Who’s your daddy? Scientists reveal secrets of the horse’s Y chromosome

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The study found that all descendants of St Simon carry variants linked to Herod and not Eclipse.
The study found that all descendants of St Simon carry variants linked to Herod and not Eclipse. © National Horseracing Museum

Scientists have delved into the Y chromosome of horses in unprecedented detail, revealing some remarkable insights into sire lines over the centuries.

They have unearthed crucial information on the origins of the domestic horse, including the sire lines of the stallions who founded the Thoroughbred breed, and even cast doubt on the ancient pedigree of a famous racing lineage.

The horse has accompanied humans since its domestication more than 5000 years ago, revolutionizing agriculture, transportation and warfare.

Vast empires were ruled from the back of the horse.

Today, there are an estimated 58 million horses worldwide, across about 700 breeds.

The spread of horse genes predictably coincided with the expansion and spread of human cultures, starting from the Early Bronze Age.

This spread was mainly achieved by breeding from a limited number of stallions, which largely explains today’s limited diversity in the Y chromosome compared to that of mitochondrial DNA – the genes passed down maternal lines.

Strategic breeding in the past 300 years caused the most dramatic change in the genetic make-up of horses, noted Sabine Felkel, Claus Vogl and Barbara Wallner, researchers with the University of Veterinary Medicine, Vienna, who designed a major study of paternal DNA.

The formation of European and American breeds is marked by the enormous impact of imported stallions.

The Godolphin Arabian
The Godolphin Arabian

According to written records, this process, intended as a refinement of local stocks, started in Europe with the popularity of Iberian sires from the 15th to the 18th century. It was followed by the so-called “Oriental wave” from the late 18th to the late 19th century. During this period, “Original Arabian” stallions were imported from Syria to Egypt to achieve speed and elegance.

From the early 19th century, systematic upgrading of horse populations was mainly done through English Thoroughbred stallions, leading to the attributes we see today in most modern horse breeds.

The 25-strong study team, writing in the journal Scientific Reports, said a precise genetic analysis of sire lines independent of pedigree was important, given the impact of stallions on breeding goals.

“Until recently,” they noted, “the only means to trace sire lines were often incomplete or even erroneous pedigree data.

“Here, we resolved the mammalian Y chromosome sequence variation of horses at a resolution comparable to that in humans.”

For their study, they generated a 6.46 Mbp sized reference of the mammalian Y chromosome for the horse that went far beyond anything done before.

They used 130 male domestic horses, nine Przewalski’s horses and one donkey, using data either obtained from previously published studies or sequenced as part of this study.

Based on male genealogy, they found that – apart from an early-branching Asian group and a few other Asian and Northern European lineages – all Western domestic horses clustered in a recently established “crown haplogroup”. A haplogroup is a genetic population which shares a common ancestor.

This cluster, they said, most likely resulted from the extreme preference of stallions of Oriental origin in Western European and North American breeds during the past few hundred years.

Indeed, more than half of the domestic horses in their dataset (76 of 130 horses) carried a haplotype designated HG Tb.

“These included English Thoroughbreds, Standardbreds, many Thoroughbred-influenced breeds (Warmbloods, American Quarter horses, Franches-Montagnes), a Lipizzan stallion, and the Akhal-Tekes.”

Previously, the researchers had identified HG Tb as a signature of the Turkoman horse, an ancient horse population from the steppes of central Asia.

“During the past 300 years HG Tb was extensively spread by the English Thoroughbred.

“The Thoroughbred sire lines trace back to three founder stallions that were imported to England at the end of the 17th century.”

The authors delved into the heritage of Thoroughbred sire lines to learn more about their origins. The male genetics of 65 males were said to be highly consistent with their paternal pedigrees.

They were able to clearly discriminate discrete sublines of the Darley Arabian, born in 1700, and Godolphin Arabian, born in 1724.

Eclipse, from a painting by George Stubbs.
Famous English racehorse Eclipse, from a painting by George Stubbs.

Only a few of the tested males traced back paternally to the Byerley Turk, born in 1680, who were characterized by a specific variation. All tested horses with the variation coalesced in Herod, born in 1758, whose ancestry in turn traces back to Byerley Turk.

They also traced another variation in 11 Thoroughbreds tracing back to St Simon, born in 1881.

According to stud records, St Simon was the son of Galopin, born in 1872, who was sired by Vedette, born in 1854.

“The line should trace back to Eclipse, born in 1764, according to stud books.”

However all descendants of St Simon carry variants linked to Herod and not Eclipse.

“Thus, an incorrect paternity assignment must have occurred in this lineage.”

This was, perhaps, not a new controversy. “In a discussion recorded in the early to mid 19th century, one party claimed that instead of Vedette a moderate performer named Delight, born in 1863, a Byerley Turk descendant, fathered Galopin. Our molecular data support this view.”

Given the dominance of crown lineages in today’s intensively bred horse populations in Central Europe and North America, the researchers broke it down into 58 smaller haplotypes (genetic groups) based on 211 variants, forming three major haplogroups.

“In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse.”

They detected two early splits in the males lines, one separating the Przewalski’s from modern domestic horses and the other between Western and Asian haplotypes.

They also observed two recent consecutive radiations, one encompassing all non-Asian domestic horses with the deepest branch leading to the Shetland Pony and the North Swedish Draft Horses, followed by the more recent crown radiation.

The researchers propose that the dispersal of the now-dominant crown started from a population already harbouring the base male-related genes on the Y chromosomes that can be seen in modern-day breeds. Breeds were refined with genetic input from North African and Iberian, Arabian, and Turkoman horses. Additionally, evidence of a Chinese lineage can be seen in this group.

The authors say their fine-scaled resolution of the individual Thoroughbred lines underlines that genetically grouping horses based on sires’ Y chromosome genes is a practically valuable and accurate method to assess male ancestry.

“We have enabled Y-chromosomal barcoding of individual sire lines and paved the way for forensic applications.”

Their work, they said, will serve as the backbone for studying the paternal ancestry of horses on a worldwide scale.

Moreover, the incorporation of ancient DNA data should cast further light on the origin of existing lineages in the near future.

The full study team comprised Sabine Felkel, Claus Vogl, Doris Rigler, Viktoria Dobretsberger, Bhanu P. Chowdhary, Ottmar Distl, Ruedi Fries, Vidhya Jagannathan, Jan E. Janečka, Tosso Leeb, Gabriella Lindgren, Molly McCue, Julia Metzger, Markus Neuditschko, Thomas Rattei, Terje Raudsepp, Stefan Rieder, Carl-Johan Rubin, Robert Schaefer, Christian Schlötterer, Georg Thaller, Jens Tetens, Brandon Velie, Gottfried Brem and Barbara Wallner, from a range of institutions.

The horse Y chromosome as an informative marker for tracing sire lines
Sabine Felkel, Claus Vogl, Doris Rigler, Viktoria Dobretsberger, Bhanu P. Chowdhary, Ottmar Distl, Ruedi Fries, Vidhya Jagannathan, Jan E. Janečka, Tosso Leeb, Gabriella Lindgren, Molly McCue, Julia Metzger, Markus Neuditschko, Thomas Rattei, Terje Raudsepp, Stefan Rieder, Carl-Johan Rubin, Robert Schaefer, Christian Schlötterer, Georg Thaller, Jens Tetens, Brandon Velie, Gottfried Brem & Barbara Wallner
Scientific Reports, volume 9, Article number: 6095 (2019) https://doi.org/10.1038/s41598-019-42640-w

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

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