Genetic diversity: Depends upon mutations, natural selection, gene flow, and genetic drift.

Genome: The complete set of chromosomes for an individual

Chromosome: a thread-like structure found in the nucleus of living cells. It contains deoxyribonucleic acid (DNA)

Gene: segments of DNA which are contained within in chromosomes

DNA:  Segments of base-pairs (adenine-thymine & cytosine-guanine). The order of these pairs form the structure of DNA

Allele: Two or more alternate forms of a gene. Examples are coat color modifier such as the Cream Gene. Horses can be dominant (CC & Cc), or recessive (cc). Some are more complex such as human blood types in which four possibilities exist (A, B, O, AB)

Single nucleotide polymorphisms: These SNP (also called ‘snips’) are changes within a single nucleotide. As an example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA. These variations may be unique to one individual or they may be found in many individuals; scientists have found more than 100 million SNPs in human populations around the world. Most commonly, these variations are found in the DNA between genes. They can act as biological markers, helping scientists locate genes that are associated with disease.The SNIP’s are important in establishing genetic variability 

“An important part of the horse genome project was the identification of over a million SNPs, which directed the development of genomic tools for mapping in the horse. The SNPs were generated from the diploid genome of Twilight and by partial sequencing of seven additional horses of diverse breeds. The reference assembly and the SNP map marked a turning point in horse genomics by providing resources for driving subsequent molecular, clinical and evolutionary studies in the horse” (Raudsepp, 2019)

“Twilight”, a Thoroughbred mare, was the first horse to have her entire genome mapped in 2006-2007

Genetic diversity: The range of different inherited traits within a species.

Mutation:  Changes in the sequence of DNA. They can be a tiny as one nucleotide change (adenine-thymine & cytosine-guanine) or consist of a larger part(s) of the gene. They occur frequently (1 per 1,000 nucleotides) which equates to 4-5 million per genome (the complete set of chromosomes per organism). Most are benign and cause no problems (disease or disability) for the organism, but some can be lethal (lethal white [foal] syndrome).  Some mutations can be advantageous such a gene coding for harder hooves in wild horses. Soft hooves could potentially render a horse lame which might make them more susceptible to predation (an example).

Natural selection: The process in which certain genes occur in better adapted horses. Individuals with mutations that are better adapted for survival pass these traits to their offspring. The mutations are inherited characteristics that allow a horse to adapt to the environment more successfully . Presently, there is no significant difference between the genome of wild horses and their domestic counterparts.

Gene flow: This refers to the migration of organisms, and the genes they carry, from one population to another. It can occur by physical movement (migration), or human mediated translocation of some horses from one management area to another.

Genetic Drift: The totally random process which changes the numbers of gene variants in a population. Genetic drift takes place when different forms of a gene, called alleles, increase and/or decrease by chance over time. Allelic frequencies measure the presence of these variations. It is common for genetic drift to occurs in small populations, because infrequently occurring alleles face a greater chance of being lost because they occur rarely. During the process of genetic drift, rare alleles are lost and the common alleles become the only allele at a particular locus. Both possibilities decrease the genetic diversity of a population. Genetic drift can result in the loss of rare alleles and decrease the gene pool.

Microsatellite markers:  These are repeating sequences of DNA (or microsatellites) and are distributed throughout the genome and passed on to the organism’s offspring. They are useful in determining paternity, as well as measuring the relatedness between individuals of a population and useful for determining genetic variability.

Patrilineal: Kinship derived from the male or father lineage

Matrilineal: Kinship derived from the female, or mother lineage

mtDNA (Mitochondrial DNA): This form of circular DNA is found in the mitochondrial cells (the ‘powerhouse of the cell’… shades of high school biology class). mtDNA is passed from mother to offspring of both genders and is very useful in determining ancestry by following the maternal lineage back in time. It plays a role in the controversy surrounding wild mustangs and the Spanish Colonial horse type.

Patrilineal Y Chromosome Analysis (Male Specific Region of the Y Chromosome- MSY): Every male horse inherits a Y chromosome from their father. Similar to matrilineal mtDNA, the male horses can trace their lineage back hundreds of years. Researchers look for mutations (which are found in many chromosomes, not just the Y chromosome). These changes in the genetic sequence are called ‘polymorphic markers’ and are useful because they are passed down from father to son on the Y chromosome to trace patrilineal ancestry.

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References

Raudsepp, T., et al. “Ten Years of the Horse Reference Genome: Insights into Equine Biology, Domestication and Population Dynamics in the Post‐Genome Era.” Animal Genetics, vol. 50, no. 6, 2019, pp. 569–597., doi:10.1111/age.12857.