Equine genetic conservation – why, how and what’s next? - Veterinary Practice
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Equine genetic conservation – why, how and what’s next?

The need for equine genetic conservation has never been more apparent, with research showing that genetic diversity in equid species has decreased the most dramatically in the past 20 years

Horses have been domesticated for approximately 5,500 years and have since been used for companionship, recreation, agriculture and warfare. Following domestication, humans have artificially selected and bred horses for particular traits and job roles, creating around 500 breeds to date. However, some breeds are at risk of extinction. Through domestication and breeding, humans have decreased genetic diversity within the equine population, simultaneously increasing the chances of deleterious genetic disorders such as Warmblood fragile foal syndrome (WFFS) and foal immunodeficiency syndrome, among others.

three horses

The Rare Breeds Survival Trust (RBST), alongside other charities, has been conserving a multitude of native rare breed animals, including equids, from extinction in the UK for the past 50 years. Their updated watchlist model (2022/23) uses effective population size and measures of inbreeding, providing an accurate representation of the current population status of different breeds.

The RBST watchlist for 2024/25 shows six priority equine breeds in the UK: Cleveland Bay horse, Dale’s pony, Eriskay pony, Exmoor pony, Hackney horse and pony and the Suffolk. A further seven breeds are also at risk: Clydesdale, Dartmoor pony, Fell pony, Highland pony, New Forest pony, Section B Welsh Pony and the Shire horse. This highlights the need to conserve our equine population to save some from going extinct and to increase equine genetic diversity for the future.

Why should we conserve our native equine breeds?

Many consider that conserving our native equine breeds is a form of keeping or holding onto tradition. These horses have been bred for job roles, some of which are now redundant, over the last 5,500 years; therefore, we have a responsibility to uphold conservation. Whether you hold this opinion or not, research shows that the current worldwide population of horses has a lack of genetic diversity compared to horses prior to domestication (Raudsepp et al., 2019). This suggests that domestication and human intervention influenced this decline.

Alarmingly, it has been found that the genetic diversity of the horse has decreased most dramatically (by 16 percent) in the last 200 years (Fages et al., 2019). This has also been attributed to extensive artificial selection. Within a population of low genetic diversity, such as the Cleveland Bay horse, Dale’s pony, Eriskay pony, Suffolk, Exmoor pony and Hackney horse and pony, there is an increased proportion of homozygous individuals, resulting in an increased number of deleterious alleles present. Ultimately, this increases the chances of animals inheriting disorders, such as foal immunodeficiency syndrome (a recessive missense mutation causing fatal anaemia), now common in the Fell and Dales ponies (Raudsepp et al., 2019).

Whether the reason for conserving our equine breeds is solely for tradition or not, there is a greater need to safeguard the current genetics and increase diversity for the future

A low genetic diversity has also been associated with a reduced potential to combat disease. In populations with a small gene pool, there is a higher risk that disease could destroy the entire population due to the lack of genetic diversity. In smaller populations of animals, there is also understandably higher inbreeding compared to larger populations. Although research is limited, inbreeding in equids has been linked to increased retained placentas, decreased motility of spermatozoa and pregnancy loss (Lawson et al., 2024). The current population of horses also has a lack of diversity in the Y chromosome – a deficiency likely caused by artificial selection and the declining number of colts kept entire (Librado et al., 2017).

Therefore, whether the reason for conserving our equine breeds is solely for tradition or not, there is a greater need to safeguard the current genetics and increase diversity for the future.

How do we conserve equine genetics?

Oocyte and spermatozoa harvesting

Oocyte and spermatozoa harvesting is one method of safeguarding equine genetics for the future.

Cryopreserving spermatozoa from stallions is commonly used and involves artificially collecting spermatozoa to preserve in liquid nitrogen for future use. Samples can be collected from a live stallion or following death through epididymal semen harvest, both of which have good pregnancy results (Dascanio and Miller, 2021). Cryopreservation of spermatozoa not only safeguards genetics for the future but also allows for multiple offspring produced from a single ejaculate.

Cryopreserving spermatozoa from stallions is commonly used and involves artificially collecting spermatozoa to preserve in liquid nitrogen for future use

Similarly, oocytes can also be harvested from live donor mares or following death directly from the ovaries in a process called ovum pick-up (OPU). Unlike spermatozoa, cryopreservation of oocytes is unsuccessful. Instead, oocytes are matured in vitro and fertilised using intracytoplasmic sperm injection (ICSI) before implantation or preservation in liquid nitrogen. OPU is becoming increasingly popular for the equine breeder, although successful pregnancy results vary (Cabeza and Gambini, 2023).

Somatic cell nuclear transfer

Somatic cell nuclear transfer (SCNT) is another method of genetic preservation but without the need to collect spermatozoa or oocytes. Instead, the technique uses tissue samples to produce a genetically identical individual. SCNT has already been used to increase the genetic diversity of today’s Przewalski’s horse population using skin biopsies taken in the 1980s; it has produced two foals to date (Cabeza and Gambini, 2023).

While this technology has caused some concern regarding cloning animals, tissue samples can be taken today for use in the future through preservation in liquid nitrogen, similar to the cryopreservation of spermatozoa (Bolton et al., 2022). This is called “cryobanking” and is much like a seed bank for flora.

Stem cell technologies

More recently, stem cell technology has been discussed not only for use in regenerative veterinary medicine for injury recovery but also for producing gametes and embryos to safeguard genetics without the need for spermatozoa or oocyte collection. This was first reported in the equid in 2011 when fibroblasts were reprogrammed into induced pluripotent stem cells in vitro (Nagy et al., 2011), but we have seen success more recently in the Grévy’s zebra (Endo et al., 2022).

Stem cell technology has been discussed […] for producing gametes and embryos to safeguard genetics without the need for spermatozoa or oocyte collection

The production of a novel synthetic embryo-like structure (iBlastoids) also shows promise for genetic conservation. iBlastoids derived from pluripotent stem cells organise into structures resembling early embryos in humans (Liu et al., 2021).

It is hoped that stem cell technology will continue to develop and be a potential method to conserve genetics for many species, including equids.

What are the barriers to success?

There is increasing concern for safeguarding equine genetic diversity; however, there are currently no regulatory bodies for the process and limited funding for doing so. Most equine rare breed breeders have a passion for conservation but are generally funding this interest alone.

Routine genetic testing of equids is suggested to confirm pedigree; however, the microsatellites used cannot identify specific genetic disorders – this requires the use of single nucleotide polymorphisms (SNPs), which is not standard practice. SNPs are a regularly used tool for genetic testing of equids for disorders such as lavender foal syndrome, WFFS and equine polysaccharide storage myopathy, among many others (Raudsepp et al., 2019). However, this is also not mandatory or regulated within equine breeding.

There is increasing concern for safeguarding equine genetic diversity; however, there are currently no regulatory bodies for the process and limited funding for doing so

While research highlights the need for equine genetic conservation, the unanswered questions are: who is responsible and who should take the lead?

What future directions can we take?

One method to conserve our equine rare breed populations is to use native breeds for versatile disciplines as either purebreds or by cross breeding. Conservation grazing is another way to use native breeds, as they are adapted to the landscape and can be managed as semi-feral groups with minimal intervention. This not only conserves genetics but could also aid in sustainability directives which could coincide with much-needed funding (Fraser et al., 2019). Encouraging equine breeders to select individuals with genetic diversity to reduce inbreeding and deleterious alleles (and not forgetting the use of the available preservation techniques!) will aid equine genetic conservation.

Encouraging equine breeders to select individuals with genetic diversity to reduce inbreeding and deleterious alleles will aid equine genetic conservation

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