The DNA of Franches-Montagnes Horses Reveals the Origin of the Breed
Photo: Christelle Althaus
The genotype information of over 1,000 horses reveals that the Franches-Montagnes can be distinguished from other historically introgressed breeds. Furthermore, it has been demonstrated, that this kind of information can also be applied to manage the inbreeding within the population.
The Franches-Montagnes (FM) breed was established in Switzerland at the end of the 19th century by cross-breeding local mares with two Anglo-Norman stallions: Vaillant (1891) and Imprévu (1886). The FM studbook was officially released in 1921. Thereafter, periodic introgression of horses from other breeds was authorised to meet market demands, initially with draught horses for agricultural work and later with stallions of the Shagya, Purebred Arabian, Nonius, Anglo-Norman, Selle Français, and Swiss Warmblood stallions in order to breed a lighter type of horse for leisure riding and carriage driving. Some of these introgressions led to the formation of new sire lines. Currently, there are 11 sire lines, 6 of which are considered original and five of which arose from stallions of other European horse breeds.
The studbook was closed in 1997 to preserve the characteristics of the last Swiss horse breed, i. e. a foal resulting from cross-breeding after this cut-off year is not registered as an FM horse. FM horses born before 1950 are considered purebred, even if their pedigree includes ancestors from other breeds. Currently, the number of ‘old-type’ horses (no cross-breeding since 1950) is declining, resulting in an increase in inbreeding in this subpopulation. Currently, there is a preference for FM horses with a high admixture proportion, which threatens the integrity of the FM horse population as a native breed from both a genetic and phenotypic perspective.
Using genotype data to visualise fine-scale population structures
To accurately interpret the kinship and inbreeding of the FM breed, scientists genotyped over 1200 horses using the Affymetrix Axiom™ array, which allows for cost-effective exploration of the genetic variance of individual horse genomes. With over 600,000 markers (single nucleotide polymorphisms [SNPs]), this genotyping allows the characterisation of each horse genome and the study of genetic diversity among modern horse breeds: related horses have more markers in common than horses with different origins. Genomic data were also applied to assess the genetic relatedness and individual inbreeding of the horses.
The study compared the genotypes of 1268 horses: 522 FM horses (including 44 old-type), 514 Warmblood (including Noé, a stallion used for one of the last cross-breeding events in 1990), 136 Purebred Arabian, 32 Shagya, and 64 Thoroughbreds (as some Warmblood stallions used for admixture with the FMs showed Thoroughbred origin in their pedigrees). The 11 sire lines of the FM breed were represented by 8–148 descendants.
To ascertain fine-scale population structures within the FM breed, researchers applied a novel three-step approach that combines the visualisation of the genetic relatedness of horses with admixture proportions and individual inbreeding. This approach also allows for the evaluation of the genetic diversity of the FM breed and old-type FMs compared to the other breeds.
The FM is clearly distinguishable from other breeds
The analyses clearly show that FMs and old-type FMs are distinguishable from the two Arabian breeds, as well as from the Warmblood and Thoroughbred breeds. The FM is therefore clearly distinguishable from other breeds historically introgressed since 1950.
Nevertheless, further substructures in the FM population were observed according to different genetic origins (old type). Furthermore, it was noticed, that the overrepresentation of the progeny of certain influential stallions that caused additional substructures in the FM breed.
Within the FM breed, admixed horses accounted for most of the genetic variance of the current breeding population, while old-type horses accounted for only a small proportion of the variance. Finally, the study revealed that some FM horses exhibit unexpectedly high Thoroughbred admixture levels.
On average, FM horses were less inbred compared to other closed-studbook breeds (except Warmblood horses), particularly owing to the admixtures, but certain data suggest a loss of diversity in the two FM subpopulations. To prevent inbreeding, the authors suggest including old-type FM horses in the FM breeding population and discouraging breeders from selecting for ‘rare’ coat colours in FM horses, such as black and grey.
Conclusions
- Established at the end of the 19th century in Switzerland, the Franches-Montagnes (FM) horse breed was subject to periodic admixtures of other breeds, including Shagya, Purebred Arabian, Nonius, Anglo-Norman, Selle Français and Swiss Warmblood.
- A study based on the genotypic data of 1268 horses, including FM, Warmblood, Purebred Arabian, Shagya, and Thoroughbred horses, shows that FM remains the only breed of Swiss origin.
- The study also shows that FM horses are, on average, less inbred compared to other European breeds, although a loss of diversity was observed due to the popularity of certain stallions.
- To prevent inbreeding, the authors suggest including old-type FM horses in the FM breeding population and encouraging breeders to select for characteristics other than coat colour.
Bibliographical reference
Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed.
