High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia

Abstract

The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia's role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey.

Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

“…Rather, the presence of only six Y chromosome haplotypes (HTs) in modern European horse breeds [2] and the limited microsatellite variability [11][12][13] suggest an extremely low effective population size of males. The decline of Y chromosome diversity in horses likely started about 5,500 years ago with genetic bottlenecks during the domestication process [14,15] and was further enhanced by multiple prehistoric and historic waves of migration [16][17][18]. Most so-called ''modern horse breeds'' are the result of centralized and organized horse breeding over the past few hundred years [19].…”

“…While this finding seems to contradict our hypothesis that there were two distinct male lineages for the Oriental founder populations, it might be explained by incomplete lineage sorting in ancestral populations or by an underestimation of private alleles. It might also simply reflect the inability of European horse traders on the Oriental horse markets in the 19 th century to accurately identify ''purebred'' Arabian stallions [16,17]. Variants specific to focal lines will be key to further studies of high-resolution, unbiased horse paternal genealogies.…”

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

“…Most studies of horses that have utilized STRUCTURE have examined a small number of breeds, often from a specific geographic locality (Barcaccia et al, 2013; Berber et al, 2014; Bömcke, Gengler, & Cothran, 2011; Conant et al, 2012; Cothran et al, 2011; Galov et al, 2013; Janova et al, 2013; Khanshour, Conant, et al, 2013; Khanshour et al, 2015; Koban et al, 2012; Kusza et al, 2013; Lopes et al, 2015; Mackowski, Mucha, Cholewinski, & Cieslak, 2015; Mujica, 2006; Pablo Gómez et al, 2017; Pires et al, 2016; Prystupa, Juras, Cothran, Buchanan, & Plante, 2012; Rendo, Iriondo, Manzano, & Estonba, 2012; Sereno, Sereno, Vega‐Pla, Kelly, & Bermejo, 2008; Tozaki et al, 2003; Uzans, Lucas, McLeod, & Frasier, 2015). The ∆ K obtained in these studies appeared reasonable for the number of breeds.…”

Türkiye’deki Alaca Atların mtDNA D-Loop Dizi Analizi İle Genetik Yapılarının Araştırılması

“…In a study conducted using the mitochondrial control region to determine the genetic variation in Ayvacık Pony, Malakan, Hınıs and Canik horses; the haplogroups showed high diversity [16] . As a result of mtDNA sequence analysis of 5 horse breeds in Turkey, 68 polymorphic regions and 151 haplotypes (Haplotype diversity, Hd: 0.9866±0.0017, nucleotide diversity, Pi: 0.021±0.00036, and average nucleotide diversity, k: 8,006) were found [17] .…”