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

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.