Research

Research: Biomedical Genomics

Our lab focuses on studying the heredity basis of equine congenital defects and economically significant traits in domestic animals (mainly the horse); interrelationships of inbreeding, genetic polymorphism, and reproductive performance in horses; population genetics of feral horses; comparative aspects of genetic variation in horses under human selection and under natural selection; genetic aspects of captivity; genetics of domestication. Management of genetic polymorphism in small populations and conservation of rare breeds; genetic relationship among domestic horse breeds; changes in gene regulation based upon environmental factors; gene mapping of the horse.

Selected Publications

• Indigenous Greek Horse Breeds: Genetic Structure and the Influence of Foreign Breeds. Emilio Katsoulakou, M., Kostaras, N., Kjöllerström, H.J., Laliotis, G.P., Bizelis, I., Cothran, E.G., Juras, R., Koutsouli, P. Agriculture. 2025; 15(5), 1-21. https://doi.org/10.3390/agriculture15050540

• The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome. Radovic,L., Remer, V., Rigler, D., Bozlak, E., Allen, L., Brem, G., Reissman, M., Brockmann, G.A., Ropka-Molik, K., Stefaniuk-Szmukier, M., Kalinkova, L., Kalashnikov, V.V., Zaitev, A.M., Raudsepp, T., Castaneda, C., von Butler-Wemken, I., Rosa, L.P., Brooks, S.A., Novoa‐Bravo, M., Kostaras, N., Abdurasulov, A., Antczak, D.F., Miller, D.C., Lopes, M.S., Machado, A.C., Lindgren, G., Juras, R., Cothran, G., Wallner, B. PNAS 121 (49) e2414408121. https://doi.org/10.1073/pnas.2414408121

• Naturally occurring horse model of miscarriage reveals temporal relationship between chromosomal aberration type and point of lethality. Lawson, J.M., Salem, S.E., Miller. D. , Kahler, A., van den Boer, W.J., Shilton, C.A., Sever, T., Mouncey, R.R., Ward, J., Hampshire, D.J., Foote, A.K., Bryan, J.S., Juras, R., Pynn, O.D., Davis, B.W., Bellone, R.R., Raudsepp,T., Mestre, A.M. DevelopmentalBiology 2024 121 (33) e2405636121. https://doi.org/10.1073/pnas.2405636121

• Relatedness and genomic inbreeding in a sample of Timor ponies. Doris E. Fröhlich, D.E., Wallner, B., Juras, R., Cothran, E.G., Velie, B.D. Journal of Equine Veterinary Science 2024 Volume 133, 105016. https://doi.org/10.1016/j.jevs.2024.105016
• Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation. Stroupe, S., Martone, C., McCann, B., Juras, R., Kjöllerström, H.J., Raudsepp, T., Beard, D., Davis, B.W., Derr, J.N. G3 Genes|Genomes|Genetics 2023 jkad156. https://doi.org/10.1093/g3journal/jkad156
• Genomic studies of Thoroughbred stallions’ ‘idiopathic’ subfertility. Castaneda, C., Hernandez-Aviles, C., Love, C.C., Varner, D.D., Juras, R., Davis, B.W., Raudsepp, .T. Journal of Equine Veterinary Science 2023 Volume 125, 104581. https://doi.org/10.1016/j.jevs.2023.104581
• Refining the evolutionary tree of the horse Y chromosome. Bozlak, E., Radovic, L., Remer, V., Rigler, D., Allen, L., Brem, G., Stalder, G., Castaneda, C., Cothran, G., Raudsepp, T., Okuda, Y., Moe, K., Moe, H., Kounnavongsa, B., Keonouchanh, S., Van, N., Vu, V., Shah, M., Nishibori, M., Kazymbet, P., Bakhtin, M., Zhunushov. A., Paul, R.., Dashnyam, B., Nozawa, K., Almarzook, S., Brockmann, G., Reissmann, M., Antczak, D., Miller, D., Sadeghi, R., von Butler-Wemken, I., Kostaras, N., Han, H., Manglai, D., Abdurasulov, A., Sukhbaatar, B., Ropka-Molik, K., Stefaniuk-Szmukier, M., Lopes, M., Câmara Machado, A., Kalashnikov, V., Kalinkova, L., Zaitev, A., Novoa‐Bravo, M., Lindgren, G., Brooks, S., Rosa, L., Orlando, L., Juras, R., Kunieda, T. & Wallner, B. Sci Rep 2023 13, 8954 https://doi.org/10.1038/s41598-023-35539-0
• Genetic Variability of Small Horse Populations from Greek Islands. Emilio Katsoulakou, M. , Papachristou, D. , Kostaras, N. , Laliotis, G. , Bizelis, I. , Cothran, E. G. , Juras, R. & Koutsouli, P. Black Sea Journal of Agriculture. 2023 6 (2) , 117-125 . DOI: 10.47115/bsagriculture.1165045
• The Second Case of Non-Mosaic Trisomy of Chromosome 26 with Homologous Fusion 26q;26q in the Horse. Ghosh, S., Kjöllerström, J., Metcalfe, L., Reed, S., Juras, R., Raudsepp, T. Animals 2022, 12, 803 https://doi.org/10.3390/ani12070803
• Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Remer V, Bozlak E, Felkel S, Radovic L, Rigler D, Grilz-Sege, G, Stefaniuk-Szmukier M, Bugno-Poniewierska M, Brooks S, Miller DC, Antczak DF, Sadeghi R, Cothran G, Juras R, Khanshour AM, Rieder S, Penedo MC, Waiditschka G, Kalinkova L, Kalashnikov VV, Zaitsev AM, Almarzook S, Reißmann M, Brockmann GA, Brem G, Wallner,B Genes 2022, 13, 229. https://doi.org/10.3390/genes13020229
• Thoroughbred stallion fertility is significantly associated with FKBP6 genotype but not with inbreeding or the contribution of a leading sire. Castaneda C, Juras R, Kjöllerström J, Hernandez Aviles C, Teague SR, Love CC, Cothran EG, Varner DD, Raudsepp T Anim Genet. 2021; doi: 10.1111/age.13142
• An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome. Jevit MJ, Davis BW, Castaneda C, Hillhouse A, Juras R, Trifonov VA, Tibary A, Pereira JC, Ferguson-Smith MA, Raudsepp T. Genes. 2021; 12(1):105. DOI: 10.3390/genes12010105 PMID: 33467186
• Two Novel Cases of Autosomal Translocations in the Horse: Warmblood Family Segregating t(4;30) and a Cloned Arabian with a de novo t(12;25). Ghosh S, Carden CF, Juras R, Mendoza MN, Jevit MJ, Castaneda C, Phelps O, Dube J, Kelley DE, Varner DD, Love CC, Raudsepp T. Cytogenet Genome Res. 2020 Dec 16:1-10. doi: 10.1159/000512206. PMID: 33326979
• Novel Complex Unbalanced Dicentric X-Autosome Rearrangement in a Thoroughbred Mare with a Mild Effect on the Phenotype. Mendoza MN, Schalnus SA, Thomson B, Bellone RR, Juras R, Raudsepp T. Genome Res. 2020 Nov 5:1-13. doi: 10.1159/000511236. PMID: 33152736
• Efficient correction of a deleterious point mutation in primary horse fibroblasts with CRISPR-Cas9. Pinzon-Arteaga C, Snyder MD, Lazzarotto CR, Moreno NF, Juras R, Raudsepp T, Golding MC, Varner DD, Long CR. Sci Rep 10, 7411 (2020). https://doi.org/10.1038/s41598-020-62723-3
• Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites. Funk SM, Guedaoura S, Juras R, Raziq A, Landolsi F, Luís C, Martínez AM, Mayaki AM, Mujica F, Oom MM, Ouragh L, Stranger YM, Vega‐Pla JL, Cothran EG. Ecology and Evolution. 2020;00:1–19 DOI: 10.1002/ece3.6195
• Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines. Castaneda C, Juras R, Khanshour A, Randlaht I, Wallner B, Rigler D, Lindgren G, Raudsepp T, Cothran EG. Genes (Basel). 2019 Aug 20;10(8). PMID: 31434327
• Comparative FISH-Mapping of MC1R, ASIP, and TYRP1 in New and Old World Camelids and Association Analysis With Coat Color Phenotypes in the Dromedary (Camelus dromedarius).  Alshanbari F, Castaneda C, Juras R, Hillhouse A, Mendoza MN, Gutiérrez GA, Ponce de León FA, Raudsepp T. Front Genet. 2019 Apr 16;10:340. PMID: 31040864
• Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park.  Ovchinnikov IV, Dahms T, Herauf B, McCann B, Juras R, Castaneda C, Cothran EG. PLoS One. 2018 Aug 1;13(8):e0200795. PMID: 30067807
• A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse.  Morgenthaler C, Diribarne M, Capitan A, Legendre R, Saintilan R, Gilles M, Esquerré D, Juras R, Khanshour A, Schibler L, Cothran G. Genet Sel Evol. 2017 Nov 15;49(1):85. PMID: 29141579
• The legend of the Canadian horse: genetic diversity and breed origin. Khanshour A, Juras R, Blackburn R, Cothran EG. J Hered. 2015 Jan-Feb;106(1):37-44. PMID: 25416795
• Copy number variation in the horse genome. Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson DL, Chowdhary BP, Raudsepp T. PLoS Genet. 2014 Oct 23;10(10):e1004712. doi: 10.1371/journal.pgen.1004712. eCollection 2014 Oct. PMID: 25340504
• Worldwide frequency distribution of the ‘Gait keeper’ mutation in the DMRT3 gene. Promerová M, Andersson LS, Juras R, Penedo MC, Reissmann M, Tozaki T, Bellone R, Dunner S, Hořín P, Imsland F, Imsland P, Mikko S, Modrý D, Roed KH, Schwochow D, Vega-Pla JL, Mehrabani-Yeganeh H, Yousefi-Mashouf N, G Cothran E, Lindgren G, Andersson L. Anim Genet. 2014 Apr;45(2):274-82. doi: 10.1111/age.12120. Epub 2014 Jan 21. PMID: 24444049
• Microsatellite analysis of genetic diversity and population structure of Arabian horse populations. Khanshour A, Conant E, Juras R, Cothran EG. J Hered. 2013 May-Jun;104(3):386-98. doi: 10.1093/jhered/est003. Epub 2013 Feb 28. PMID: 23450090
• Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL. Andersson LS, Wilbe M, Viluma A, Cothran G, Ekesten B, Ewart S, Lindgren G. PLoS One. 2013 Sep 23;8(9):e75639. doi: 10.1371/journal.pone.0075639. eCollection 2013. PMID: 24086599
• Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Andersson LS, Larhammar M, Memic F, Wootz H, Schwochow D, Rubin CJ, Patra K, Arnason T, Wellbring L, Hjälm G, Imsland F, Petersen JL, McCue ME, Mickelson JR, Cothran G, Ahituv N, Roepstorff L, Mikko S, Vallstedt A, Lindgren G, Andersson L, Kullander K. Nature. 2012 Aug 30;488(7413):642-6. doi: 10.1038/nature11399. PMID: 22932389
• A microsatellite analysis of five Colonial Spanish horse populations of the southeastern United States. Conant EK, Juras R, Cothran EG. Anim Genet. 2012 Feb;43(1):53-62. doi: 10.1111/j.1365-2052.2011.02210.x. Epub 2011 May 23. PMID: 22221025
• Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations. Prystupa JM, Juras R, Cothran EG, Buchanan FC, Plante Y. Animal. 2012 Jan;6(1):19-30. doi: 10.1017/S1751731111001212. PMID: 22436150
• Genetic diversity in the modern horse illustrated from genome-wide SNP data. Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MC, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. PLoS One. 2013;8(1):e54997. doi: 10.1371/journal.pone.0054997. Epub 2013 Jan 30. PMID: 23383025
• Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing. Khanshour AM, Cothran EG. BMC Genet. 2013 Sep 13;14:83. doi: 10.1186/1471-2156-14-83. PMID: 24034565
• Targeted analysis of four breeds narrows equine Multiple Congenital Ocular Anomalies locus to 208 kilobases. Andersson LS, Lyberg K, Cothran G, Ramsey DT, Juras R, Mikko S, Ekesten B, Ewart S, Lindgren G. Mamm Genome. 2011 Jun;22(5-6):353-60. doi: 10.1007/s00335-011-9325-7. Epub 2011 Apr 5. PMID: 21465164
• Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds. Bömcke E, Gengler N, Cothran EG. Genet Mol Biol. 2011 Jan;34(1):68-76. doi: 10.1590/S1415-47572010005000113. Epub 2011 Mar 1. PMID: 21637546
• Genetic analysis of the Venezuelan Criollo horse. Cothran EG, Canelon JL, Luis C, Conant E, Juras R. Genet Mol Res. 2011 Oct 7;10(4):2394-403. doi: 10.4238/2011.October.7.1. PMID: 22002132
• Maternal lineages in native Canadian equine populations and their relationship to the Nordic and Mountain and Moorland pony breeds. Prystupa JM, Hind P, Cothran EG, Plante Y. J Hered. 2012 May-Jun;103(3):380-90. doi: 10.1093/jhered/ess003. Epub 2012 Apr 13. PMID: 22504109
• XX/XY Blood lymphocyte chimerism in heterosexual dizygotic twins from a American Bashkir Curly horse. Case Report. Juras R, Raudsepp T, Das PJ, Conant E, Cothran EG 2010. Case Report. Journal of Equine Veterinary Science, 30 (10): 575-580
• Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation. Luís C, Juras R, Oom MM, Cothran EG. Anim Genet. 2007 Feb;38(1):20-7. PMID: 17257184
• Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management. Luís C, Cothran EG, Oom MM. J Hered. 2007 May-Jun;98(3):232-7. Epub 2007 Apr 2. PMID: 17404326
• A missense mutation in PMEL17 is associated with the Silver coat color in the horse. Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S, Lindgren G. BMC Genet. 2006 Oct 9;7:46. PMID: 17029645
• Genetic structure and phylogenetic relationships of the Polish Heavy horse. Iwańczyk E, Juras R, Cholewiński G, Cothran EG. J Appl Genet. 2006;47(4):353-9. PMID: 17132900
• Limited number of patrilines in horse domestication. Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H. Nat Genet. 2004 Apr;36(4):335-6. Epub 2004 Mar 14. PMID: 15034578
• Genetic Analysis of Three Lithuanian Native Horse Breeds. Juras R, Cothran EG, Klimas R. Acta Agriculturae Scandinavica, Section A – Animal Science Volume 53, Issue 4, 2003. Pages 180-185. DOI: 10.1080/09064700310012971
• Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism. Yang YH, Kim KI, Cothran EG, Flannery AR. Biochem Genet. 2002 Jun;40(5-6):175-86. PMID: 12137332
• Rejection of MITF and MGF as the genes responsible for appaloosa coat colour patterns in horses. Terry RB, Bailey E, Lear T, Cothran EG. Anim Genet. 2002 Feb;33(1):82-4. No abstract available. PMID:11849149
• Genetic differentiation associated with gait within American standardbred horses. Cothran EG, MacCluer JW, Weitkamp LR, Bailey E. Anim Genet. 1987;18(4):285-96. PMID: 3481678
• Genetic analysis of three South African horse breeds. Cothran EG, van Dyk E. J S Afr Vet Assoc. 1998 Dec;69(4):120-5. PMID: 10192084
• Inbreeding and reproductive performance in standardbred horses. Cothran EG, MacCluer JW, Weitkamp LR, Pfennig DW, Boyce AJ. J Hered. 1984 May-Jun;75(3):220-4. PMID: 6736603