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. 2022 Jan 26;13(2):229.
doi: 10.3390/genes13020229.

Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses

Affiliations

Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses

Viktoria Remer et al. Genes (Basel). .

Abstract

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.

Keywords: Arabian horse; Y chromosome; foundation sire; genotyping; haplotype; horse breeding; male genealogy; paternal lineage tracing; pedigree.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of the data; in the writing of the manuscript; or in the decision to publish the results. The statements made herein are solely the responsibility of the authors.

Figures

Figure 1
Figure 1
NGS HT Network. The MSY HT network from 118 WGS sequenced males and 39 TES males, based on a total of 1639 variants (281 crown, 1358 outside the crown). HTs are indicated as circles, with circle size being proportional to frequency. HT-IDs and sample information are provided in Table S1. HTs first described in this study based on TES data are shown in bold. Variants are indicated on branches and underlined when selected for genotyping. The position of the crown MRCA is marked with a cross. The 14 crown HGs are indicated in the outer circle, with the breeds listed beside them. Blue HTs were detected in Arabians, and light blue HTs were detected in a horse that traced back to an imported Arabian in the paternal lineage. The signatures of the three founders of the English Thoroughbred (Tb-oB1, Tb-oB31, and Tb-d) are marked with red lines.
Figure A1
Figure A1
Target-enriched sequencing depth.
Figure A2
Figure A2
NGS data analysis pipeline. Two NGS data sets were merged to produce the final structure: mappings of 118 WGS males to LipY764 from a previous study and newly generated TES data of 39 males. The 77 novel variants ascertained in the TES dataset were merged with 2199 previously defined variants resulting in a total of 2267 variants. Those variants were genotyped in the mapping files, missing positions imputed, and HTs constructed by concatenating the polymorphic sites. HTs were visualized in a network format. A total of 118 variants was selected for genotyping. Detailed descriptions of the workflow, including programs, and parameters, is provided in the Material and Methods section.
Figure 2
Figure 2
MSY HTs in Arabian sire lines. Simplified crown HT network based on 118 variants. Genotyping results from 145 males are shown in blue circles with size proportional to frequency. Details on samples are given in Table 1, and Table S5 (samples are indicated in Column J; Foundation sires shown in Column AI). Foundation sires are shown for each HT, with the number of samples for each line in parenthesis. HTs/foundation sires that are only active in breeds other than Arabians are given in light blue. Genealogies of the English Thoroughbred founders are outlined with red crosses and the thoroughbred specific subhaplogroups with the branches in red.
Figure 3
Figure 3
Genealogical cases. (a) Paternal genealogies of 15 genotyped male horses after Siglavy, 1810. (b) Paternal genealogies of eight genotyped male horses after Ilderim db. Dotted lines indicate that at least one generation is omitted. Abbreviation of horse breeds other than Arabian is given by: L = Lipizzaner, ShA = Shagya Arabian, Trak = Trakehner, AA = Anglo Arabian. The number of genotyped horses and HTs is listed on the bottom (dark HTs were detected in Arabians, light blue HTs in other breeds). The complete tail-male line reconstruction is provided in Table S5.
Figure 4
Figure 4
MSY Haplotypes in globally active Arabian lines, Middle Eastern Arabians, and other breeds. Haplogroup (bold) and haplotype distribution in breed or breed groups in absolute numbers (N = total number). Thoroughbred HG/HTs are marked in red, Arabian in blue, and Akhal Teke/Turkoman in yellow. The Tb-oB1* subhaplogroup was detected in Thoroughbreds, Akhal Teke/Turkoman, and in a small subset of Arabians, but the ancestry of horses carrying this haplogroup remains unresolved.

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