Horse Genetics. Ernest Bailey
The scientific name of the species is given in the far-left column, followed in subsequent columns by common names and the number of chromosomes reported for each species. The practice is to type the genus and species name in full the first time it is used, and then simply abbreviate the first letter(s) thereafter. So Equus caballus becomes E. caballus. In some literature, the horse is designated Equus ferus and includes both the domestic horse and the Przewalski horse. When using that convention, the domestic horse is given the subspecies designation “caballus” (E. f. caballus) and the Przewalski horse is likewise designated E. f. przewalskii. As described in Chapter 2, the two species diverged between 41,000 and 70,000 years ago and are distinguishable species at the DNA level. Therefore, we will use the convention of referring to them with the species designations, E. caballus and E. przewalskii.
The chromosomes of domestic horses and donkeys are well known from clinical karyotyping studies, as well as genome mapping studies, and excellent ideograms exist that depict the number and structure of the chromosomes in these species (Bowling et al., 1997; Raudsepp et al., 2000; Di Meo et al., 2009). However, relatively fewer karyotyping studies have been undertaken for the wild equids, and some variation has been noted in their karyotypes. We do not know whether the individuals studied had clinically abnormal karyotypes or whether this variation represents hybridization between chromosomally heterogeneous populations that were brought together in recent history.
Endangered species
The conservation status of the different species of Equus according to the IUCN is identified on the far right of Table 3.1. Those listed as critically endangered (Somali wild ass), endangered (Przewalski’s horse, kulan, onager, and Grevy’s zebra), and vulnerable (mountain zebra) are those considered at risk of extinction. Those identified as of least concern (kiang and common or plains zebra) are considered stable populations for the present.
Genomic differences among the species of Equidae
The relationships among the species of Equidae continue to be clarified as we obtain more DNA sequence information. Whole genome sequence is reported for most, if not all, of the Equidae species and subspecies in publicly available databases.
Horses
This group comprises two species, commonly known as Przewalski’s horse (E. przewaslkii) and the domestic horse (E. caballus). The domestic horse is well known and is the primary subject of this book. One likely ancestor of the horse, sometimes called a tarpan (E. ferus ferus and E. f. sylvestris), has become extinct in the wild but the natural distribution was throughout modern-day Europe, Asia, and the Middle East (Groves and Ryder, 2000). Przewalski’s horse (Fig. 3.4) is a closely related species that was driven to extinction in the wild during the 1900s, and then reintroduced to the Hustai National Park of Mongolia in 1992 using captive born Przewalski’s horses (Boyd and King, 2011). Before its initial extinction in the wild, the natural distribution of Przewalski’s horses appears to have been from eastern Germany through to the northern regions of Asia, especially Mongolia. The extant Przewalski’s horse population is descended from only 12 horses brought into zoo populations in the early 1900s. Today, the number of Przewalski’s horses exceeds 1800, including more than 300 living in the wild.
Fig. 3.4. Przewalski Horse (E. przewalskii) (picture provided by Zoological Society of San Diego).
The relationship between Przewalski’s horses and domestic horses continues to be a topic of research and discussion. Hybrids of the two species can be fertile, and indeed, are likely to have produced occasional hybrids that contributed to the genomic constitution of domestic horses (Gaunitz et al., 2018). Differences in overall genome organization are minimal. The most obvious difference is the number of chromosomes with E. caballus having 64 and E. przewalskii having 66. The difference appears to be the result of what is called a “Robertsonian translocation” when two smaller chromosomes fuse to form a single larger chromosome (Myka et al., 2003). Chromosome EPR23 of the E. przewalskii is homologous to the long arm of E. caballus chromosome ECA5. Chromosome EPR24 is homolgous to the short arm of ECA5. It appears that chromosome ECA5 of E. caballus is the product of an ancient, evolutionary fusion between two chromosomes in a species that is an ancestor of E. caballus and E. przewalskii (Myka et al., 2003). However, the mitochondrial genome and the Y chromosome of Przewalski’s horses and domestic horses are distinctly different, demonstrating that they are clearly different species (Oakenfull and Ryder, 1998; Oakenfull et al., 2000; Wallner et al., 2003; Lindgren et al., 2004; Lau et al., 2009).
Asses
Asses evolved in northern Africa. Following domestication, the donkey is found throughout the world because of its usefulness in agriculture. The Somali wild ass continues to exist in the wild in regions of Ethiopia and Eritrea. At present, the number of Somali wild asses may be less than 200 and the species is considered critically endangered (Moehlman et al., 2008c).
The ass karyotype differs numerically from that of the horse by just a single chromosome pair, but the morphology and banding patterns of the individual chromosomes are quite different from those of the horse. Chromosome painting studies have demonstrated large numbers of rearrangements in genome organization when comparing asses with horses (Raudsepp and Chowdhary, 2001). The karyotypes of the Somali wild ass (Fig. 3.5) and the domestic ass cannot be distinguished. A simple chromosome polymorphism has been described several times that involves the same large metacentric chromosome (Benirschke and Ryder, 1985; Bowling and Millon, 1988). Studies of mitochondrial DNA from the extant asses and museum specimens of the extinct Nubian wild ass (E. africanus africanus) indicated that the domestic donkey appears to have descended from the Nubian wild ass and another unknown, ancestral species, but to be distinct from the Somali wild ass (Kimura et al., 2011).
Fig. 3.5. Somali wild ass (E. africanus somaliensis) (picture provided by Zoological Society of San Diego).
Asiatic Wild Asses
The taxonomy of the Asiatic wild asses has a