Оглавление
Ernest Bailey. Horse Genetics
Genetic Relationships Among Breeds
Summary
References
Website
Evolution and Migration of Early Equids. Earliest ancestor of horses
Climate, environment and evolution
Domestication of horses
Relationship of modern domestic horses to the Przewalski horse and other wild horse populations
Archeological evidence for domestication of horses
Ancient DNA
Which horse species was first domesticated?
Other sites of domestication
Genomic Data on Horse Evolution and Domestication
Domestication and selection for coat color
Summary
References
Classification and Differences Among the Equidae. Species classification and population standings
Chromosomal differences among the Equidae species
Endangered species
Genomic differences among the species of Equidae
Horses
Asses
Asiatic Wild Asses
Zebras
Species Hybrids
Rare fertility in mules and hinnies
Feral Species
Summary
References
What Are Genes?
DNA
DNA structure
DNA replication
The central dogma of genetics (DNA ≥ RNA ≥ protein)
Genetic code
Identification of genetic variation at the DNA level for horses
Mutations and variants affecting proteins
Effect of amino acid substitutions
Mutation versus variant
Other roles of DNA: introns and exons, and regulatory DNA sequences
Examples of DNA changes affecting genes. Nucleotide substitution changing an amino acid
Deletion/loss of DNA resulting in loss of the codon reading frame
Changes in gene expression (alternate splicing)
Chromosome inversions
Changes affecting gene expression
Where Are Genes Found? Genes in the nucleus
Genes in mitochondria
Behavior of Chromosomes
Mitosis
Linkage
The inheritance of gender
References
Genes and alleles
Genotypes: Homozygous and Heterozygous
Dominant and recessive; phenotype and genotype
Breeding heterozygous and homozygous horses
Schematic representation of pedigrees
Practices for the Naming of Genes
Mendelian Ratios. Nomenclature for ambiguous genotypes
Altered ratios for lethal alleles
Partial dominance among alleles
Co-dominance among alleles
Expected ratios, statistical tests and alternative models
Two loci: the “dihybrid” cross
Epistasis and Hypostasis
Sex-linked genes
Epigenetics
Epigenetic programming of tissues during development
Environmentally induced epigenetic changes
Parent of origin effects
Polygenic (Multiple Gene) Traits
Determination of Inheritance Patterns
Summary
References
Genome Projects
Completion of the Human Genome Project and realization of the horse reference genome
Horse Genome Sequencing. The sequencing of Twilight’s genome
Composition of the genome
Coding DNA/RNA
Non-coding DNA/RNA
Genetic variants
Sex Chromosomes
Mitochondria DNA sequence
Whole genome sequencing and why we have reference genomes
Genome Browsers
Genome-wide Association Studies (GWAS)
Functional Genomics. DNA transcription
RNA-Seq
Chromatin and epigenetic markers
Genome Annotation
Summary
References
Websites
General Comments about Coat Color Genetics
Important note regarding molecular designations
Extension and Agouti Loci: The Basic Coat Colors
Extension Locus
Trait inheritance and gene symbol
Molecular genetics and gene location
Gene function
Breeds
Agouti Locus
Trait inheritance and gene symbol
Molecular genetics and gene location
Gene function
Breeds
References
Cream Dilution Locus
Trait inheritance and gene symbol
Genetics of CR and cr in bay, chestnut, and black horses
Molecular genetics and gene location
Gene function
Breeds
Health concerns
Dun Locus
Trait inheritance and gene symbol
Molecular genetics and gene location
Gene action
Breeds
Silver Dilution Locus
Trait inheritance and gene symbol
Molecular genetics and gene location
Gene function
Breeds
Health concerns
Champagne Dilution Locus
Molecular genetics and gene location
Gene function
Breeds
References
Tobiano Locus
Combination with colors and other patterns
Trait inheritance and gene symbol
Molecular genetics and gene location
Breeds
Dominant White Locus
Trait inheritance and gene symbol
Homozygous lethal white
Molecular genetics and gene location
Breeds
Health concerns
Sabino (SB1) Locus
Trait inheritance and gene symbol
Molecular genetics and gene location
Breeds
Roan Locus
Trait inheritance and gene symbol
Homozygous lethal roan
Roan phenocopy: rabicano
Molecular genetics and gene location
Breeds
Summary
References
Website
Frame Overo Locus
Trait inheritance and gene symbol
Molecular genetics and gene location
Gene function
Breeds
Health concerns
Splashed White Loci
Trait inheritance and gene symbol
Additional Variants of MITF
Molecular genetics and gene location
Gene function
Breeds
Health concerns
References
Leopard Complex/Appaloosa Locus
Trait Inheritance and gene symbol
Molecular genetics and gene location for LP
Modifying Genes for LP
Gene function
Breeds
Health concerns
References
Gray Locus
The gray trait
Trait inheritance and gene symbol
Molecular genetics and gene location
Gene function
Breeds
Health concerns
Genetics of Brindle
Genetics of Tiger Eye
Genetics of Curly
Population Distributions
References
References
Parentage
Two rules of parentage testing
Parentage testing detects errors in pedigrees but does not prove parentage
Blood typing tests
DNA Tests
Technical note
Microsatellite DNA markers
Testing microsatellites
Polymerase chain reaction
Measuring the length of a microsatellite
International Collaboration and Oversight of Horse Parentage Testing
Example of a Parentage Case Using Microsatellite DNA Markers
Special cases
Future developments for parentage testing
References
Websites
References
Examples of Diseases With Different Modes of Inheritance or Different Natural History. Partially dominant disease variant with some desirable effects
Recessive disease gene inadvertently spread by popular breeding stock
Dominant disease genes only apparent under some management conditions
Phenocopies: same disease phenotype can be caused by variants in different genes
Other Mendelian diseases
How are Mendelian disease genes discovered?
Candidate gene approach
Mapping and family studies
Genome-wide association studies
Complex genetic diseases
Disease correlations
Complex hereditary diseases: to what extent does genetics influence phenotype?
Examples of QTL studies
Database of Horse Diseases: OMIA
References
Website
Sex Chromosomes and Autosomes
The standard horse karyotype
Cytogenetics and Genomics
Fluorescence in situ hybridization (FISH)
Chromosome painting
Identification of chromosomes in a karyotype
Variation in Chromosome Arrangements. Mosaicism
Chromosome polymorphisms not associated with disease
Diseases associated with gain or loss of autosomes
Fertility problems associated with autosome rearrangements
Gain or loss of sex chromosomes. Loss of the X chromosome
Gain of X chromosomes
Gain of Y chromosomes
Disorders of Sexual Development (DSD)
XY sex reversal
XX sex reversal
Prevalence of Chromosome Abnormalities Among Horses
Future of Clinical Cytogenetics
References
Marker Assisted Selection
Major Gene for Racing Distance: MSTN
Major Gene for Gait: DMRT3
Genes for Size or Stature
Summary for Major Genes
References
Measuring Variation
Nature of Heritability
Determining Heritability
The Effect of Selection on Heritability Scores
General Observations About Heritability
Heritability estimates for racing
Heritability of other horse traits
Estimated Breeding Values (EBV) for Performance Traits
Best linear unbiased prediction (BLUP)
Summary
References
Establishing Pedigrees
The pedigree format: standard diagram
Estimates of relatedness and “percentage of blood”
Evaluation of pedigree influences
Inbreeding, Linebreeding, Outcrossing, and Assortative Mating. Inbreeding and linebreeding
Toward homozygosity
Closed stud books
Inbreeding in short versus long pedigrees
Outcrossing
Assortative mating
Tail-male and tail-female lineages. Tail-male lineage
Tail-female lineage, strain breeding and families
Questioning Breeding Myths in the Light of Genetics
Nicks
Using genetics to guide a breeding program
References
Microbiome
Mitochondria
What are mitochondria?
Are mitochondria descended from bacteria?
Mitochondrial DNA does not contain all the mitochondrial genes
Reproduction of mitochondria
Maternal inheritance of mitochondria
Mitochondria and studies of breeds and evolution
Mitochondria and performance
References
Genetics of Resistance and Susceptibility to Infectious Diseases
Inbreeding and Diversity in Horse Breeds
Genetics of Complex Traits
Summary
