Admixture in Horse Breeds Illustrated from Single Nucleotide Polymorphism Data César Torres, Yaniv Brandvain University of Minnesota, Department of Plant Biology, LSSURP Sciences Program INTRODUCTION More than 300 horse breeds exist in the modern world. Many of these horse breeds are thought to have closely related evolutionary paths, but with the horse genome being sequenced recently (2007), genome-wide single nucleotide polymorphism (SNP) studies confirming evolutionary relationships are lacking. This project determines whether there is admixture between horse breeds that are thought to be evolutionary related by using the program Treemix to create a phylogenic tree, which illustrates admixture in the multiple horse breeds. Allele frequencies across 34,648 SNP sites formatted from the genotype of 36 breeds (795 individuals in total) obtained with an Illumina Beadchip, were used as the input data for the program. We found evidence for admixture events between several breeds of horses, most of which were admixed with the Thoroughbred. Some horses were found to not have evidence of admixture. While for the Caspian, a breed rediscovered in 1965, some admixture evidence was found, implying they might not be 100% pure Caspian. This was confirmed with F3 statistics tests (three population test). These findings will facilitate future studies of the origin of the domestic horse and its evolutionary path by providing new insights on each breed and how they are related to each other. In the future we will use denser chips to obtain more SNP sites allowing us to find regions of introgression and determine whether or not they are coding sequences. METHODS Samples of 36 horse breeds (795 individuals) genotyped on the Illumina 50k SNP Beadchip (DNA Microarray) were obtained and formatted into allele frequencies. Out of the 50k SNP sites, only 34,648 were used due to triple allelic sites being removed. The program Treemix used the allele frequencies at the 34k SNP sites to infer the patterns of population splits and admixture. The program uses the similarities between allele frequencies to determine which horse breeds are related to each other and if there is admixture between any of them illustrating it with a red arrow. These trees were used to base our hypotheses. F3 statistic tests (also known as three population tests) were used to further confirm if there was admixture between the horse breeds. This test compares three populations or breeds in the form of (A; B, C), where a negative F3 statistic value implies admixture in individuals of the group A. RESULTS FIGURE 1: Treemix tree with multiple admixture arrows. Thoroughbred can be seen involved in multiple admixture patterns. FIGURE 2: F3 statistic results for horses thought to have admixture from the Thoroughbred. FIGURE 3: F3 statistic results for horses thought to have no admixture. CONCLUSIONS A diverse number of horse breeds including the Quarter Horse, Swiss Warmblood, Paint Horse and Hanoverian; seem to have admixture with the Thoroughbred from US and UK. This can be confirmed by their negative f3 statistic values ranging as low as for the Swiss Warmblood. A very interesting result is that the Thoroughbred US seemed to yield a more negative f3 statistic value than the Thoroughbred UK when compared with the Quarter Horse. This implies that the Thoroughbred US might have some admixture with the Quarter Horse. Also both the Thoroughbred US and Thoroughbred UK were shown to have admixture from each other. In addition, no evidence was found of admixture in the Mangalarga Paulista, Exmoor, North Swedish Horse, Puerto Rican Paso Fino, Arabian or Icelandic, implying that these breeds might be pure. As of the Caspian breed, few negative f3 statistic values were found, illustrating traces of admixture. This is evidence for thinking that the horses rediscovered might not be pure Caspian horses. FUTURE PLANS Since a higher number of SNP sites are needed to determine regions of introgression, denser chips will be used. Denser chips will also allow to determine whether or not these sites are are coding sequences. Linkage disequilibrium dating can be used to determine at what time the breeds’ history the admixture occurred. REFERENCES/ ACKNOWLEDGMENTS Pickrell and Pritchard (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics. In Press. Sponsored by NSF-REU in Molecular Genetics & Proteomics Funded by UPR-PRISE Program NIH Grant #R25GM A A A A B B No admixture 50% snps Breed 1 Breed 2 Breed 3 A A A A B B Admixture from Breed 3 to Breed 2 <50% snps >50% snps Breed 1 Breed 2 Breed 3 Admixture among horse breeds F3 Rank F3 value (<0 suggests admixture) o Quarter Horse ; Thoroughbred, _______ o Swiss Warmblood ; Thoroughbred, _______ o Paint Horse ; Thoroughbred, _______ o Hanoverian ; Thoroughbred, _______ o Other F3 Breeds: Putatively pure horse breeds Mangalarga Paulista Exmoor North Swedish Horse Puerto Rican Paso Fino Arabian IcelandicCaspian