G C A T T A C G G C A T genes Article Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines Caitlin Castaneda 1 , Rytis Juras 1, Anas Khanshour 2, Ingrid Randlaht 3, Barbara Wallner 4, Doris Rigler 4, Gabriella Lindgren 5,6 , Terje Raudsepp 1,* and E. Gus Cothran 1,* 1 College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA 2 Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA 3 Estonian Native Horse Conservation Society, 93814 Kuressaare, Saaremaa, Estonia 4 Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria 5 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden 6 Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium * Correspondence:
[email protected] (T.R.);
[email protected] (E.G.C.) Received: 9 August 2019; Accepted: 13 August 2019; Published: 20 August 2019 Abstract: The Estonian Native Horse (ENH) is a medium-size pony found mainly in the western islands of Estonia and is well-adapted to the harsh northern climate and poor pastures. The ancestry of the ENH is debated, including alleged claims about direct descendance from the extinct Tarpan. Here we conducted a detailed analysis of the genetic makeup and relationships of the ENH based on the genotypes of 15 autosomal short tandem repeats (STRs), 18 Y chromosomal single nucleotide polymorphisms (SNPs), mitochondrial D-loop sequence and lateral gait allele in DMRT3.