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Y chromosome genetic variation and deep genealogies provide new insights on Lipizzan sire lines

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Lara Radovic at University of Veterinary Medicine Vienna
Lara Radovic
V. Remer
V. Remer
V. Remer
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S. Reiter
S. Reiter
S. Reiter
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Elif Bozlak at University of Veterinary Medicine Vienna
Elif Bozlak
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Abstract

The male-specific region of the Y chromosome (MSY) is paternally inherited and enables to trace patrilines through genetic analysis. MSY markers and haplotypes in combination with pedigree information provide precise insights into genealogical systems. While the use of the Y chromosomal genetic genealogy is well established in humans, we recently could develop an equine MSY marker system from NGS data capable to perform a genetic fine-scale analysis of sire lines in horses. This approach has been successfully applied to solve genealogical questions in the English Thoroughbred. In this work, we study sire line genealogies in Lipizzan horses by combining MSY and pedigree information. The Lipizzan breed is characterized by deep pedigree records that trace back to founder sires born in the 18th and early 19th century. We inferred Lipizzan specific MSY haplotypes based on NGS data from 15 Lipizzan males mapped to a 5.8 Mb horse MSY draft reference (LipY764). Haplotype distribution was then studied by screening 52 selected haplotype determining variants in 132 stallions representing the 8 existing Lipizzan sire lines. Samples were derived from 7 European Lipizzan state stud farms. Genomic DNA was isolated from blood and genotyping was performed with the KASP genotyping method. MSY haplotype spectra in Lipizzans were compared with other breeds, and the results confirmed a presumed Arabian and Spanish origin in 2 Lipizzan sire lines. Surprisingly, horses from the remaining 6 sire lines grouped into haplogroup Tb. This haplogroup was recently characterized as a signature of the Turkoman horse, and the allocation of Lipizzans into Tb points to a possible Turkish influence in the Lipizzans. In addition, we detected 6 haplotypes that arose via de novo mutation in the timeframe of pedigree documentation. In 2 sire lines the MSY pattern in sub-lines did not accord with the paternal lineage documentation. In 5 horses belonging to a side-branch of the Favory line, a unique haplotype was detected. This finding indicates another foundation sire in the Lipizzan horse. In conclusion, MSY haplotyping confirmed historic breed documentation and offered new insights on the male breed ancestry. Furthermore, we demonstrated that our approach is suitable to study sire lines on a genealogical scale. MSY analysis can be used for studying the paternal ancestry and as a forensic tool, to solve open questions in the paternal lineages, even if they occurred multiple generations back in time.
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Journal of Equine Veterinary Science 100 (2021)
Contents lists available at ScienceDirect
Journal of Equine Veterinary Science
journal homepage: www.j-evs.com
Journal of Equine Veterinary Science 100 (2021) 103501
https://doi.org/10.1016/j.jevs.2021.103501
38 Y chromosome genetic variation and deep genealogies provide new
insights on Lipizzan sire lines
L. Radovic
1
,
2
,
∗
, V. Remer
1
, S. Reiter
1
, E. Bozlak
1
,
2
, S. Felkel
3
, G. Grilz-Seger
1
, G. Brem
1
,
B. Wallner
1
1
University of Veterinary Medicine Vienna, Vienna, 1210, Austria
2
Vienna Graduate School of Population Genetics, Vienna, 1210, Austria
3
University of Life Sciences and Natural Resources, Vienna, 1180, Austria
The male-specific region of the Y chromosome (MSY) is pa-
ternally inherited and enables to trace patrilines through genetic
analysis. MSY markers and haplotypes in combination with pedi-
gree information provide precise insights into genealogical sys-
tems. While the use of the Y chromosomal genetic genealogy is
well established in humans, we recently could develop an equine
MSY marker system from NGS data capable to perform a genetic
fine-scale analysis of sire lines in horses. This approach has been
successfully applied to solve genealogical questions in the English
Thoroughbred. In this work, we study sire line genealogies in Lipiz-
zan horses by combining MSY and pedigree information. The Lip-
izzan breed is characterized by deep pedigree records that trace
back to founder sires born in the 18th and early 19t h century. We
inferred Lipizzan specific MSY haplotypes based on NGS data from
15 Lipizzan males mapped to a 5.8 Mb horse MSY draft reference
(LipY764). Haplotype distribution was then studied by screening
52 selected haplotype determining variants in 132 stallions rep-
resenting the 8 existing Lipizzan sire lines. Samples were derived
from 7 European Lipizzan state stud farms. Genomic DNA was iso-
lated from blood and genotyping was performed with the KASP
genotyping method. MSY haplotype spectra in Lipizzans were com-
pared with other breeds, and the results confirmed a presumed
Arabian and Spanish origin in 2 Lipizzan sire lines. Surprisingly,
horses from the remaining 6 sire lines grouped into haplogroup
Tb. This haplogroup was recently characterized as a signature of
the Turkoman horse, and the allocation of Lipizzans into Tb points
to a possible Turkish influence in the Lipizzans. In addition, we de-
tected 6 haplotypes that arose via de novo mutation in the time-
frame of pedigree documentation. In 2 sire lines the MSY pattern
in sub-lines did not accord with the paternal lineage documen-
tation. In 5 horses belonging to a side-branch of the Favory line,
a unique haplotype was detected. This finding indicates another
foundation sire in the Lipizzan horse. In conclusion, MSY haplotyp-
ing confirmed historic breed documentation and offered new in-
sights on the male breed ancestry. Furthermore, we demonstrated
that our approach is suitable to study sire lines on a genealogical
scale. MSY analysis can be used for studying the paternal ances-
try and as a forensic tool, to solve open questions in the paternal
lineages, even if they occurred multiple generations back in time.
Keywords: Lipizzan, Y Chromosome, Sire Lines
... Due to the close association with the patriline, the MSY became the most popular marker in human genetic genealogy [17,18]. In horses, MSY analysis could reveal the influence and origin of breeding stallions, similar to human family history research, or even be useful for forensic applications [19]. ...
Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses
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  • Jan 2022
The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.
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