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Conservation genomics of endangered indigenous European horse breeds

Periodic Reporting for period 1 - ENDANGEREDHORSES (Conservation genomics of endangered indigenous European horse breeds)

Reporting period: 2017-03-15 to 2019-03-14

Horses have been used throughout human history for transportation, warfare and plowing fields. Their central importance for human development has attracted a lot of attention from geologists as well as the ancient DNA community.

Since the Industrial revolution, horses have diminished in terms of their importance. However, there are several thousands of horse breeds today. Especially in Europe, several of these horse breeds are iconic and representative of certain regions like the Camargue or the Friesian horses. Certain breeds used for racing or dressage can reach a very high market price. However, very little is known about their history and their origin. Furthermore very little is known about the state of their genetic diversity and whether long-term conservation can be achieved.

The goal of this project was to sequence a large number of horses breeds and ideally various individuals per breed. The goal was to reconstruct population histories as well as try to identify some genomic targets for selection.
The different horse breeds have been sampled, DNA has been extracted and sequenced at a high-coverage. The same processing was applied to various horse samples from previous studies. Various techniques were used to identify the ancestral population and to identify the proportion of ancestral populations in different breeds.

In general, we find that horse breeds can be classified into three categories: 1) highly related to Arabian horses 2) having little or no Arabian ancestry 3) being a mixture of the first two categories. We find that the most divergent horse breeds are found in Asia followed by Central Asia and followed by northern Europe. We find that these horses have the highest genetic diversity indicating that they are more ancient populations and not Arabian horses which underwent selection. Furthermore, we showed that certain horse breeds have a critical paucity of genetic diversity due to continuous inbreeding.

The technique used to infer the level of inbreeding as well as remaining genetic diversity was presented by Gabriel Renaud at the 8th International Symposium on Biomolecular Archaeology (ISBA) in 2018 And was recently accepted in Genetics: Gabriel Renaud, Kristian Hanghøj, Thorfinn Korneliussen, Eske Willerslev, and Ludovic Orlando. Joint estimates of heterozygosity and runs of homozygosity for modern and ancient samples. This was accepted for publication in Genetics, 2019. The main paper describing the results of the different horse breeds is being drafted as we speak.
Conservation efforts can suffer from a lack of genetic diversity. This lack of genetic diversity can be due to two main causes namely recent inbreeding or in overall lack of individuals in the population. The effects of recent inbreeding can be recoverable through better mating practices. However, the lack of individuals in a mating population is not something that can be mitigated. Being able to distinguish both has implication for conservation. This is why our method to detect inbreeding and evaluate the genetic diversity is important. Although it was only applied to horses, it can be applied to different organisms to help guide conservation efforts of certain populations.

Our work on horse breeds highlights the uniqueness of certain horse breeds especially those with very low Arabian ancestry. Horse breeds like the Icelandic horses will garner additional attention in the future and will probably result in further economic downfalls to increased tourism and increased interest in such horse breeds.