Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

Eight Y chromosome genes show copy number variations in horses

Abstract. Copy number variations (CNVs), which represent a significant source of genetic diversity on the Y chromosome in mammals, have been shown to be associated with the development of many complex phenotypes, such as reproduction and male fertility. The occurrence of CNVs has been confirmed on the Y chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y chromosome (ECAY) genes are largely unknown. To demonstrate the copy number variations of Y chromosome genes in horses, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of the eukaryotic translation initiation factor 1A Y (EIF1AY), equine testis-specific transcript on Y 1 (ETSTY1), equine testis-specific transcript on Y 4 (ETSTY4), equine testis-specific transcript on Y 5 (ETSTY5), equine transcript Y4 (ETY4), ubiquitin activating enzyme Y (UBE1Y), sex determining region Y (SRY), and inverted repeat 2 Y (YIR2) across 14 Chinese domestic horse breeds in this study. Our results revealed that these eight genes were multi-copy; furthermore, some of the well acknowledged single-copy genes such as SRY and EIF1AY were found to be multi-copy in this research. The median copy numbers (MCNs) varied among different breeds for the same gene. The CNVs of Y chromosome genes showed different distribution patterns among Chinese horse breeds, indicating the impact of natural selection on copy numbers. Our results will provide fundamental information for future functional studies.

Decline of genetic diversity in ancient domestic stallions in Europe

Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.

Improved de novo genomic assembly for the domestic donkey

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.

Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers

Studies of mitochondrial DNA (mtDNA) as well as the non-recombining part of the Y chromosome help to understand the origin and distribution of maternal and paternal lineages. The Kabardian horse from Northern Caucasia which is well-known for strength, stamina and endurance in distance riding has a large gap in its breeding documentation especially in the recent past. A 309 bp fragment of the mitochondrial D-loop (156 Kabardian horses) and six mutations in Y chromosome (49 Kabardian stallions), respectively, were analyzed to get a better insight into breeding history, phylogenetic relationship to related breeds, maternal and paternal diversity and genetic structure. We found a high mitochondrial diversity represented by 64 D-loop haplotypes out of 14 haplogroups. The most frequent haplogroups were G (19.5%), L (12.3%), Q (11.7%), and B (11.0%). Although these four haplogroups are also frequently found in Asian riding horses (e.g. Buryat, Kirghiz, Mongolian, Transbaikalian, Tuvinian) the percentage of the particular haplogroups varies sometimes remarkable. In contrast, the obtained haplogroup pattern from Kabardian horse was more similar to that of breeds reared in the Middle East. No specific haplotype cluster was observed in the phylogenetic tree for Kabardian horses. On Kabardian Y chromosome, two mutations were found leading to three haplotypes with a percentage of 36.7% (haplotype HT1), 38.8% (haplotype HT2) and 24.5% (haplotype HT3), respectively. The high mitochondrial and also remarkable paternal diversity of the Kabardian horse is caused by its long history with a widely spread maternal origin and the introduction of Arabian as well as Thoroughbred influenced stallions for improvement. This high genetic diversity provides a good situation for the ongoing breed development and performance selection as well as avoiding inbreeding.

Asian horses deepen the MSY phylogeny

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.