Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds

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.

Figure 1. The localisation of the BAC-clones on the horse Y chromosome (ECAY).

The heterochromatic, male specific euchromatic (MSY) and the pseudoautosomal region (PAR) of the horse Y chromosome are shown at the top. The seven MSY contigs (I-VII) described in the study of Raudsepp et al., 2004 are illustrated in the middle and indicated as boxes; gaps between contigs are spanned with dotted lines. The locations of some MSY genes are given (italics). The chromosomal position of each BAC clone used in this study is marked by an arrow. On the bottom the approximate positions of the BAC clones on the horse Y-chromosomal gene map after Paria et al. 2011 are indicated.

Figure 2. Haplotype network of the six modern and two Przewalski horse HTs.

Circles represent the haplotypes with the area proportional to the observed frequency in 20 male horses in the initial Y-chromosomal sequence analysis (Table S4). HT1, n = 7 (three Lipizzan, two Arabian, one Shetland pony, one Shire horse); HT2, n = 5 (five Lipizzan); HT3, n = 3 (one Thoroughbred, one Trakehner, one Quarter horse); HT 4 (one Icelandic horse), HT5 (one Norwegian Fjord horse), HT6 (one Shetland pony), HTPrz1 (one Przewalski horse), HTPrz2 (one Przewalski horse). A dashed line between the haplotypes indicates, that the polymorphism is located on the highly variable contig YE3, which was omitted when estimating divergence time and nucleotide diversity.

Figure 3. Geographic distribution and history of Y-haplotypes in modern horse breeds.

(a) Geographic distribution of Y-chromosomal haplotypes in a set of modern horse breeds. Only a few important breeds are specified, the full list with information on breeds and HT frequencies is given in Table S7. (b) Origin of modern domestic horse founders deduced from pedigree data. Each founder is represented by a drum with its size proportionally to the number of offspring in the dataset. The number in the drums serve as founder identifiers. Detailed information on founders (name, year of birth, breed, origin, information on import) is listed in Table 1. (c) Male introgression routes deduced from the pedigree and the distribution of HT2 and HT3 in our dataset. HT2 (yellow arrows) arrived from South-East at early times and has been spread during the Neapolitan and Oriental introgression waves, but did not reach Northern Europe and the Iberian peninsula. The English wave in red is well documented through pedigree data and the spread of HT3 (red arrows). Due to the ubiquitous occurrence of HT1, this haplotype is not considered. The black solid lines reflect the limits of the observation of HT2 and HT3.

Figure 4. Pedigree of Darley Arabians progeny depicting the origin of HT3 from HT2.

Breeds of analysed males are listed on the bottom and the haplotypes of their ancestors are reconstructed (HT2-yellow, HT3-red, unknown-grey). Selected famous stallions are shown by name; dotted lines connect relatives where at least one ancestor is omitted. No descendants from “Pot8os” and “Waxy” were available apart from “Whalebone, 1807”. The mutation leading to HT3 must have occurred either in the germline of stallion “Eclipse” or in his son “Pot8os” or in his grandson “Waxy” and rose to very high frequency in the English Thoroughbred and many sport horse breeds through the progeny of the stallion “Whalebone”.