Horse-breeding practices are the major driver of a loss of genetic diversity on the male Y chromosome.

Need to preserve genetic diversity of male horses featured in review –

Horse breeding practices are the primary driver of a loss of genetic diversity on the male Y chromosome.
Image by Daron Herbert

According to the researchers, modern horse populations have extremely low genetic diversity on the male Y chromosome, mainly due to the strategies of breeders.

Scientists cautioned in a just-published review that examines the diversity of the horse’s Y chromosome.

Irene Cardinali and her fellow researchers, writing in the journal Genoastated that current equine genetic variation reflects the profound influence of intensive breeding programs over the past 200 years.

They set out in their review to examine the current state of knowledge on trends and prospects for variation in the equine male specific region of the Y chromosome, which was first assembled in 2018.

Compared to 12 species of mammals, horses are now the most represented, with 56 genes documented in the male-specific region of the Y chromosome.

“However, in contrast to the high mitochondrial DNA variability observed in many horse breeds from different geographic areas, modern horse populations exhibit extremely low Y-chromosome genetic diversity.

“Selective pressures employed by breeders using pedigree data (which is not always error free) as a predictive tool represent the primary cause of this lack of Y chromosome variation.”

On a more positive note, the researchers said the information gained from recent small-scale Y chromosome genotyping in many horse breeds around the world has been extremely beneficial.

They have contributed to answering genealogical, forensic and demographic questions leading to the re-evaluation of the Y chromosome as a powerful genetic marker to prevent biodiversity loss through selective breeding practices.

The information will also allow scientists to better understand the historical development of horse breeds.

Research has shown that, when looking at the male-specific region of the Y chromosome, modern horse breeds cluster genetically for the most part in what is known as the “crown group”, whose most common ancestor recent was born about 1000 to 2000 years ago from the eastern founder. stallions.

This group split from northern European horses about 1300 years ago (haplogroup N, found in Norwegian Fjord horse, Swedish Coldblood horse and Shetland ponies) and sister clade I (found in Icelandic horses ) about 1000 years ago.

“However, all modern European breeds clustered in the crown group and showed an influence of Oriental stallions with male-specific Y-chromosome ancestry belonging to the Arabian and Turkmen lines of origin, the latter profoundly influencing the English thoroughbred stallions.”

Then, 211 other variants and 58 haplotypes were described after analyzing Y-chromosome data from 130 domestic horses and nine Przewalski horses, confirming the clear separation between the crown group (found in modern horses from Central Europe and South, North American, and most East Asian horses) and crownless haplotypes (found in Przewalski’s horses and some northern European and Asian breeds).

The major male-specific Y-chromosome clades that belong to the crown group are A (first described in an Arabian horse), H (first described in a Spanish horse), L (first described in in Lipizzaner horses) and T (first described in Thoroughbreds), while the non-crown group is mainly represented by I (found in Icelandic horse), J (in Jeju horse), N (typical of breeds European horses), O (found in the Mongolian horse), P (in Przewalski’s horse) and Y (in the Yakutian horse).

In summary, of the 169 horse breeds worldwide analyzed so far for the Y chromosome, 46 have been classified into haplogroups. Thirty-eight breeds belonged to the crown group, seven to the non-crown group, and only one Asiatic breed (the Yakutian horse) represents both.

In a global context, the uncrowned group so far includes the Icelandic Horse, Jeju Pony, Mongolian Horse, North Swedish Draft Horse, Norwegian Fjord Horse, Przewalski Horse and Shetland Pony, who, like many other native breeds, carry specific breed variants. which have not been replaced by Arab and Turkmen lineages.

The authors noted that recent studies of ancient specimens have attempted to describe the times and patterns of horse variation loss across the male line, and different scenarios have been proposed.

“The correlation between the genetic admixtures observed in European populations and the spread of the Yamnaya culture from the Pontic-Caspian steppe initially suggested that this region was the center of horse domestication,” they said.

The loss of Y-chromosome diversity in the horse started from there, they note, with one male line gradually replacing all others except the line found only in Yakutian horses and of a rather marked genetic diversity observed today in other Asian breeds.

However, in 2018, researchers who conducted an analysis on the male lines of 96 ancient European stallions dating from the Copper and Bronze Ages to the Middle Ages stated that the loss of different Y chromosome lines in modern horses is due to an artificial selection that began in the Iron Age and not by founder or demographic effect.

Undoubtedly, the genetic diversity of paternal lines has declined over the past 2000 years, the review team said.

The authors said that the highly repetitive structure of the Y chromosome makes its sequencing and assembly very difficult, but the long-standing debates about the origin, spread and genetic variability of domestic horses and the many studies focusing on the homolog female have allowed researchers to uncover the evolutionary processes that affected paternal lines.

They said recent developments in small-scale horse Y-chromosome analysis have helped in tracing male lineages and provided different scenarios for when and what causes the loss of Y-chromosome diversity.

“The discovery of new variants and a better understanding of the pathways by which domestication occurred have been possible through the analysis of modern and ancient horse populations.”

Although further investigation is still needed, the variation within the Y chromosome represents a powerful lineage and pedigree tracer crucial to bolster horse management, the review team said.

The information, they said, can be used to help prevent further loss of biodiversity within male lines and aid in scientific understanding of historical breed development.

The study team included Cardinali, Andrea Giontella, Maurizio Silvestrelli and Hovirag Lancioni, all from the University of Perugia; and Anna Tommasi, from the University of Pavia.

Cardinals, I.; Giontella, A.; Tommasi, A.; Silvestrelli, M.; Lancioni, H. Unlocking the diversity of horse Y chromosomes. Genes 2022, 13, 2272.

The study, published under a Creative Commons Licensecan be read here.

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