Horse genetics

Cover......Page 1
Horse Genetics......Page 4
Copyright......Page 5
Contents......Page 6
Preface to the First Edition......Page 8
Preface to the Second Edition......Page 10
Preface to the Third Edition......Page 12
1 Nature of Horse Breeds......Page 14
 Genetic Relationships Among Breeds......Page 17
 Website......Page 19
  Climate, environment and evolution......Page 20
  Domestication of horses......Page 23
   Archeological evidence for domestication of horses......Page 24
   Which horse species was first domesticated?......Page 25
 Genomic Data on Horse Evolution and Domestication......Page 26
 References......Page 27
  Species classification and population standings......Page 29
  Chromosomal differences among the Equidae species......Page 30
  Endangered species......Page 32
  Horses......Page 33
  Asiatic Wild Asses......Page 34
  Zebras......Page 36
  Rare fertility in mules and hinnies......Page 38
 References......Page 39
 What Are Genes?......Page 42
  DNA replication......Page 43
  Genetic code......Page 44
 Identification of genetic variation at the DNA level for horses......Page 45
   Effect of amino acid substitutions......Page 46
  Other roles of DNA: introns and exons, and regulatory DNA sequences......Page 48
   Nucleotide substitution changing an amino acid......Page 49
  Genes in the nucleus......Page 50
  Genes in mitochondria......Page 51
  Meiosis......Page 52
 The inheritance of gender......Page 53
 References......Page 54
  Genotypes: Homozygous and Heterozygous......Page 55
  Breeding heterozygous and homozygous horses......Page 56
 Schematic representation of pedigrees......Page 58
 Practices for the Naming of Genes......Page 59
  Nomenclature for ambiguous genotypes......Page 60
   Partial dominance among alleles......Page 61
    Expected ratios, statistical tests and alternative models......Page 62
   Epistasis and Hypostasis......Page 63
 Epigenetics......Page 64
  Environmentally induced epigenetic changes......Page 65
  Parent of origin effects......Page 66
 Determination of Inheritance Patterns......Page 67
 Summary......Page 68
 References......Page 69
 Genome Projects......Page 70
  The sequencing of Twilight’s genome......Page 71
   Non-coding DNA/RNA......Page 72
 Sex Chromosomes......Page 73
  Whole genome sequencing and why we have reference genomes......Page 74
 Genome-wide Association Studies (GWAS)......Page 75
  DNA transcription......Page 76
  Chromatin and epigenetic markers......Page 77
 Summary......Page 78
 References......Page 79
 Websites......Page 81
 General Comments about Coat Color Genetics......Page 82
 Extension Locus......Page 83
  Trait inheritance and gene symbol......Page 84
  Gene function......Page 85
  Trait inheritance and gene symbol......Page 86
  Gene function......Page 88
 References......Page 89
 Cream Dilution Locus......Page 91
  Trait inheritance and gene symbol......Page 93
  Genetics of CR and cr in bay, chestnut, and black horses......Page 94
  Molecular genetics and gene location......Page 95
  Breeds......Page 96
  Trait inheritance and gene symbol......Page 97
  Gene action......Page 99
 Silver Dilution Locus......Page 100
  Trait inheritance and gene symbol......Page 101
  Gene function......Page 102
 Champagne Dilution Locus......Page 103
  Molecular genetics and gene location......Page 104
 References......Page 105
 Tobiano Locus......Page 107
  Combination with colors and other patterns......Page 108
  Trait inheritance and gene symbol......Page 109
 Dominant White Locus......Page 110
  Homozygous lethal white......Page 113
 Sabino ( SB1) Locus......Page 114
  Trait inheritance and gene symbol......Page 115
 Roan Locus......Page 116
  Trait inheritance and gene symbol......Page 117
  Roan phenocopy: rabicano......Page 118
 Summary......Page 119
 References......Page 120
 Website......Page 121
 Frame Overo Locus......Page 122
  Molecular genetics and gene location......Page 124
  Health concerns......Page 125
 Splashed White Loci......Page 126
  Trait inheritance and gene symbol......Page 127
  Molecular genetics and gene location......Page 129
  Breeds......Page 130
 References......Page 131
  Trait Inheritance and gene symbol......Page 133
  Molecular genetics and gene location for LP......Page 135
   Modifying Genes for LP......Page 136
  Health concerns......Page 137
 References......Page 138
  The gray trait......Page 139
  Trait inheritance and gene symbol......Page 140
  Molecular genetics and gene location......Page 142
  Health concerns......Page 143
 Genetics of Brindle......Page 144
 Genetics of Curly......Page 145
 References......Page 146
13 Putting it All Together: Color by Design......Page 148
 References......Page 152
  Two rules of parentage testing......Page 153
 DNA Tests......Page 154
  Microsatellite DNA markers......Page 155
 International Collaboration and Oversight of Horse Parentage Testing......Page 156
 Example of a Parentage Case Using Microsatellite DNA Markers......Page 157
  Special cases......Page 158
 References......Page 160
 Websites......Page 161
15 Blood Groups and Neonatal Isoerythrolysis......Page 162
 References......Page 164
16 Medical Genetics......Page 166
  Partially dominant disease variant with some desirable effects......Page 168
   Dominant disease genes only apparent under some management conditions......Page 169
   Phenocopies: same disease phenotype can be caused by variants in different genes......Page 170
   Other Mendelian diseases......Page 172
    Genome-wide association studies......Page 173
  Complex hereditary diseases: to what extent does genetics influence phenotype?......Page 174
  Examples of QTL studies......Page 175
 Database of Horse Diseases: OMIA......Page 176
 References......Page 177
 Website......Page 180
  The standard horse karyotype......Page 181
 Cytogenetics and Genomics......Page 182
  Identification of chromosomes in a karyotype......Page 183
  Chromosome polymorphisms not associated with disease......Page 185
 Fertility problems associated with autosome rearrangements......Page 186
   Loss of the X chromosome......Page 187
 Disorders of Sexual Development (DSD)......Page 188
 Prevalence of Chromosome Abnormalities Among Horses......Page 189
 References......Page 190
 Marker Assisted Selection......Page 194
 Major Gene for Racing Distance: MSTN......Page 195
 Major Gene for Gait: DMRT3......Page 197
 Summary for Major Genes......Page 198
 References......Page 199
 Measuring Variation......Page 201
 Nature of Heritability......Page 202
 The Effect of Selection on Heritability Scores......Page 203
  Heritability estimates for racing......Page 204
  Heritability of other horse traits......Page 205
 Estimated Breeding Values (EBV) for Performance Traits......Page 206
  Best linear unbiased prediction (BLUP)......Page 207
 References......Page 208
 Establishing Pedigrees......Page 210
  Estimates of relatedness and “percentage of blood”......Page 211
  Evaluation of pedigree influences......Page 212
   Toward homozygosity......Page 214
   Closed stud books......Page 215
  Outcrossing......Page 216
  Tail-female lineage, strain breeding and families......Page 217
 Questioning Breeding Myths in the Light of Genetics......Page 218
 References......Page 219
 Microbiome......Page 221
   Are mitochondria descended from bacteria?......Page 224
   Maternal inheritance of mitochondria......Page 225
   Mitochondria and performance......Page 226
 References......Page 227
 Genetics of Resistance and Susceptibility to Infectious Diseases......Page 229
  Inbreeding and Diversity in Horse Breeds......Page 230
  Summary......Page 231
Index......Page 232
Back Cover......Page 242