Abstract
The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.
Highlights
Mitochondrial DNA and the paternally transmitted portion of the Y chromosome (NRY) are inherited uniparentally and do not recombine
Gene conversion i.e. the transfer of a short sequence from the homologous, but non-recombining region on the X- to the Ychromosome can contribute to Y-chromosomal variation [4,5]. Mitochondrial DNA (mtDNA)- and NRY-variant distributions have been widely analysed in humans and in a broad range of wild and domesticated animals to provide indications of the origin of species, domestication processes, the characterization of genetic diversity within and between populations and sex specific demographic behaviors [6]
Y-chromosomal specificity was checked by comparative amplification of the long-range PCR (LRP) on male and female DNA (Fig. S2)
Summary
Mitochondrial DNA (mtDNA) and the paternally transmitted portion of the Y chromosome (NRY) are inherited uniparentally and do not recombine. They accumulate mutations, such as single nucleotide polymorphisms (SNPs), insertions and deletions (Indels) and structural rearrangements [1,2,3]. Genealogies inferred from the distribution of mutations on mtDNA and NRY haplotypes reflect gender-specific population genetic forces. MtDNA- and NRY-variant distributions have been widely analysed in humans and in a broad range of wild and domesticated animals to provide indications of the origin of species, domestication processes, the characterization of genetic diversity within and between populations and sex specific demographic behaviors [6]. Y-chromosomal and mtDNA variation has been used to study the domestication and population structure of the domestic dog [8,9,10], pig [11,12], sheep [13] and cattle [14]
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