Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

Abstract

The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses.

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

“…Together with its inheritance from father to son, it is a highly informative marker for the paternal origin of species, populations or individuals with a much stronger phylogeographic differentiation than observed for mitochondrial or autosomal DNA. The highly informative Y-chromosomal markers are now widely exploited in population-genetic studies of humans (Jobling and Tyler-Smith, 2017; Kivisild, 2017), cattle (Edwards et al, 2011; Xia et al, 2019), horse (Wallner et al, 2017; Wutke et al, 2018; Felkel et al, 2019a) water buffalo (Zhang et al, 2016), sheep (Meadows and Kijas, 2009; Zhang et al, 2014), camel (Felkel et al, 2019b), pigs (Guirao-Rico et al, 2018) and dogs (Natanaelsson et al, 2006; Oetjens et al, 2018).…”

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

“…8(1): 40-46 ________________________________________________________________________________________________________ variation of pre-domestic horses (Lippold et al, 2011), no diversity was detected in the Y chromosome of domestic horses awhile (Brandariz-Fontes et al, 2013;Lindgren et al, 2004). In the last years, a few polymorphic sites were found in modern horses leading to a small number of haplotypes in contemporary domestic stallions (Ling et al, 2010;Wallner et al, 2013Wallner et al, , 2017Kreutzmann et al, 2014). This study addresses the maternal and paternal genetic variation of Kabardian horses -a breed with excellent endurance for mountain rides.…”

Synteny search identifies carnivore Y chromosome for evolution of male specific genes

“…Moreover, many mammalian genome projects have focused on females to obtain reliable X chromosome sequences (Hughes et al 2012). As a consequence, the complete sequences of Y chromosome have only been determined for a handful of mammals, such as humans (Homo sapiens) (Skaletsky et al 2003), chimpanzees (Pan troglodytes) (Hughes et al 2010), rhesus macaques (Macaca mulatta) (Hughes et al 2012), gorillas (Tomaszkiewicz et al 2016) (Western lowland gorilla), pigs (Sus scrofa) (Skinner et al 2016) and mice (Mus musculus) (Soh et al 2014), as well as partially sequenced for cattle (Bos taurus) (Chang et al 2013), dogs (Canis lupus familiaris), cats (Felis catus) (Li et al 2013), polar bears (Ursus maritimus) (Bidon et al 2015), horse (Equus caballus) (Wallner et al 2017), marmosets (Callithrix jacchus), opossums (Monodelphis domestica) and rats (Rattus norvegicus) (Bellott et al 2014).…”