| Contributors | p. XV |
| Cattle | p. 1 |
| Introduction | p. 1 |
| History | p. 1 |
| Economic Importance | p. 1 |
| Molecular Genetics | p. 3 |
| Genetic-Mapping Resources | p. 3 |
| Quantitative Trait Loci | p. 5 |
| Using Genotypes in Breeding Cattle | p. 8 |
| Future Scope of Work | p. 9 |
| References | p. 10 |
| Water Buffalo | p. 19 |
| Introduction | p. 19 |
| Taxonomic Description | p. 19 |
| Economic Importance | p. 21 |
| Breeding Objectives | p. 22 |
| Molecular Genetics | p. 23 |
| Classical Mapping Efforts | p. 23 |
| Construction of Genetic Maps and Comparative Mapping | p. 24 |
| Future Scope of Work | p. 28 |
| References | p. 28 |
| Sheep | p. 33 |
| Introduction | p. 33 |
| Economic and Biomedical Importance | p. 33 |
| History | p. 34 |
| The Sheep Karyotype | p. 34 |
| Molecular Genetics | p. 35 |
| Linkage Maps | p. 36 |
| Mapped Traits in Sheep | p. 36 |
| Resources for Mapping and Sequencing the Ovine Genome | p. 39 |
| Future Scope of Work | p. 41 |
| References | p. 41 |
| Deer | p. 47 |
| Introduction | p. 47 |
| Taxonomic Description | p. 47 |
| Economic Importance | p. 48 |
| Karotype of Cervids | p. 48 |
| Molecular Genetics | p. 48 |
| Genetic Analysis Using Molecular Markers | p. 48 |
| The Deer Genetic Map | p. 60 |
| Genes | p. 61 |
| Quantitative Trait Loci in Deer | p. 62 |
| Chronic Wasting Disease of North American Cervids | p. 65 |
| Future Scope of Work | p. 66 |
| References | p. 67 |
| Poultry | p. 75 |
| Introduction | p. 75 |
| Brief History and Zoological Description | p. 75 |
| Chickens | p. 77 |
| Economic Importance and Nutritional Value | p. 82 |
| Breeding Objectives | p. 85 |
| Classic Genetics | p. 86 |
| Brief History of Poultry Genetics | p. 86 |
| Early Classical Mapping Efforts | p. 86 |
| First Chicken Map | p. 99 |
| Subsequent Classical Mapping | p. 100 |
| Molecular Genetics and Whole-Genome Sequence | p. 101 |
| First-generation Molecular Maps | p. 101 |
| Physical Maps | p. 103 |
| Whole-Genome Sequence | p. 105 |
| Chicken Genome and Sequence Features | p. 107 |
| Genetics and Molecular Mapping in Other Birds | p. 110 |
| QTL and Functional Genomics | p. 120 |
| QTL Analysis | p. 120 |
| QTL: Growth, Meat Quality, and Productivity | p. 120 |
| QTL: Egg Quality and Productivity | p. 122 |
| QTL: Disease Resistance | p. 122 |
| QTL: Behavior | p. 123 |
| Toward Functional Genomics of Poultry | p. 123 |
| Other Molecular Applications | p. 124 |
| Biodiversity Studies | p. 124 |
| Molecular Sexing | p. 125 |
| Conclusions | p. 126 |
| References | p. 126 |
| Turkey | p. 143 |
| Introduction | p. 143 |
| Origin and Domestication | p. 143 |
| Taxonomy and Zoological Description | p. 144 |
| Modern Breeding Objectives | p. 144 |
| Economic Importance | p. 145 |
| Karyotype and Genome | p. 147 |
| Classical Mapping Efforts and Limitations | p. 147 |
| Construction of Genetic Maps | p. 148 |
| Genetic Markers | p. 148 |
| Primary Genetic Linkage Maps | p. 151 |
| Second-generation Linkage Map | p. 151 |
| Integrative Mapping | p. 153 |
| Comparative Mapping | p. 154 |
| Other Comparative Studies | p. 155 |
| Physical Mapping | p. 157 |
| The Next-Generation Physical Maps | p. 157 |
| Advanced Works, Functional Genomics | p. 158 |
| ESTs, Microarrays, and SAGE | p. 158 |
| Candidate Gene Mapping | p. 159 |
| Conclusion | p. 160 |
| References | p. 160 |
| Rabbit | p. 165 |
| Introduction | p. 165 |
| History | p. 165 |
| Taxonomic Position | p. 165 |
| Physical Characteristics | p. 166 |
| Breeds | p. 166 |
| Domestication, Phylogeny, and Genetic Diversity | p. 167 |
| Economic Importance | p. 171 |
| Molecular Genetics | p. 175 |
| Cytogenetics | p. 175 |
| Genetic Molecular Markers | p. 176 |
| Physical Mapping Tools | p. 204 |
| Sequencing Data | p. 204 |
| Bioinformatics Tools | p. 205 |
| Expected Tools and Development | p. 206 |
| Genome Mapping | p. 206 |
| Future Scope of Work | p. 220 |
| Using Rabbits to Study the Domestication Process | p. 220 |
| Using Rabbits to Study Color Patterns | p. 220 |
| Using Rabbits to Study Early Embryonic Development | p. 220 |
| Using Rabbits to Produce Embryonic Stem Cells and Validate Candidate Genes | p. 221 |
| Perspectives of the Rabbit as a Farm Animal | p. 221 |
| References | p. 223 |
| Dog | p. 231 |
| Introduction | p. 231 |
| Dog Breeds | p. 231 |
| Genetic Diversity and Dog Breeds | p. 233 |
| The Superfamily Canoidae | p. 234 |
| Mitochondrial DNA (MtDNA) Analysis of Canids | p. 234 |
| The Domestic Dog Population | p. 236 |
| Molecular Genetics of Dogs | p. 237 |
| Canine Linkage and Radiation Hybrid Maps | p. 237 |
| Comparative Maps | p. 238 |
| Survey Sequence and a Canine Gene Map | p. 239 |
| The 7.5x Canine Genome Sequence | p. 240 |
| Single Gene Traits | p. 241 |
| Complex Traits | p. 244 |
| Resources | p. 249 |
| Future Scope of Work | p. 250 |
| References | p. 251 |
| Pig | p. 257 |
| Introduction | p. 257 |
| History and Description | p. 257 |
| Economic Importance | p. 258 |
| Breeding Objectives | p. 258 |
| Molecular Genetics of Pigs | p. 259 |
| Genetic Maps | p. 259 |
| Physical and RH Maps | p. 260 |
| Pig-Human Comparative Maps | p. 260 |
| Quantitative Trait Loci | p. 261 |
| Candidate Gene Discovery | p. 262 |
| Marker-Assisted Breeding | p. 264 |
| Functional Genomics | p. 265 |
| Expressed Sequence Tags | p. 265 |
| DNA Microarrays | p. 265 |
| Future Scope of Work | p. 266 |
| Swine Genome Sequencing | p. 266 |
| Expression QTL | p. 266 |
| Conclusion | p. 268 |
| References | p. 268 |
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