milk quality and lactation
		15.9.2 Meat quality of transgenic rabbits
	15.10 Conclusion
	Acknowledgements
	References
16 Pluripotent Stem Cells in Rabbits
	16.1 Introduction
	16.2 Genome Modifications in Rabbits
		16.2.1 Modelling human diseases in rabbits
		16.2.2 Modelling human early  developmentin rabbits
		16.2.3 Rabbits as bioreactors
		16.2.4 Transgenesis in rabbits
		16.2.5 Rabbit iPSCs and the preservation of genetic resources
	16.3 Rabbit Embryonic Stem Cells (Rabbit ESCs)
		16.3.1 Derivation of rabbit ESCs
		16.3.2 Characterization of rabbit ESCs
		16.3.3 Signalling pathways in rabbit ESCs
	16.4 Rabbit Induced Pluripotent Stem Cells (Rabbit iPSCs)
		16.4.1 Reprogramming of somatic cells into rabbit iPSCs
		16.4.2 Characterization of rabbit iPSCs
	16.5 Transcription Factors and miRNAsInvolved in Rabbit Pluripotency
		16.5.1 Naïve versus primed states of pluripotency
		16.5.2 Transcriptome of rabbit ESCs and rabbit iPSCs
		16.5.3 miRNAsome of rabbit ESCs and iPSCs
	16.6 In Vitro Differentiation of Rabbit ESCs and iPSCs
	16.7 Current Bottlenecks
	16.8 Conclusion
	References
17 Biotechnology Applications in the Rabbit
	17.1 Introduction
	17.2 Transgenic Rabbits for Biotechnology  Applications
		17.2.1 Targeted production of pharmaceutical proteins
		17.2.2 The purification steps of recombinant proteins from milk and other tissues
		17.2.3 Animal systems and tissues used to produce recombinant proteins
	17.3 Rabbit Antibodies
	17.4 Biotechnology Applications: Cryopreservation of Rabbit Lines
	17.5 Concluding Remarks
	References
18 The Rabbit as a Biomedical Model
	18.1 Introduction
	18.2 Rabbit Models for Atherosclerosis
	18.3 Rabbit Models for Heart Disease
	18.4 Rabbit Models for Alzheimer’s Disease
	18.5 Rabbit Models for Ophthalmological Research
	18.6 Rabbit Models for Osteoarthritis
	18.7 Rabbit Models for Infectious and Autoimmune Disease
	18.8 Rabbit Models for Studying Reproductive Physiology
	18.9 Respiratory System
		18.9.1 Asthma and COPD
		18.9.2 Cough
		18.9.3 Tuberculosis
	References
Index
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