The horse Y chromosome as an informative marker for tracing sire lines

Abstract

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski’s horses. Among domestic horses we confirmed the predominance of a young’crown haplogroup’ in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse ‘Galopin’, born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

A First Y-Chromosomal Haplotype Network to Investigate Male-Driven Population Dynamics in Domestic and Wild Bactrian Camels

“…Felkel et al (2019) calculated a mutation rate of 1.68 × 10 -8 mutations/site/generation for the horse Y based on deep pedigrees and this rate is highly similar to the genome-wide estimate in humans (Kong et al, 2012). Since no pedigrees have been available to calculate a camel specific mutation rate, we used the horse rate to date nodes in the resulting camel Y network using rho statistics implemented in Network (for details see Supplementary Methods; variants and contigs used for dating are indicated in Supplementary Tables S3, S4, respectively; the haplotype network based on variants used for dating is shown in Supplementary Figure S6).…”

“…We mapped the Illumina short reads from the eight male and six female Bactrian camels to the raw assembly output using bwa aln, removed PCR duplicates and filtered for mapping quality > 20 using samtools. We next splitted the assembly into 50 bp windows and followed the probabilistic approach of Felkel et al (2019), which uses the differences of normalized mapping coverages in males and females to classify the windows into single copy (scY) and multi copy (mcY) MSY and not MSY (nonMSY). For the classification we did not consider DC269 on which the reference is based.…”

“…We and others have recently shown the value that de novo assemblies of the MSY, generated from short read next generation sequencing (NGS) data, had for tracing male lineages (Wallner et al, 2017). We also described in detail the need to accurately define single copy regions in the assembly (Felkel et al, 2019) to unambiguously call variants in these regions only. With this approach ( de novo assembly and SNV calling in single copy MSY regions) we elevated the resolution and accuracy of paternal lineage tracing in horses to a level similar to that in humans (Wallner et al, 2017; Felkel et al, 2019), where MSY haplotype (HT) trajectories are well described (Jobling and Tyler-Smith, 2017).…”

“…To trace the paternal lineages and reconstruct male-driven population dynamics in Old World camels, specifically in the highly endangered wild camel, we adopted the approach recently described in horses (Wallner et al, 2017; Felkel et al, 2019) and de novo assembled the Bactrian camel MSY from short read NGS data. The assembly was used as a reference for mapping and single copy MSY variant calling using short read data from five wild and three domestic Bactrian camels one dromedary as outgroup.…”

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).…”