Puerto Ricans bred horses for the “gait-keeper” gene for centuries, study finds

A Puerto Rican Paso Fino mare with tiger eye, an eye color so far only found in Puerto Rican Paso Finos, according to Wikipedia. It usually lightens the eyes to a striking amber, yellow, or bright orange color. Photo: Arsdelicata, CC BY-SA 3.0, via Wikimedia Commons
Platanera Dorada, a Puerto Rican Paso Fino mare with tiger eye, an eye color so far found only in Puerto Rican Paso Finos, according to Wikipedia. It usually lightens the eyes to a striking amber, yellow, or bright orange color. Photo: Arsdelicata, CC BY-SA 3.0, via Wikimedia Commons

The Puerto Rican Paso Fino horse, famed for its smooth four-beat gait, most likely descended from the Puerto Rican Criollo horse, researchers report.

The results of genetic testing, reported in the journal Scientific Reports, point to the Iberian origins of the breed.

Remarkably, the DMRT3 mutant allele – the so-called “gait-keeper” gene found in gaited breeds – was almost as common in the Criollo horse as the Paso Fino, Walter Wolfsberger, Nikole Ayala and their fellow researchers reported.

The study team said several local varieties and breeds have been established in the New World since the first Spanish settlers brought horses to the Americas centuries ago.

These breeds were generally a consequence of the mix of the different breeds arriving from Europe.

In some instances, local horses were selectively bred for specific traits, such as appearance, endurance, strength, and gait.

Researchers in the University of Puerto Rico study looked at the genetics of the Puerto Rican Criollo and Paso Fino.

A gaucho rides a native Criollo horse. Photo by Comparceiro (originally posted to Flickr as ABRINDO TÓCA) CC BY-SA 2.0 via Wikimedia Commons
A gaucho riding a Criollo horse. Photo by Comparceiro / CC BY-SA 2.0 via Wikimedia Commons

“While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established,” they noted.

They started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a fragment of the mitochondrial DNA in 200 horses from 27 locations on the Caribbean island.

They then genotyped all 200 horses for the gait-keeper gene previously associated with the paso gait, as well as other genetic work, which was further combined with the publicly available Paso Fino genomes from other studies.

Their analysis showed an undeniable genetic connection between the two horse breeds in Puerto Rico, consistent with the hypothesis that the local Criollo horses are the descendants of the original genetic pool – a mix of horses imported from the Iberian Peninsula and elsewhere in Europe.

Some of the original founders of the Criollo population must have carried the gait-keeper gene. From these horses, desired traits were selected by the local farmers over several centuries.

They propose that the frequency of the mutant gait-keeper gene originally increased in the local horses through selection for the smooth ride and other characteristics long before the Paso Fino breed was established.

The genetic evidence supports this view. The researchers said they identified a signature of selection in the genomic region containing the DMRT3 gene in the Criollo horses, but not the Paso Finos.

The lack of the detectable signature of selection associated with the DMRT3 in the Paso Finos would be expected if this native breed was originally derived from the genetic pool of Criollo horses established earlier, and most of the founders already had the mutant allele.

Consequently, selection specific to Paso Fino horses later focused on alleles in other genes, including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others, that have not been previously associated with the prized paso gait in Puerto Rico or anywhere else.

Discussing their findings, the researchers said that, over the centuries, the two breeds gained their distinctive appearance that is reflected in the genetic structure revealed by their analysis.

They said their study of mitochondrial DNA diversity in the two breeds also points to their mainly Iberian origins.

The genetic testing showed that Puerto Rican horses share genome variation components with a number of horses worldwide.

In particular, the Criollo horses appear to have genomic fragments in common with the Northern European and Asian horse breeds, specifically the Finnhorse, Mongolian and Tuvan breeds.

“This appears to be the same component present in the Iberian (Lusitano), Middle Eastern (Caspian horse), or US derivatives from the Spanish stock brought to Florida in the 1500s (the Florida Cracker).”

Both Puerto Rican breeds display a common genetic component that seems to be unique to the local island horses and cannot be found in any of the other surveyed horse breeds.

This component represents a larger part of genetic variation in the Criollo horse, but completely dominates the Paso Fino genomes. The most likely explanation of this observation is that the Criollo has a unique mixture that incorporates variation from a diverse set of breeding lines brought on ships to the island.

Given the results, the authors said the most likely historic scenario is that the Puerto Rican Paso Fino is a distinct horse breed that has been selected from the Puerto Rican Criollo. The genetic pool of the Criollo was likely a result of admixture between the horses historically imported to Puerto Rico from Spain and other regions of the Old World.

“Some of the founders of this pool must have originally brought the gait-keeper DMRT3 mutant allele with them. Local farmers must have been selectively breeding for the mutant allele, and over several centuries, it has increased in frequency in the non-purebred population of horses on the island.”

Consequently, the founders of the Paso Fino were initially picked out from the existing Criollo pool, but since the DMRT3 mutant allele was already nearly fixed, the selection in the purebred horses was focused on other genes that may or may not be associated with the paso gait.

The study team said, in order to reinforce their hypothesis and identify the specific functional mutations selected by Paso Fino breeders, a comprehensive phenotype-genotype analysis based on horse pedigrees and sequencing data from these candidate genes needs to be conducted.

The study team comprised Wolfsberger, Ayala, Stephanie Castro-Marquez, Valerie Irizarry-Negron, Antoliy Potapchuk, Khrystyna Shchubelka, Ludvig Potish, Audrey Majeske, Luis Figueroa Oliver, Alondra Diaz Lameiro, Juan Carlos Martínez-Cruzado, Gabriella Lindgren and Taras K. Oleksyk.

Wolfsberger, W.W., Ayala, N.M., Castro-Marquez, S.O. et al. Genetic diversity and selection in Puerto Rican horses. Sci Rep 12, 515 (2022). https://doi.org/10.1038/s41598-021-04537-5

The study, published under a Creative Commons License, can be read here



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