Thunder Hill Equine Drum Horses

Horse Colours Explained:

The genetics of horse colour are both easy and difficult to understand at the same time. To begin there must be a rudimentary understanding of how genetics work, so that the colour concepts being discussed can be more easily understood. . Horse people know the basic names of horse colour and many breeders have a good idea what colour a foal would be when born but there are always surprises. Early geneticists and researchers had determined many colour principles but it has only been in the last 20 years that the research has expanded exponentially. The first equine genome was only sequenced in 2007. This endeavor and subsequent work has allowed geneticists to identify mutations for the basic coat colours, and locate modifying genes for the other coat colours and various white pattern.

Genes are considered the basic building blocks of an organism’s genome and are the fundamental physical and functional units of heredity. Horses have approximately 20,000 genes. Genes use only 4 nucleotide bases to create 20 different amino acids which in turn are used to create proteins. The bases are grouped into 3’s which are called codons that are used to create the amino acids, with 64 possible combinations. There are more possible combinations than actual amino acids which allows most amino acids to have more than one set of base codons to create it. This is a built in back up to allow amino acids to continue as required in spite of changes. Even the changing of one base could change an amino acid which changes the protein which change the function of the gene. These changes are referred to as mutations. Genes are located on chromosomes which are organized package of DNA found in the nucleus of a cell. Horses have 32 pairs of chromosomes in comparison to humans 23 pairs. A horse inherits half of a chromosome pair from each parent, and the corresponding half of a gene pair. Each half of a gene pair is called an allele. If the alleles that are inherited from each parent are the same they are referred to as homozygous. If the alleles from each parent are different they are heterozygous.

When we are discussing horse colour we are looking at specific genes and their alleles. All horse colour beyond the original wild colour is a result of mutations to the gene/allele. Alleles can be dominant, partially dominant, or recessive when being used in the context of colour. A dominant allele will be expressed in both homozygous and heterozygous states. A partially dominant allele will be expressed differently in its homozygous and heterozygous states. A recessive allele will only be expressed in its homozygous state.

Horse colours are divided into different categories: base colours, dilutions, hair structure anomalies, modifications and uncategorized colour anomalies. Base colours are the result of interaction of the 2 genes that control the production of colour pigment: Extension and Agouti. Base colours are Bay, Black, and Red (possibly Seal Brown as well). Dilutions are gene alleles that dilute or lighten the base colour of the horse. Dilution genes are Champagne, Cream, Pearl, and Silver. Mushroom, Lavender foal and Macchiato will also be discussed as part of the dilution group. Hair structure anomalies are colour modifications that are a result of differences to the actual hair itself and are not fully related to colour pigment. Hair structure anomalies are Dun and Akhal-Teke Satin. Modifications are any gene alleles that modify areas of a horse’s body coat, mane, tail and skin with various shapes of white depigmentation, also known as pattern genes. Modification genes are Grey, Roan, Leopard, Tobiano, Frame, Sabino 1, Splashed White 1-4+, and White Spotting 1-22+. Uncategorized colour anomalies are any colour change or pattern that varies from the base colours and does not fit into any of the other categories.

Glossery of Genetic Terms

Chromosome: An organized package of DNA found in the nucleus of the cell. Different organisms have different numbers of chromosomes. Humans have 23 pairs of chromosomes --22 pairs of numbered chromosomes, callled autosomes, and one pair of sex chromosomes, X and Y. Horses have 32 pairs of chromosomes-- 31 pairs of numbered chromosomes as well as the sex chromosome pair. Each parent contributes one chromosome to each pair so that offspring get half of their chromosomes from their mother and half from their father.
-- Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Gene: The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides (molecules) located in a particular position on a particular chromosome that encodes a specific functional product (i.e., a protein or RNA molecule). The closer two genes are to each other on the chromosome, the more likely it is that they will be inherited together. Horses have approximately 20,000 genes.
-- Definition adapted from: Human Genome Project Information, at the U.S. Department of Energy

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Allele: One of two or more versions of a gene. An individual inherits two alleles for each gene, one from each parent. Though the term "allele" was originally used to describe variation among genes, it now also refers to variation among non-coding DNA sequences.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Dominant gene: An allele which is expressed whenever it is present. When referring to horse colours the dominant form of an allele is capitalized, E or A for example.
--Definition adapted from: Horse Genome Project, from the University of Kentucky

Partial Dominant gene: An allele that expresses differently depending on if it is homozygous or heterozygous. The cream gene is a Partial Dominant.
--Definition adapted from: Horse Genome Project, from the University of Kentucky

Recessive gene: An allele which is only expressed in the absence of a dominant gene. Horses with one copy of a dominant allele and one copy of a recessive allele are said to be carriers of the recessive allele (gene). When referring to horse colours the recessive form of an allele is lowercase, for example e or a.
--Definition adapted from: Horse Genome Project, from the University of Kentucky

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Dilution gene: A mutation to a gene that lightens the base coat colour of the horse.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Modifier gene: A mutation to a gene that changes the colour of a horse, generally by depigmentation (white hairs) of the coat.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Exon: The portion of a gene that codes for amino acids that are ultimately expressed in the protein synthesis. (E)xon = (E)xpressed
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Intron: The part of a gene sequence that is not expressed in the protein. The non-coding part of the gene sequence that breaks up, comes between or interferes with the exons. (I)ntron = (I)n-between
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Non-coding DNA: The sequences of DNA that do not code for proteins. The majority of non-coding DNA is located between genes with a small amount appearing as introns. The function of non-coding DNA has not been determined but is felt to play a role in the regulation of gene expression.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

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Gene Map/ Genome Map: The known order for a set of genes or DNA markers at intervals along a chromosome. A minimum density map will have 300 markers while a high density map will have 10,000 markers.
--Definition from: Horse Genome Project, from the University of Kentucky

Genome: The entire set of genetic instructions (genes and associated regulatory DNA) found in a cell. In humans, the genome consists of 23 pairs of chromosomes containing approximately 3.1 billion bases of DNA sequence. Horses have on their 32 pairs of chromosomes approximately 3 billion DNA bases.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Genome Sequence: The complete DNA sequence determined for all chromosomes in a cell for an individual, including all 20,000 genes and approximately 3 billion DNA bases.
--Definition from: Horse Genome Project, from the University of Kentucky

DNA (Deoxyribonucleic acid): The chemical name for the molecule that carries genetic instructions and is the major component of chromosomes. The DNA molecule consists of two strands that wind around one another to form a shape known as a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases--adenine (A), cytosine (C), guanine (G), and thymine (T). The two strands are held together by bonds between the bases; adenine bonds with thymine (A-T or T-A), and cytosine bonds with guanine (C-G or G-C). The sequence of the bases along the backbones serves as instructions for assembling protein and RNA molecules. A gene may be 1000 to 2000 bases long.
--Definition from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

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Heterozygous: When an organism has inherited different forms (alleles) of a particular gene from each parent, for example Ee or Aa.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Homozygous: A genetic condition where an individual inherits the same alleles for a particular gene from both parents, for example EE and ee.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Genetic variation: Refers to diversity in gene frequencies. Genetic variation can refer to differences between individuals or to differences between populations. Mutation is the ultimate source of genetic variation, but mechanisms such as sexual reproduction and genetic drift contribute to it as well. Mutations can be identified as changes in the composition of the DNA at a unique site.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute, and Horse Genome Project from the University of Kentucky

Genotype: An individual's collection of genes. The term also can refer to the two alleles inherited for a particular gene.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Phenotype: An individual's observable traits, such as height, eye color, and hair colour. The genetic contribution to the phenotype is called the genotype, while the phenotype is how the gene gets expressed. The genotype causes an individual to have brown hair and the phenotype is an expression of what shade of brown.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

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Single nucleotide polymorphisms (SNPs): A type of polymorphism involving variation of a single base pair. SNPs (pronounced "snips") are the most common type of genetic variation and occur when one base is switched with another: for instance thymine switched with cytosine. There are approximately 10,000 SNPs in a genome.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Linkage: The close association of genes or other DNA sequences on the same chromosome. The probability of being inherited together is increased by proximity of the two genes on the same chromosome. The likelihood of inheritance linkage is measured in centiMorgans (cM). 1 cM = 1% chance of linkage = approximately one million base pairs.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Polymorphism: One of two or more variants of a particular DNA sequence that is at least 1% of the population. Most common occurrence is a single nucleotide polymorphism (SNP) involving a single base pair.
--Definition adapted from: Talking Glossary of Genetic Terms, from the National Human Genome Research Institute

Missense Mutation: A change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.
--Definition from: Genetics Home Reference Handbook

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Nonsense Mutation: A change in one DNA base pair that cause the altered DNA sequence to prematurely signal the cell to stop building a protein. This type of mutation results in a shorthand protein that may function improperly or not at all.
--Definition from: Genetics Home Reference Handbook

Insertion Mutation: Changes the number of DNA bases in a gene by adding a piece of DNA. As a result the protein made by the gene may not function properly. Inserts one or more bases or part of a chromosome into another.
--Definition from: Genetics Home Reference Handbook

Deletion Mutation: Changes the number of DNA bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighbouring genes. The deleted DNA may alter the function of the resulting protein(s).
--Definition from: Genetics Home Reference Handbook

Duplication Mutation: Consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein. Gene duplication is an important mechanism by which evolution occurs.
--Definition from: Genetics Home Reference Handbook

Frameshift Mutation: Occurs when the addition or deletion of DNA bases changes a genes reading frame. A reading frame consists of groups of 3 bases that each code for one amino acid. A Frameshift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually non-functional. Insertions, deletions, and duplications can all be frameshift.
--Definition from: Genetics Home Reference Handbook

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Repeat Expansion Mutation: Nucleotide repeats are short DNA sequences that are repeated a number of times in a row; for example, a trinucleotide repeat is made up of 3 base pair sequences and a tetranucleotide repeat is made up of 4 base pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.
--Definition from: Genetics Home Reference Handbook

Splice Site Mutation: A change in the genetic sequence that occurs at the boundary of the exons and introns. The consensus sequences at these boundaries signal where to cut out introns and rejoin exons in the mRNA. A change in these sequences can eliminate splicing at that site which would change the reading frame and protein sequence. This leaves the intron as part of the protein.
--Definition from: University of Vermont website

Translocation Mutation: A structural abnormality of chromosomes where genetic material is exchanged between two or more non-homologous chromosomes.
--Definition from: University of Vermont website

Point Mutation: A single base change in the DNA sequence. A point mutation may be silent, missense or nonsense.
--Definition from: University of Vermont website

Silent Mutation: A change in the genetic sequence that does not change the protein sequence. This can occur because of redundancy in the genetic code where an amino acid may be encoded by multiple codons.
--Definition from: University of Vermont website

Substitution Mutation: A mutation where one base pair is replaced by a different base pair. The term also refers to the replacement of one amino acid in a protein with a different amino acid.
--Definition from: University of Vermont website

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