08/03/2023

Publications:  

1. Todd E, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury J-M, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. Imputed genomes of historical horses provide insights into modern breeding.  iScience. In Press.

 

2. Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi H-R, Naboulsi R, Petersen JL, Lindgren G. Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Heredity. 2023. doi:10.1038/s41437-023-00624-7.

 

3. Valberg SJ, Williams Z, Finno CJ, Schultz A, Velez-Irizarry D, Henry M, Gardner K, Petersen JL. Type 2 polysaccharide storage myopathy in Quarter Horses is a novel glycogen storage disease causing exertional rhabdomyolysis.  Equine Veterinary Journal. 2023 55(4): 618-631. doi:10.1111/evj.13876

 

4. Peng SC, Dahlgren AR, Donnelly CG, Hales EN, Petersen JL, Bellone RR, Kalbfleisch T, Finno CJ. Functional annotation of the animal genomes: an integrated annotation resource for the horse.  PLoS Genetics. 2023 19(3):e1010468. doi:10.1371/journal.pgen.1010468.

 

5. Valberg SJ, Henry ML, Herrick KL, Velez-Irizarry, Finno CJ, Petersen JL. Absence of myofibrillar myopathy in Quarter Horses with a histopathologic diagnosis of type 2 polysaccharide storage myopathy and lack of association with commercial genetic tests. Equine Veterinary Journal. 2023 55(2):230-238. doi:10.1111/evj.13574.

 

6. Klouth E, Zablotski Y, Petersen JL, de Bruijn CM, Gröndahl G, Müller S, Goehring LS. Epidemiological Aspects of Equid Herpesvirus-associated Myeloencephalopathy (EHM) outbreaks. Viruses. 2022 14(11):2576.  doi:10.3390/v14112576.

 7.      Shilton CA, Townsend SS, Kahler A, Wathes CD, Castaneda C, Ghosh S, Davis BW, Raudsepp T, de Mestre AM. Microdeletions on chromosomes 2 and 20 are associated with equine early pregnancy loss. J Equine Vet Sci 2023 125, June, https://doi.org/10.1016/j.jevs.2023.104784. 8.      Kahler A, Mouncey R, Raudsepp T, de Mestre A. CfDNA of feto-placental origin is not detectable in plasma of pregnant mares by optimised sexing-qPCR. J Equine Vet Sci 2023 125, https://doi.org/10.1016/j.jevs.2023.104770. 9.      Ramirez-Agamez L, Castaneda C, Grahn RA, Hernandez-Aviles C, Raudsepp T, Love CC. A study on methods for preimplantation genetic diagnosis on equine embryos. J Equine Vet Sci 2023 125, June, https://doi.org/10.1016/j.jevs.2023.104673. 10.   Castaneda C, Hernandez-Aviles C, Love CC, Varner DD, Juras R, Davis BW, Raudsepp T. Genomic studies of Thoroughbred stallions’ ‘idiopathic’ subfertility. J Equine Vet Sci 2023 125, June, https://doi.org/10.1016/j.jevs.2023.104581. 11.   Batcher K, Varney S, Raudsepp T, Jevit MJ, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One, Accepted May 30, 2023.

 

12. Ward J, Raudsepp T, Levine D, Turner R. Theriogenology Query: Severe Hypospadias/Disorder of Sexual Development in a Miniature Equid Hybrid. JAVMA, accepted May 23, 2023, In press.


13. Kania J, Wilson K, Raudsepp T, Castaneda C, Jevit M, Horteloup P, Saklou N, Jula C, Funk R. Double cervices in a Gypsy Vanner mare. Clinical Theriogenology, published April 6, 2023; DOI: https://doi.org/10.58292/ct.v15.9395.

 

14. Shilton CA, Kahler A, Roach JM, Raudsepp T, de Mestre AM. Lethal variants of equine pregnancy: is it the placenta or foetus leading the conceptus in the wrong direction? Reprod Fertil Dev. 2022 Dec;35(2):51-69. doi: 10.1071/RD22239. PMID:

 

15. Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 (Bethesda). 2022 Dec 1;12(12): jkac278. doi: 10.1093/g3journal/jkac278. PMID:

 

16. Beaumont RE, Smith EJ, Zhou L, Marr N, Thorpe CT, Guest DJ. Exogenous interleukin-1 beta stimulation regulates equine tenocyte function and gene expression in three-dimensional culture which can be rescued by pharmacological inhibition of interleukin 1 receptor, but not nuclear factor kappa B, signaling. Molecular and Cellular Biochemistry. 2023. doi: 10.1007/s11010-023-04779-z.

 

17. Bailey E. Spotlight: Ancient DNA reveals an early adoption of horse culture by Native Americans. 2023. Trends in Genetics (in press)

 

18. Thieulent CJ, Carossino M, Balasuriya UBR, Graves K, Bailey E, Eberth J, Andrews FM, Keowen M,   Go YY  Development of a TaqMan^® allelic discrimination PCR assay for rapid detection of equine CXCL16 allelic variants associated with the establishment of long-term equine arteritis virus carrier state in stallions. Frontiers in Genetics 2022; 13:871875. doi: 10.3389/fgene.2022.871875

 

19. AbouEl Ela NH, El Araby IE, Saleh AA, Abd El‐fattah AH, Hagag NM, Brooks SA, Radwan MA, Kalbfleisch T. Evidence for origin of lavender foal syndrome among Egyptian Arabian horses in Egypt. Equine Veterinary Journal. 2023;55(3):487-93.

 

20. Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T. Refining the evolutionary tree of the horse Y chromosome. Scientific Reports. 2023;13(1):8954.

 

21. Bruno S, Senczuk G, Landi V, Di Civita M, Brooks SA, Almathen F, Faye B, Gaouar SSB, Piro M, Kim KS. Analysis of dromedary genetic diversity and structure using whole-genome sequence data. Proceedings of the 6^th Conference of the International Society of Camelid Research and Development (ISOCARD) 2023.

 

22. Bruno S, Senczuk G, Landi V, Di Civita M, Brooks SA, Almathen F, Faye B, Gaouar SSB, Piro M, Kim KS. The illumina® agricultural greater good initiative: development of a medium-Density SNP chip for camels. Proceedings of the 6^th Conference of the International Society of Camelid Research and Development (ISOCARD) 2023.

 

23. Ciosek J, Kimes A, Vinardell T, Miller DC, Antczak DF, Brooks S. Juvenile idiopathic epilepsy in Arabian horses is not a single-gene disorder. Journal of Heredity. 2023 doi: 10.1093/jhered/esad029..

 

24. McFadden A, Martin K, Foster G, Vierra M, Lundquist EW, Everts RE, Martin E, Volz E, McLoone K, Brooks SA. 5′ UTR Variant in KIT Associated With White Spotting in Horses. Journal of Equine Veterinary Science. 2023;127:104563.

 

25. Powell BB, Horvath KC, Gilliam TL, Sibille KT, Keil A, Miller-Cushon EK, Wickens CL, Brooks SA. Behavioral and Physiological Reactions to a Sudden Novel Object in the Weanling Horse: Quantitative Phenotypes for Future GWAS. Genes. 2023;14(3):593.

 

26. Rosa LP, Whitaker B, Allen K, Peters D, Buchanan B, McClure S, Honnas C, Buchanan C, Martin K, Lundquist E. Genomic loci associated with performance limiting equine overriding spinous processes (kissing spines). Research in Veterinary Science. 2022;150:65-71.

 

27. Shah I, Gray N, Groth D, Brooks S, Munyard K. A copy number variant near KITLG is associated with the roan pattern in alpacas. Animal Production Science. 2023. doi:10.1071/AN22463

 

28. Taylor WTT, Librado P, Hunska Tašunke Icu M, Shield Chief Gover C, Arterberry J, Luta Wiƞ A, Nujipi A, Omniya T, Gonzalez M, Means B. Early dispersal of domestic horses into the Great Plains and northern Rockies. Science. 2023;379(6639):1316-23.

 

29. Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L. The genomic history and global expansion of domestic donkeys. Science. 2022;377(6611):1172-80.

 

30. Clark BL, Bamford NJ, Stewart AJ, McCue ME, Rendahl ME, Bailey SR, Bertin Francoise-Rene, Norton EM. Evaluation of an HMGA2 variant contribution to height and basal insulin concentrations in ponies. J Vet Intern Med 2023 May-Jun; 37(3):1186-1192. PMID: 37148171. PMCID: PMC10229368

 

 

Appendix A: Grants and Contracts Received

 

Bailey E (Principal Investigator), Kalbfleisch T (Co-I), Petersen J (Co-I). Comparing Genetic Diversity of North American Thoroughbred Horses from two periods: 2005-2019 and 1965-1984; Koller Endowment. 2023-2024 $135,300

 

Durward-Akhurst S (co-PI), McCue ME (co-PI). A robust pipeline to functionally annotate non-traditional model pangenomes. University of Minnesota Informatics Institute. 2023 $50,000.

 

Durward-Akhurst S (Principal Investigator). Genetic mechanisms of sudden cardiac death in racehorses as a model for sudden arrhythmic death syndrome in human athletes. UMN CTSI pre-K award. $50,000

 

Durward-Akhurst S (Principal Investigator). Investigation of arrhythmic-SCD causing mutations in racehorses. UMN College of Veterinary Medicine Animal Health Grant. $60,000

 

Guest D (Principal Investigator). Bad memories: do horse tendon cells become primed to inflammation? Horserace Betting Levy Board, £173,000

 

Guest D (Principal Investigator). Utilising novel therapeutics to reduce inflammation in equine adult tenocytes Petplan Charitable Trust, £10,000.

 

McCoy AM (Principal Investigator). Effects of Early Exercise on Muscle Expression of

Myokines in Foals. USDA Hatch Funds FY23. 9/2023-9/2024. $17,385.

 

McCoy AM (Principal Investigator). Molecular markers of early equine post-traumatic osteoarthritis. USDA-AFRI-NIFA. 5/2023-4/2026. $627,000.

 

McCoy AM (Mentor). Alterations in the peritoneal environment of horses with intestinal disease: a multiomics approach. Morris Animal Foundation. 7/2023-6/2025. S124,956.

 

McCue ME (Principal Investigator), Durward-Akhurst S (co-I). Mendelian and oligogenic disease mutation discovery: best practices and automated tools. UMN College of Veterinary Medicine Multistate. $70,000

 

Mienaltowski M (Principal Investigator). Delivery of Exogenous EGR1 mRNA to Improve Tendon Formation. UC Davis Center for Equine Health Research Grant. $28,735

 

Raudsepp T (Collaborator). Genetic Analysis for the Wild Horse and Burro Program (WHBP). DOI-Bureau of Land Management. 2021-2025. $152,187.

 

Raudsepp T (Co-PI). Understanding the co-evolution of phylogenomic signal, gene linkage, and recombination rate through comparative genomics. NSF-DEB #2150664. 07/01/2022-06/30/2025. $1,200,000. (includes horse and equids)

 

Raudsepp T (Principal Investigator). Preliminary population genetic analysis of the Estonian Draft Horse: comparison with Swedish Ardennes. Estonian Ministry of Rural Affairs. July-December 2022. $5000.

 

Raudsepp T (Principal Investigator). Exploring the Genomic Component of Equine Sex Development and Reproduction. USDA-AFRI, Animal Health and Production and Animal Products: Animal Reproduction. Proposal Number: 2022‐08309. May 2023 - 2026. $644,320.

 

Raudsepp T (Principal Investigator). Genomics of Thoroughbred stallion subfertility. Grayson-Jockey Club Research Foundation. April 1, 2023-March 31, 2025. $77,371.

 

Raudsepp T (Principal Investigator). Exploring the Genomic Component of Reproductive Health in Mares: Molecular Signatures for X-Monosomy-Like Gonadal Dysplasia. American Quarter Horse Research Foundation. October 1, 2023-September 30, 2024. $39,021.

 

 

 

Appendix B: Research presentations and other outreach activities

 

Research presentations

January 2023. Plant and Animal Genome 30, San Diego, CA

Arias X, Janes JG, Hagen DE, Petersen JL, Murdoch BM, Steffen D, Norton E, McCarthy FM, Kalbfleisch T. A genetic data portal to enable discovery of deleterious genetic variants in farmed animals.

 

Bannasch D, Batcher KL, Varney S, Raudsepp T, Jagannathan V, Leeb T. Ancient segmentally duplicated Lcorl retrocopies in equids.

 

Bishop RC, Arrington J, McCoy AM. Alterations in the peritoneal fluid proteome of horses with intestinal disease.

 

Ciosek JL, Alhaddad H, Brooks SA. Genome wide association study for skull morphology in Arabian horses.

 

Cullen JN, Schaefer RJ, Mickelson JR, McCue ME, Tissue-Specific Distribution and Complexity of Small Non-Coding RNA Expression in the Horse.

 

Dimmler KE, Sinclair R, Edwards J, Sinclair H, Juras R, Shelton D, Cox M, McCue ME, Szauter P. Characterization of a Glycine-to-Alanine substitution in a triple helical domain of COL63A in horses.

 

Finno CJ, Peng S, Barber AM, Bellone RR, Kingsley NB, Cappelletti E, Piras FM. Giulotto E, Kalbfleisch, Petersen JL. Equine FAANG update: from starting gate to winner’s circle.

 

Hughes LE, Marlowe JL, Durward-Akhurst SA, McCue ME. Evaluation of Candidate Gene Prediction Programs in Equine Disease.

 

Li K, Hussien N, Petersen JL, Loux SC, Laird-Smith M, Bailey E, Kalbfleisch T. A comparison of trio binned horse and donkey assemblies with current reference assemblies.

 

Marlowe JL, Cullen JN, McCue ME, Durward-Akhurst SA. Exploring drivers of discortance between variant calling and variant filtration methods to inform decvisions for a best practices WGS variant prioritization pipeline.

 

Medeiros BB, Barcelos KMC, da Paz Carvalho MC, Miranda VR, de Iliveira Maia K, Reinhardt, Patterson Rosa L. The weight of genetic drift: a pedigree-based evaluation of the Breton Draft Horse population in Brazil.

 

Mienaltowski MJ, Callahan M, Gonzales N, Wong AO. Bolstering Tenogenic Phenotype in Equine Tendon Cells with Vitamin C Supplementation.

 

Petersen JL, Barber, AM, Finno CJ, Bellone RR, Peng S, Kingsley NB, Cappelletti E, Piras FM, Giulotto, Kalbfleisch T. The Equine FAANG Project: A Portal to Connect Genome to Phenome.

 

Powell BB, Brooks SA. Preliminary identification of a quantitative trait locus for body size proportion in the American Quarter Horse.

 

Santos H, de Toledo AP, Staiger EA, Paschoal VR, Patterson Rosa L. ANALOC-E: A Deep Phenotyping Tool for Horse Locomotion

 

Smythe MP, Dewberry S, Staiger EA, Allen K, Brooks SA. Quantifying locomotor phenotypes in fragile foal syndrome carriers using artificial intelligence.

 

Yousefi Mashouf N, Spina A, Eberth J, Bellone RR, Graves KT, Bailey E. Investigation of myostatin gene variants in Thoroughbred and related horse breeds.

 

Hands-on Demo of Containerized Workflows and a Data Repository to Support Efficient, Standardized, Interoperable Genomic Analysis: An Equine Example.

 

Durward-Akhurst SA, Marlowe JL, Cullen JN, Mickelson JM, McCue ME. Building and using the Equine Variant Database.

 

Cullen JN, Kalbfleisch T, Durward-Akhurst SA, Marlowe JL, McCue ME, Friedenberg SG. Downloading and Running Containers in HPC/Cloud Environments.

 

March 2023.  Invited – Midwest Section of the American Society of Animal Sciences.  Functional annotation of the equine genome: from sample collection to FAIR data.  J Petersen*, R Bellone, T Kalbfleisch, E Giulotto, C Finno.

 

April 2023.  Invited – University of Kentucky, Gluck Equine Research Center.  Using genetic information to understand and inform the management of horse breeds.  J Petersen*, A Fuller, I Grazian.

 

Outreach Activities

 

March 2023. Invited – American Shire Association Annual Meeting, Blair, NE.  Equine genetics:

focus on the Shire.  J Petersen*.

 

March 2023. Talk for British science week on the racehorse genetics and bone fracture. D. Guest

March 2023. 4-H Area North Virtual Youth equine Symposium presentation, virtual, 1 hr, 20 participants. S. Brooks

Equine Genetics Online Short Courses, part I and II, virtual asynchronous, 18 hrs in total, 15 participants. S. Brooks

 

 

03/08/2024

AbouEl Ela, N.H., El Araby, I.E., Saleh, A.A., Abd El-fattah, A.H., Hagag, N.M., Brooks, S.A., Radwan, M.A. and Kalbfleisch, T. (2023) 'Evidence for origin of lavender foal syndrome among Egyptian Arabian horses in Egypt', Equine Veterinary Journal, 55(3), 487-493, available: http://dx.doi.org/10.1111/evj.13604.

 

Bacon, E.K., Donnelly, C.G., Bellone, R.R., Finno, C.J. and Velie, B.D. (2023) 'Melanocortin-1 receptor influence in equine opioid sensitivity', Equine Veterinary Education, 35(3), 152-162, available: http://dx.doi.org/10.1111/eve.13661.

 

Bailey, E. (2023) 'Ancient DNA reveals an early adoption of horse culture by Native Americans', Trends in Genetics, 39(11), 808-809, available: http://dx.doi.org/10.1016/j.tig.2023.06.010.

 

Batcher, K., Varney, S., Raudsepp, T., Jevit, M., Dickinson, P., Jagannathan, V., Leeb, T. and Bannasch, D. (2023) 'Ancient segmentally duplicated LCORL retrocopies in equids', PLoS ONE, 18(6 JUNE), available: http://dx.doi.org/10.1371/journal.pone.0286861.

 

Beaumont, R.E., Smith, E.J., Zhou, L., Marr, N., Thorpe, C.T. and Guest, D.J. (2023) 'Exogenous interleukin-1 beta stimulation regulates equine tenocyte function and gene expression in three-dimensional culture which can be rescued by pharmacological inhibition of interleukin 1 receptor, but not nuclear factor kappa B, signaling', Molecular and Cellular Biochemistry, available: http://dx.doi.org/10.1007/s11010-023-04779-z.

 

Bishop, R.C., Wilkins, P.A., Kemper, A.M., Stewart, R.M. and McCoy, A.M. (2023) 'Effect of Firocoxib and Flunixin Meglumine on Large Colon Mural Thickness of Healthy Horses', Journal of Equine Veterinary Science, 126, available: http://dx.doi.org/10.1016/j.jevs.2023.104562.

 

Bozlak, E., Radovic, L., Remer, V., Rigler, D., Allen, L., Brem, G., Stalder, G., Castaneda, C., Cothran, G., Raudsepp, T., Okuda, Y., Moe, K.K., Moe, H.H., Kounnavongsa, B., Keonouchanh, S., Van, N.H., Vu, V.H., Shah, M.K., Nishibori, M., Kazymbet, P., Bakhtin, M., Zhunushov, A., Paul, R.C., Dashnyam, B., Nozawa, K., Almarzook, S., Brockmann, G.A., Reissmann, M., Antczak, D.F., Miller, D.C., Sadeghi, R., von Butler-Wemken, I., Kostaras, N., Han, H., Manglai, D., Abdurasulov, A., Sukhbaatar, B., Ropka-Molik, K., Stefaniuk-Szmukier, M., Lopes, M.S., da Câmara Machado, A., Kalashnikov, V.V., Kalinkova, L., Zaitev, A.M., Novoa‐Bravo, M., Lindgren, G., Brooks, S., Rosa, L.P., Orlando, L., Juras, R., Kunieda, T. and Wallner, B. (2023) 'Refining the evolutionary tree of the horse Y chromosome', Scientific Reports, 13(1), available: http://dx.doi.org/10.1038/s41598-023-35539-0.

 

Cappelletti, E., Piras, F.M., Sola, L., Santagostino, M., Petersen, J.L., Bellone, R.R., Finno, C.J., Peng, S., Kalbfleisch, T.S., Bailey, E., Nergadze, S.G. and Giulotto, E. (2023) 'The localization of centromere protein A is conserved among tissues', Communications Biology, 6(1), available: http://dx.doi.org/10.1038/s42003-023-05335-7.

 

Carver, C., Bruemmer, J., Coleman, S., Landolt, G. and Hess, T. (2023) 'Effects of corn supplementation on serum and muscle microRNA profiles in horses', Food Science and Nutrition, 11(6), 2811-2822, available: http://dx.doi.org/10.1002/fsn3.3259.

 

Ciosek, J., Kimes, A., Vinardell, T., Miller, D.C., Antczak, D.F. and Brooks, S. (2023) 'Juvenile idiopathic epilepsy in Arabian horses is not a single-gene disorder', Journal of Heredity, 114(5), 488-491, available: http://dx.doi.org/10.1093/jhered/esad029.

 

Clark, B.L., Bamford, N.J., Stewart, A.J., McCue, M.E., Rendahl, A., Bailey, S.R., Bertin, F.R. and Norton, E.M. (2023) 'Evaluation of an HMGA2 variant contribution to height and basal insulin concentrations in ponies', Journal of Veterinary Internal Medicine, 37(3), 1186-1192, available: http://dx.doi.org/10.1111/jvim.16723.

 

Clifton, D.L., Boyd, J.A. and Patterson Rosa, L. (2023) 'Using genetics to trace the ancestry and ‘breed-type’ of rescued horses', Animal Genetics, 54(6), 813-815, available: http://dx.doi.org/10.1111/age.13362.

 

Donnelly, C.G. and Finno, C.J. (2023) 'Vitamin E depletion is associated with subclinical axonal degeneration in juvenile horses', Equine Veterinary Journal, 55(5), 884-890, available: http://dx.doi.org/10.1111/evj.13907.

 

Donnelly, C.G., Johnson, A.L., Reed, S. and Finno, C.J. (2023) 'Cerebrospinal fluid and serum proteomic profiles accurately distinguish neuroaxonal dystrophy from cervical vertebral compressive myelopathy in horses', Journal of Veterinary Internal Medicine, 37(2), 689-696, available: http://dx.doi.org/10.1111/jvim.16660.

 

Elcombe, M.E., Bellone, R.R., Magdesian, K.G. and Finno, C.J. (2023) 'Prevalence of the RAPGEF5 c.2624C>A and PLOD1 c.2032G>A variants associated with equine familial isolated hypoparathyroidism and fragile foal syndrome in the US Thoroughbred population (1988–2019)', Equine Veterinary Journal, 55(4), 666-671, available: http://dx.doi.org/10.1111/evj.13883.

 

Esdaile, E., Knickelbein, K.E., Donnelly, C.G., Ferneding, M., Motta, M.J., Story, B.D., Avila, F., Finno, C.J., Gilger, B.C., Sandmeyer, L., Thomasy, S. and Bellone, R.R. (2023) 'Additional evidence supports GRM6 p.Thr178Met as a cause of congenital stationary night blindness in three horse breeds', Veterinary Ophthalmology, available: http://dx.doi.org/10.1111/vop.13151.

 

Gossett, C.L., Guyer, D., Hein, J. and Brooks, S.A. (2023) 'Digital Phenotyping Reveals Phenotype Diversity and Epistasis among White Spotting Alleles in the American Paint Horse', Genes, 14(11), available: http://dx.doi.org/10.3390/genes14112011.

 

Hardefeldt, L.Y. and Bailey, K.E. (2023) 'Challenges to appropriate antimicrobial use in horses', Equine Veterinary Education, 35(11), 567-570, available: http://dx.doi.org/10.1111/eve.13882.

 

Jevit, M.J., Castaneda, C., Paria, N., Das, P.J., Miller, D., Antczak, D.F., Kalbfleisch, T.S., Davis, B.W. and Raudsepp, T. (2023) 'Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features', Scientific Reports, 13(1), available: http://dx.doi.org/10.1038/s41598-023-47583-x.

 

Kent, E., Coleman, S., Bruemmer, J., Casagrande, R.R., Levihn, C., Romo, G., Herkelman, K. and Hess, T. (2023) 'Comparison of an Antioxidant Source and Antioxidant Plus BCAA on Athletic Performance and Post Exercise Recovery of Horses', Journal of Equine Veterinary Science, 121, available: http://dx.doi.org/10.1016/j.jevs.2022.104200.

 

Klecel, W., Drobik-Czwarno, W. and Martyniuk, E. (2023) 'Judging the Arabian Beauty: What are the Relationships Between Different Scoring Categories?', Journal of Equine Veterinary Science, 123, available: http://dx.doi.org/10.1016/j.jevs.2023.104247.

 

Knych, H.K., Finno, C.J., Katzman, S., Ryan, D., McKemie, D.S., Kass, P.H. and Arthur, R.M. (2023) 'Clodronate detection and effects on markers of bone resorption are prolonged following a single administration to horses', Equine Veterinary Journal, 55(4), 696-706, available: http://dx.doi.org/10.1111/evj.13866.

 

Louie, E.W., Berryhill, E.H., Nieto, J., Wensley, F., Knych, H., Finno, C.J. and Morgan, J.M. (2023) 'Changes in Heart Rate Variability with Induction of Gastric Ulcers in Adult Horses', Journal of Equine Veterinary Science, 121, available: http://dx.doi.org/10.1016/j.jevs.2022.104192.

 

Manfredi, J.M., Jacob, S. and Norton, E. (2023a) 'A one-health lens offers new perspectives on the importance of endocrine disorders in the equine athlete', Journal of the American Veterinary Medical Association, 261(2), 153-164, available: http://dx.doi.org/10.2460/javma.22.11.0485.

 

Manfredi, J.M., Jacob, S.I., Boger, B.L. and Norton, E.M. (2023b) 'A one-health approach to identifying and mitigating the impact of endocrine disorders on human and equine athletes', American Journal of Veterinary Research, 84(2), available: http://dx.doi.org/10.2460/ajvr.22.11.0194.

 

McCoy, A.M. and Scolman, K.N. (2023) 'Impact of periarticular osteophytes of the distal tarsus diagnosed in nonlame yearling Standardbred horses on racing performance', Veterinary Surgery, 52(7), 1050-1056, available: http://dx.doi.org/10.1111/vsu.13987.

 

McCoy, A.M., Secor, E.J., Roady, P.J., Gray, S.M., Klein, J. and Gutierrez-Nibeyro, S.D. (2023) 'Plantar osteochondral fragments in young Standardbreds are associated with minimal joint inflammation at the time of surgical removal', Equine Veterinary Journal, 55(1), 33-41, available: http://dx.doi.org/10.1111/evj.13575.

 

McCue, P.M., Bisiau, C., Divine, C. and May, E. (2023) 'Congenital, Inherited Bilateral Amastia in a Quarter Horse Mare', Journal of Equine Veterinary Science, 128, available: http://dx.doi.org/10.1016/j.jevs.2023.104874.

 

McFadden, A., Martin, K., Foster, G., Vierra, M., Lundquist, E.W., Everts, R.E., Martin, E., Volz, E., McLoone, K., Brooks, S.A. and Lafayette, C. (2023a) '5′UTR Variant in KIT Associated With White Spotting in Horses', Journal of Equine Veterinary Science, 127, available: http://dx.doi.org/10.1016/j.jevs.2023.104563.

 

McFadden, A., Martin, K., Foster, G., Vierra, M., Lundquist, E.W., Everts, R.E., Martin, E., Volz, E., McLoone, K., Brooks, S.A. and Lafayette, C. (2023b) 'Two Novel Variants in MITF and PAX3 Associated With Splashed White Phenotypes in Horses', Journal of Equine Veterinary Science, 128, available: http://dx.doi.org/10.1016/j.jevs.2023.104875.

 

Moshage, S.G., McCoy, A.M. and Kersh, M.E. (2023) 'Elastic Modulus and Its Relation to Apparent Mineral Density in Juvenile Equine Bones of the Lower Limb', Journal of Biomechanical Engineering, 145(8), available: http://dx.doi.org/10.1115/1.4062488.

 

Mousavi, S.F., Razmkabir, M., Rostamzadeh, J., Seyedabadi, H.R., Naboulsi, R., Petersen, J.L. and Lindgren, G. (2023) 'Genetic diversity and signatures of selection in four indigenous horse breeds of Iran', Heredity, 131(2), 96-108, available: http://dx.doi.org/10.1038/s41437-023-00624-7.

 

Orellana-Guerrero, D., Uribe-Salazar, J.M., El-Sheikh Ali, H., Scoggin, K.E., Ball, B., Daels, P., Finno, C.J. and Dini, P. (2023) 'Dynamics of the Equine Placental DNA Methylome and Transcriptome from Mid- to Late Gestation', International Journal of Molecular Sciences, 24(8), available: http://dx.doi.org/10.3390/ijms24087084.

 

Palomino Lago, E., Jelbert, E.R., Baird, A., Lam, P.Y. and Guest, D.J. (2023) 'Equine induced pluripotent stem cells are responsive to inflammatory cytokines before and after differentiation into musculoskeletal cell types', In Vitro Cellular and Developmental Biology - Animal, 59(7), 514-527, available: http://dx.doi.org/10.1007/s11626-023-00800-3.

 

Peng, S., Dahlgren, A.R., Donnelly, C.G., Hales, E.N., Petersen, J.L., Bellone, R.R., Kalbfleisch, T. and Finno, C.J. (2023) 'Functional annotation of the animal genomes: An integrated annotation resource for the horse', PLoS genetics, 19(3), e1010468, available: http://dx.doi.org/10.1371/journal.pgen.1010468.

 

Pfeifle, R.L., Ericsson, A.C., McCoy, A.M., Boothe, D.M., Wooldridge, A.A., Groover, E.S., Sierra-Rodriguez, T. and Lascola, K.M. (2023) 'Multidose misoprostol pharmacokinetics and its effect on the fecal microbiome in healthy, adult horses', American Journal of Veterinary Research, 84(3), available: http://dx.doi.org/10.2460/ajvr.22.09.0161.

 

Powell, B.B., Horvath, K.C., Gilliam, T.L., Sibille, K.T., Keil, A., Miller-Cushon, E.K., Wickens, C.L. and Brooks, S.A. (2023) 'Behavioral and Physiological Reactions to a Sudden Novel Object in the Weanling Horse: Quantitative Phenotypes for Future GWAS', Genes, 14(3), available: http://dx.doi.org/10.3390/genes14030593.

 

Roxon, C.A., Linton, J.K., Habecker, P.L., Castaneda, C., Raudsepp, T. and Sertich, P.L. (2023) 'Equine dystocia complicated by fetal congenital anomaly', Journal of the American Veterinary Medical Association, 261(11), 1728-1731, available: http://dx.doi.org/10.2460/javma.23.06.0338.

 

Schaefer, R.J., Cullen, J., Manfredi, J. and McCue, M.E. (2023) 'Functional Contexts of Adipose and Gluteal Muscle Tissue Gene Co-expression Networks in the Domestic Horse', in Integrative and Comparative Biology, 238-249, available: http://dx.doi.org/10.1093/icb/icaa134.

 

Smith, E.J., Beaumont, R.E., McClellan, A., Sze, C., Palomino Lago, E., Hazelgrove, L., Dudhia, J., Smith, R.K.W. and Guest, D.J. (2023) 'Tumour necrosis factor alpha, interleukin 1 beta and interferon gamma have detrimental effects on equine tenocytes that cannot be rescued by IL-1RA or mesenchymal stromal cell–derived factors', Cell and Tissue Research, 391(3), 523-544, available: http://dx.doi.org/10.1007/s00441-022-03726-6.

 

Taylor, W.T.T., Librado, P., Icu, M.H.T., Gover, C.S.C., Arterberry, J., Wih, A.L., Nujipi, A., Omniya, T., Gonzalez, M., Means, B., Crane, S.H., Knife, B.D., Wih, W., Collin, C.T., Ward, C., Pasqual, T.A., Chauvey, L., Tonasso-Calviere, L., Schiavinato, S., Seguin-Orlando, A., Fages, A., Khan, N., Sarkissian, C.D., Liu, X., Wagner, S., Leonard, B.G., Manzano, B.L., O’Malley, N., Leonard, J.A., Bernáldez-Sánchez, E., Barrey, E., Charliquart, L., Robbe, E., Denoblet, T., Gregersen, K., Vershinina, A.O., Weinstock, J., Šikanjić, P.R., Mashkour, M., Shingiray, I., Aury, J.M., Perdereau, A., Alquraishi, S., Alfarhan, A.H., Al-Rasheid, K.A.S., Vukičević, T.T., Buric, M., Sauer, E., Lucas, M., Brenner-Coltrain, J., Bozell, J.R., Thornhill, C.A., Monagle, V., Perri, A., Newton, C., Hall, W.E., Conver, J.L., Le Roux, P., Buckser, S.G., Gabe, C., Belardi, J.B., Barrón-Ortiz, C.I., Hart, I.A., Ryder, C., Sponheimer, M., Shapiro, B., Southon, J., Hibbs, J., Faulkner, C., Outram, A., Rosa, L.P., Palermo, K., Solé, M., William, A., McCrory, W., Lindgren, G., Brooks, S., Eché, C., Donnadieu, C., Bouchez, O., Wincker, P., Hodgins, G., Trabert, S., Bethke, B., Roberts, P., Jones, E.L., Collin, Y.R.H. and Orlando, L. (2023) 'Early dispersal of domestic horses into the Great Plains and northern Rockies', Science, 379(6639), available: http://dx.doi.org/10.1126/science.adc9691.

 

Todd, E.T., Fromentier, A., Sutcliffe, R., Running Horse Collin, Y., Perdereau, A., Aury, J.M., Èche, C., Bouchez, O., Donnadieu, C., Wincker, P., Kalbfleisch, T., Petersen, J.L. and Orlando, L. (2023) 'Imputed genomes of historical horses provide insights into modern breeding', iScience, 26(7), available: http://dx.doi.org/10.1016/j.isci.2023.107104.

 

Valberg, S.J., Henry, M.L., Herrick, K.L., Velez-Irizarry, D., Finno, C.J. and Petersen, J.L. (2023a) 'Absence of myofibrillar myopathy in Quarter Horses with a histopathological diagnosis of type 2 polysaccharide storage myopathy and lack of association with commercial genetic tests', Equine Veterinary Journal, 55(2), 230-238, available: http://dx.doi.org/10.1111/evj.13574.

 

Valberg, S.J., Williams, Z.J., Finno, C.J., Schultz, A., Velez-Irizarry, D., Henry, M.L., Gardner, K. and Petersen, J.L. (2023b) 'Type 2 polysaccharide storage myopathy in Quarter Horses is a novel glycogen storage disease causing exertional rhabdomyolysis', Equine Veterinary Journal, 55(4), 618-631, available: http://dx.doi.org/10.1111/evj.13876.

 

Valberg, S.J., Williams, Z.J., Henry, M.L. and Finno, C.J. (2023c) 'Cerebellar axonopathy in Shivers horses identified by spatial transcriptomic and proteomic analyses', Journal of Veterinary Internal Medicine, 37(4), 1568-1579, available: http://dx.doi.org/10.1111/jvim.16784.

 

Ward, J., Raudsepp, T., Levine, D. and Turner, R. (2023) 'Ambiguous external genitalia in a 5-year-old intact miniature equid', Journal of the American Veterinary Medical Association, 261(9), 1391-1393, available: http://dx.doi.org/10.2460/javma.23.03.0175.

 

Williams Louie, E., Nieto, J., Wensley, F., Morgan, J.M., Finno, C.J. and Berryhill, E.H. (2023) 'Efficacy of the oral supplement, Equine Omega Complete, for the prevention of gastric ulcers and alpha-tocopherol supplementation in horses', Journal of Veterinary Internal Medicine, 37(6), 2529-2534, available: http://dx.doi.org/10.1111/jvim.16877.

03/28/2025

Culwell, J., North, E., Nicodemus, M.C., Cavinder, C., Williams, T. (2024) PSIV-9 Pedigree tracing to determine the origin of the golden coat phenotype within the Golden American Saddlebred horse. Journal of Animal Science, 102 (3), 549–550. https://doi.org/10.1093/jas/skae234.617.

 Pepper, B., North, E., Culwell, J., Nicodemus, M.C., Cavinder, C., Harvey, K., Williams, T. (2024) Pedigree tracing to determine the origins of the modern Palomino Horse Breeders of America stock-type horse. Journal of Equine Veterinary Science, 143, 105209. https://doi.org/10.1016/j.jevs.2024.105209.

 Alhaddad, H., Powell, B., Del Pinto, L., Sutter, N., Brooks, S. and Alhajeri, B. (2024) 'Geometric morphometrics of face profile across horse breeds and within Arabian horses', Journal of Equine Veterinary Science, 132, 104980.

 Ciosek, J., Wickens, C. and Brooks, S.A. (2024) 'A Primer on Genetic Testing for Horse Owners and Breeders: VM261, 4/2024', EDIS, 2024(3).

 Johns, L., Smythe, M., Dewberry, L., Staiger, E., Allen, K. and Brooks, S. (2024) 'Digital video analysis reveals gait parameters that predict performance in the jumping test phase of three-day eventing', Journal of Equine Veterinary Science, 141, 105166.

McFadden, A., Martin, K., Vierra, M., Robilliard, H., Lundquist, E.W., Everts, R.E., Brooks, S.A. and Lafayette, C. (2024a) 'Three HPS5 mutations associated with depigmentation in diverse horse breeds', Livestock Science, 282, 105454.

McFadden, A., Vierra, M., Martin, K., Brooks, S.A., Everts, R.E. and Lafayette, C. (2024b) 'Spotting the Pattern: A Review on White Coat Color in the Domestic Horse', Animals, 14(3), 451.

McFadden, A., Vierra, M., Robilliard, H., Martin, K., Brooks, S.A., Everts, R.E. and Lafayette, C. (2024c) 'Population Analysis Identifies 15 Multi-Variant Dominant White Haplotypes in Horses', Animals, 14(3), 517.

Radovic, L., Remer, V., Rigler, D., Bozlak, E., Allen, L., Brem, G., Reissman, M., Brockmann, G.A., Ropka-Molik, K. and Stefaniuk-Szmukier, M. (2024) 'The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome', Proceedings of the National Academy of Sciences, 121(49), e2414408121.

 Wang, J., Hu, Y., Xiang, L., Morota, G., Brooks, S.A., Wickens, C.L., Miller-Cushon, E.K. and Yu, H. (2024) 'ShinyAnimalCV: open-source cloud-based web application for object detection, segmentation, and three-dimensional visualization of animals using computer vision', Journal of Animal Science, 102, skad416.

 Durward-Akhurst, S. A. (Corresponding Author), Marlowe, J. L., Schaefer, R. J., Springer, K., Grantham, B., Carey, W. K., . . . McCue, M. E. (2024). The genetic burden and frequency of disease-associated variants in the equine population. Nature Scientific Reports, 14. PubMed Central ID Number: PMC11006912 doi: 10.1038/s41598-024-57872-8

Marlowe, J. L., McCue, M. E. (Lead Author), & Durward-Akhurst, S. A. (Lead Author) Simulated whole genome sequencing data of Equus Caballus as a novel benchmark truth set. Nature Scientific Data. [Submitted:2024]

Palomino Lago, E. (Lead Author), Baird, A., Blott, S., McPhail, R., Ross, A., Durward-Akhurst, S. A., & Guest, D. (Corresponding Author) (2024). A functional single nucleotide polymorphism upstream of the collagen type III gene is associated with catastrophic fracture risk in Thoroughbred horses. Animals, 14(1).  doi: 10.3390/ani14010116

 Esdaile E, Knickelbein KE, Donnelly CG, Fereding M, Motta MJ, Story BD, Avila F, Finno CJ, Gilger BC, Sandmeyer L, Thomasy S, Bellone RR. Additional evidence supports GRM6 p.Thr178Met as a cause of congenital stationary night blindness in three horse breeds. Vet Ophthalmol 2024;27(3):248-255.

 Ma Y, Peng S, Donnelly CG, Ghosh S, Miller AD, Woolard K, Finno CJ. Genetic polymorphisms in vitamin E transport genes as determinants for risk of equine neuroaxonal dystrophy. J Vet Intern Med 2024;38(1):417-423.

 Wilcox CV, Knych HK, Katzman SA, Arthur RM, Rodriguez V, Finno CJ. Effect of clodronate on gene expression in the peripheral blood of horses. J Vet Pharmacol Ther 2024;47(3):187-192.

 Powers A, Peek SF, Reed S, Donnelly CG, Tinkler S, Gasper D, Woolard WD, Finno CJ. Equine neuroaxonal dystrophy / degenerative myeloencephalopathy in Gypsy Vanner horses. J Vet Intern Med 2024;38(3):1792-1798.

 Willis AT, Dahlgren AR, Woolard KD, Ghosh S, Donnelly CG, de la Concha-Bermejillo A, Pacheco A, Watson KD, Berryhill E, Aleman A, Wensley F, Humphreys S, Whitehead AE, Goldsmith D, Chesen B, Ragsdale J, Rompkins JE, Nash R, Plunkett AH, Qualls HJ, Rodriguez K, Hochanadel D, Miller AD, Finno CJ. Clinicopathologic and pedigree investigation of a novel spinocerebellar neurological disease in juvenile Quarter Horses in North America. J Vet Intern Med 2024;38(3):1808-1814.

 Bacon EK, Donnelly CG, Bellone RR, Haase B, Finno CJ, Velie B. Preliminary investigation of potential links between pigmentation variants and opioid analgesic effectiveness in horses during cerebrospinal fluid centesis. BMC Vet Res 2024;20(1):311

 Bailey E, Finno CJ, Cullen JN, Kalbfleisch T, Petersen JL. Analysis of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations. Sci Rep 2024;14(1):22930.

 Heath H, Peng S, Szmatola T, Ryan S, Bellone RR, Kalbfleish T, Petersen JL, Finno CJ. A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome. BMC Genomics, in press.

 Mienaltowski MJ, Callahan M, Gonzales NL, Wong A. Examining the Potential of Vitamin C Supplementation in Tissue-Engineered Equine Superficial Digital Flexor Tendon Constructs. Int J Mol Sci. 2023 Dec 4;24(23):17098. doi: 10.3390/ijms242317098. PMID: 38069418; PMCID: PMC10707379.

 Mienaltowski MJ, Callahan M, De La Torre U, Maga EA. Comparing microbiotas of foals and their mares' milk in the first two weeks after birth. BMC Vet Res. 2024 Jan 8;20(1):17. doi: 10.1186/s12917-023-03864-1. PMID: 38191395; PMCID: PMC10775675.

 Smith, E. J., Beaumont, R. E., Dudhia, J. & Guest, D. J. Equine Embryonic Stem Cell-Derived Tenocytes are Insensitive to a Combination of Inflammatory Cytokines and Have Distinct Molecular Responses Compared to Primary Tenocytes. Stem Cell Rev Rep, May;20(4):1040-1059. doi:10.1007/s12015-024-10693-8 (2024).

 Palomino Lago E, Ross AKC, McClellan A, Guest DJ. Identification of a global gene expression signature associated with the genetic risk of catastrophic fracture in iPSC-derived osteoblasts from Thoroughbred horses. Anim Genet. 2025 Feb;56(1):e13504. doi: 10.1111/age.13504. PMID: 39801206.

03/12/2026

Marlowe, J. L., Barrey, E., Durward-Akhurst, S.A.*, and McCue, M. E.* Simulated whole genome sequencing data of Equus Caballus as a novel benchmark truth set. Submitted December 2025

Martin EJ, Hecht S, Craig L, Durward-Akhurst SA, Marlowe JL, Hines MT. Gardner-like Syndrome in a Pony. In review, September 2025.

Mayra Mendoza, Hailey Anderson, Giora Avni, Gila Kahila Bar-Gal, Rytis Juras, Terje Raudsepp. A unique case of mosaicism for two Robertsonian translocations, rob(17;27) and rob(17;29), in a subfertile mare (Equus caballus). Accepted Nov 27, 2025; Cytogenet Genome Res., Dec 8:1-18. doi:10.1159/000549928. Online ahead of print.

Nicole M. Foley, Richie Rasulis, Zoya Wani, Mayra N. Mendoza Cerna$, Klaus Peter Koepfli, Terje Raudsepp, and William J. Murphy. An ancient X chromosome recombination desert is a supergene in placental mammals. Nature, 12 November 2025; doi: https://doi.org/10.1038/s41586-025-09740-2.

Seyoung Lee, Eunsang Choi, Jungmin Lee, Sarah No, Sea-Hwan Sohn, Mayra Mendoza, Terje Raudsepp, Jong-pil Seo. 2025. Miniature Pony with 64,XY SRY-Positive Disorder of Sexual Development: Karyotyping and Genetic Marker Test. J Vet Clin, 2025, 42(4), 214-217; https://doi.org/10.17555/jvc.2025.42.4.214; Published online August 31, 2025.

Jonah N. Cullen, Jakub Cieslak, Jessica L. Petersen, Rebecca R. Bellone, Carrie J. Finno, Ted S Kalbfleisch, Kirstine Calloe, Stefano Capomaccio, Katia Cappelli, Stephen J Coleman, Ottmar Distl, Sian A Durward-Akhurst, Elena Giulotto, Natasha A Hamilton, Emmeline W Hill, Lisa M Katz, Dan A Klaerke, Gabriella Lindgren, David E MacHugh, Mariusz Mackowski, James N MacLeod, Julia Metzger, Barbara A Murphy, Ludovic Orlando, Terje Raudsepp, Maurizio Silvestrelli, Eric Strand, Teruaki Tozaki, Dagmar S Trachsel, Laura S Valderrama Figueroa, Brandon D Velie, Claire M Wade, Bianca Waud, James R Mickelson, Molly E. McCue. Charting the equine miRNA landscape: an integrated pipeline and browser for annotating, quantifying, and visualizing expression. PLoSGen (accepted August 6, 2025).

Cliona A. Ryan, Donagh P. Berry, Monika Bugno-Poniewierska, Mary-Kate Burke, Terje Raudsepp, Sonja Egan and Jennifer L. Doyle. 2025. Two Cases of Chromosome 27 Trisomy in Horses Detected Using Illumina BeadChip Genotyping. Animals, 15(13), 1842; published October 23, 2025; https://doi.org/10.3390/ani15131842.

T Raudsepp, S Stroupe, C Hernández-Avilés, R Juras, HJ Kjöllerström, H Anderson, BW Davis. 2025. Whole genome sequence-based analysis of Thoroughbred stallions with impaired acrosomal exocytosis and subfertility. Journal of Equine Veterinary Science, 145, 105317.

Bucci MP, Dewberry LS, Staiger EA, Allen K, Brooks SA. AI-assisted digital video analysis reveals changes in gait among three-day event horses during competition. Journal of Equine Veterinary Science. 2025;146:105344.

Everts RE, Caron R, Foster G, McLoone K, Martin K, Brooks SA, Lafayette C. Identification of Two Genetic Haplotypes Associated with the Roan Coat Color in the American Quarter Horse and Other Equine Breeds. Animals. 2025;15(12):1705.

Hernandez AS, Wickens C, Brooks S. Managing Heat Stress in Horses: VM278, 11/2025. EDIS. 2025;2025(6).

Hernandez S, Nastrini E, Norton E, McCoy A, Brooks S, Mienaltowski M. US stakeholder survey examining understanding of equine genetics and concerns for genetic diseases. Journal of Equine Veterinary Science. 2025;148:105508.

Klecel W, Rahael H, Brooks SA. refineDLC: an advanced post-processing pipeline for DeepLabCut outputs. Biology Methods and Protocols. 2025;10(1):bpaf084.

Obradovic NA, McFadden A, Martin K, Vierra M, McLoone K, Martin E, Thomas A, Everts RE, Brooks SA, Lafayette C. Three Novel KIT Polymorphisms Found in Horses with White Coat Color Phenotypes. Animals. 2025;15(7):915.

Pepper, B., North, E., Culwell, J., Nicodemus, M.C., Cavinder, C., Harvey, K., Williams, T. (2025) Pedigree Tracing to Determine the Origin of the Golden Coat Phenotype within the Golden American Saddlebred Horse. Journal of Equine Veterinary Science, Volume 156, 105752. https://doi.org/10.1016/j.jevs.2025.105752.

Ellsworth, S., Nicodemus, M.C., Lemley, C.O., Harvey, K., North, E., Beranger, J., Culwell, J. (2025) Spatiotemporal gait parameters associated with speed of the intermediate gaits of Spanish Colonial Horse breeds: A preliminary study, Journal of Equine Rehabilitation, Volume 3, 100033, https://doi.org/10.1016/j.eqre.2025.100033.

Finno CJ. Genetics of muscle disease. Vet Clin North Am Equine Pract 2025;41(1):17-29.

Heath H, Peng S, Szmatola T, Ryan S, Bellone RR, Kalbfleish T, Petersen JL, Finno CJ*. A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome. BMC Genomics 2025;26(1):88.

Finno CJ, Rogers SL, Donnelly CG, Affolter VK, Woolard K, Miller AD, Bellone RR, Petersen JL. Spatial transcriptomics defines the cell-specific RNA landscape of equine dorsal root ganglia. Vet Pathol 2025;62(40): 3009858241312623, online ahead of print.

van der Graaf L, Leigh W, Szmatoła T, Roberts K, Ryan S, Brown B, Van Buren S, Finno CJ*, Petersen JL. A missense mutation in the KCNE4 gene is not predictive of equine anhidrosis. Anim Genet 2025;56(1):e70004.

Barber AM, Kingsley NB, Peng S, Giulotto E, Bellone RR, Finno CJ, Kalbfleisch T, Petersen JL. Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions. Front Genet 2025;16:1534461.

Finno CJ. How nutrigenomics impacts equine health- A case study of vitamin E. J Equine Vet Sci 2025;148:105421.

Bacon EK, Donnelly CG, Finno CJ*, Haase B, Velie BD. Exploring the genetic influences on equine analgesic efficacy through genome-wide association analysis of ranked pain responses. Vet J 2025;312:106347.

Cappelletti E, Piras FM, Biundo M, Bellone RR, Finno CJ, Kalbfleisch TS, Petersen JL, Nergadze SG, Giulotto E. CENP-A and centromere evolution in equids. Chromosome Res 2025;33(1):13.

Bacon EK, Finno CJ*, Donnelly CG, Haase B, Knych HK, Velie BD. Evaluating the extent to which ataxia and responsiveness to stimuli reflect the efficacy of xylazine sedation using pharmacokinetics. J Equine Vet Sci 2025;152:105652.

Maas LT, Louie EW, Finno CJ, Donnelly CG, Stern JA, Hill AE, Morgan JM. Cardiac arrhythmia prevalence and risk factors in 24-h electrocardiograms of sedentary horses. Equine Vet J 2025; Jul 18. doi: 10.1111/evj.14543. Online ahead of print.

Van Buren SL, Brown CT, Szmatoła T, Finno CJ.* A comparative review of short genetic variant databases across humans and animal species. Brief Bioinform 2025;26(4):bbaf356.

Van Buren SL, Petersen JL, Brown CT, Finno CJ.* Genotype concordance and trait mapping efficacy comparing data from the Equine 670 K SNP array with whole genome sequence in 21 horses. Anim Genet 2025;56(4): e70037.

Cullen JN, Cieslak J, Petersen JL, Bellone RR, Finno CJ, Kalbfleisch TS, Calloe K, Capomaccio S, Cappelli K, Coleman SJ, Distl O, Durward-Akhurst SA, Giulotto E, Hamilton NA, Hill EW, Katz LM, Klaerke DA, Lindgren G, MacHugh DE, Mackowski M, MacLeod JN, Metzger J, Murphy BA, Orlando L, Raudsepp T, Silvestrelli M, Strand E, Tozaki T, Trachsel DS, Valderrama Figueroa LS, Velie BD, Wade CM, Waud B, Mickelson JR, McCue ME. Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression. PLoS Genet 2025;21(9): e1011835.

Petersen JL, Finno CJ. Additional evidence fails to associate variation in KCNE4 with equine anhidrosis. Animal Genetics. In Press.

Shi Y, Maga EA, Mienaltowski MJ. Fecal microbiota changes associated with pathogenic and non-pathogenic diarrheas in foals. BMC Res Notes. 2025 Jan 23;18(1):34. doi: 10.1186/s13104-025-07110-9. PMID: 39849534; PMCID: PMC11760091.

Michael J. Mienaltowski, Sarah Hernandez, Emma Nastrini, Carissa L. Wickens, Molly E. McCue, Laura Patterson Rosa, Elaine M. Norton, Annette M. McCoy, Samantha A. Brooks. United States stakeholder insights on genetic testing for equine health and breeding. bioRxiv 2025.07.29.667538; doi: https://doi.org/10.1101/2025.07.29.667538.

Beaumont, R.E., C. Flood, and D.J. Guest, Inhibition of interleukin-1 receptor-associated kinase (IRAK)-4 provides partial rescue of interleukin-1 beta induced functional and gene expression changes in equine tenocytes. Molecular Biology Reports, 2025. 53(1):54. doi: 10.1007/s11033-025-11219-2

Ross E. Beaumont, Emily J. Smith, Clara David, Yasmin Z. Paterson, Elena Faull, Deborah J. Guest. Equine adult, fetal and ESC-tenocytes have differential migratory, proliferative and gene expression responses to factors upregulated in the injured tendon, Cells & Development (2025) 181, 204003. doi.org/10.1016/j.cdev.2025.204003.

Barber AM, Kingsley NB, Peng S, Giulotto E, Bellone RR, Finno CJ, Kalbfleisch T, Petersen JL. Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions. Front Genet. 2025 Feb 27;16:1534461. doi: 10.3389/fgene.2025.1534461. PMID: 40084169; PMCID: PMC11903428.

Castiglione GM, Chen X, Xu Z, Dbouk NH, Bose AA, Carmona-Berrio D, Chi EE, Zhou L, Boronina TN, Cole RN, Wu S, Liu AD, Liu TD, Lu H, Kalbfleisch T, Rinker D, Rokas A, Ortved K, Duh EJ. Running a genetic stop sign accelerates oxygen metabolism and energy production in horses. Science. 2025 Mar 28;387(6741):eadr8589. doi: 10.1126/science.adr8589. Epub 2025 Mar 28. PMID: 40146832.

Cappelletti E, Piras FM, Biundo M, Bellone RR, Finno CJ, Kalbfleisch TS, Petersen JL, Nergadze SG, Giulotto E. CENP-A and centromere evolution in equids. Chromosome Res. 2025 Jun 30;33(1):13. doi: 10.1007/s10577-025-09773-3. PMID: 40586953; PMCID: PMC12208984.

Steensma MJ, Ducro BJ, Dibbits B, Doekes HP, van Schipstal JGC, Kalbfleisch T, Groenen MAM, Derks MFL. High-quality, haplotype-resolved reference genomes of the Dutch warmblood horse and Friesian horse using trio binning. BMC Genomics. 2025 Sep 1;26(1):790. doi: 10.1186/s12864-025-11985-0. PMID: 40890628.

Burnett M, Norton E. Advancing equine health through genetic and environmental research: a one health approach. Am J Vet Res. 2025 Apr 2;86(5):ajvr.25.03.0079. doi: 10.2460/ajvr.25.03.0079.

Bailey VN, Gilbert BM, Vetter M, Oberhaus EL. Melatonin receptors and thyroid stimulating hormone in the equine pars tuberalis: Potential modulators of seasonal reproduction in the mare. J Neuroendocrinol. 2025 Oct;37(10):e70077. doi: 10.1111/jne.70077. Epub 2025 Aug 10.

Variation in Four Horse Gait Categories Illustrated by Quantitative Analysis With ANALOC-E. Staiger EA, Pereira de Toledo A, Rizzato Paschoal V, Patterson Rosa L. Vet Med Int. 2025 Aug 6;2025:4906015. doi: 10.1155/vmi/4906015. eCollection 2025. PMID: 40809801

Appendix B: Research presentations

 January 2026. Plant and Animal Genome 33, San Diego, CA

Ryan et al. Altered gene expression in the liver and small intestine of horses with equine neuroaxonal dystrophy. (University of California-Davis)

Roberts et al. Identifying and quantifying predictive protein biomarkers for equine neuroaxonal dystrophy. (University of California-Davis)

Balasubramaniam et al. Runs of homozygosity in Thoroughbred horses: comparison between fractur cases and the general population. (University of Nebraska)

McCoy at el. Alterations in gastric microbiota in horses with colic. (University of Illinois)

McCoy et al. Utility of circulating inflammatory gene expression in detecting early post-traumatic osteoarthritis. (University of Illinois)

Psifidi et al. Integrating ATAC-seq and RNA-seq to investigate the transcriptomic and regulatory signature of equine recurrent rhabdomyolysis. (Royal Veterinary College, University of Minnesota)

Anderson et al. Investigating structural variants involved in disorders of sex development in horses (Texas A&M University)

Cullen et al. Updating Axiom MNEc670 Equine SNP array to the new T2T genome. (University of Minnesota, Texas A&M University, University of Kentucky)

Hegdahl et al. Comparative analysis of genetic diversity through time using pedigree and SNP-based analysis of the American Shire Horse. (University of Nebraska)

AboudEl Ela et al. Developing of cost-efficient genomic strategies through imputation of skim sequencing in Thoroughbred horses. (University of Kentucky)

Robyn et al. Generation of telomere-to-telomere genomes from a Grevy’s Zebra x Horse hybrid for integration into the equid pangenome project. (University of Kentucky)

Derks et al. Deficiency in homozygous haplotypes reveals recessive lethal variations affecting fertility in the Friesian horse. (Wangeningen University and Research)

Cullen et al. The Equine Pangenome: a new reference for the horse. (University of Minnesota, Texas A&M University, University of Kentucky)

 June 2025. Equine Sciences Society, Ft. Collins, CO

I Amarante, F Araujo, L Patterson Rosa. Investigating genetic variants and pedigree-based diversity in Brazil’s Friesian horse population. (Universidade Federal de Lavras, Long Island University)

HC Anderson, SC Stroupe, R Juras, BW Davis, T Raudsepp. Mutations in the androgen receptor gene and other sex development key genes are associated with equine disorders of sex development. (Texas A&M University)

BPG Araujo, RS Moura, CA Perazza, LNR Patterson, SLC Meirelles. Lineage differentiation in the Mangalarga Marchador breed through private microsatellite alleles. (Universidade Federal de Lavras, Universidade de Mogi das Cruzes, and Long Island University)

EK Bacon, D Parnell, J McElroy, G Muscatello, BD Velie. How prior Thoroughbred racing performance influences competition level in a horse’s post-racing eventing career. (University of Sydney, University of Melbourne)

BN Brown, S Ghosh, A Miller, GA Cortopassi, RA Grahn, RR Bellone, CJ Finno. Identification of a cryptic exon in FDXR associated with equine juvenile spinocerebellar ataxia in Quarter Horses. (UC Davis, Cornell University)

J Culwell, MC Nicodemus, E North, A Irons, M Vandiver, T Williams. Pedigree tracing to determine coat color phenotype found within the Mountain Pleasure Horse Breed. (Mississippi State University, University of Mississippi, Unity Environmental University)

CE Fedorka, KE Scoggin, S Coleman, J Hatzel, M Burleson, MHT Troedsson. Unveiling the equine placental transcriptome: a novel study on ICSI-derived pregnancies. (Colorado State University, University of Kentucky, Spy Coast Farm, Lexington, KY)

SM Hammack, SG Moshage, ME Kersh, AM McCoy. Exercise-induced changes in foal myokine gene expression are specific to muscle type. (University of Illinois Urbana-Champaign)

TR Hegdahl, NP Balasubramaniam, JL Petersen. Temporal analysis of genetic diversity in the American Shire horse from 1999 to 2023. (University of Nebraska -Lincoln)

AO Wong, MJ Mienaltowski. Targeting glycolysis in tendon constructs to enhance healing and reduce fibrosis. (UC Davis)

S Hernandez, E Nastrini, E Norton, AM McCoy, SA Brooks, MJ Mienaltowski. U.S. stakeholder survey examining understanding of equine genetics and concerns for genetic diseases. (UC Davis, University of Arizona, University of Illinois Urbana-Champaign, University of Florida)

A Johnston, A McLean, C Xue, S Jacob, E Norton. Establishing metabolic parameters in mules. (University of Arizona, UC Davis, Ross University, Michigan State University)

E Molloy, S Stimpson, B Davis, B Esparza, O Illanes, L Patterson Rosa. Characterizing the Grey locus genetic variation in a mare with widespread metastases and heart failure through targeted sequencing. (Long Island University, Texas A&M University)

M Parr, E Shepherd, M Hines, L Strickland, T Freeman, S Moisa, J Beever, J Ivey. Metabolic gene expression differences in emaciated and moderately conditioned horses: RNA-seq analysis of post-mortem skeletal muscle. (University of Tennessee)

F Raza, CH Isaac, M Cercone. Unraveling left recurrent laryngeal neuropathy in horses: Insights from gene expression profiles. (Cornell University)

 Others self-reported by stations

Culwell, J., Nicodemus, M.C., DeMorato, S., Glenn, A., Evans, H., Williams, T. (2025). Breed-Specific Predisposition to Equine Recurrent Uveitis Within an Academic Institution Multi-Breed Teaching Herd. Proceedings of the 2025 Summer Mississippi State University Honors College Undergraduate Research Symposium. Pg. 18. https://www.urcd.msstate.edu/sites/www.urcd.msstate.edu/files/2025-08/Summer%202025%20URS%20Booklet.pdf.

Culwell, J., Nicodemus, M.C., North, E., Irons, A., Vandiver, M., Williams, T. (2025). Pedigree tracing to determine coat color phenotype found within the Mountain Pleasure Horse Breed. Journal of Equine Veterinary Science, Volume 148, 105514, https://doi.org/10.1016/j.jevs.2025.105514.

DeMorato, S., Nicodemus, M.C., North, E. (2025). Genetic Ocular Diseases in Stock-type Horse Breeds: A Selected Review of Recent Literature. Proceedings of the 2025 Spring Mississippi State University Honors College Undergraduate Research Symposium. Pg. 52. https://www.urcd.msstate.edu/sites/www.urcd.msstate.edu/files/2025-05/Spring%202025%20Symposium%20Booklet.pdf.

Vandiver, M., Nicodemus, M.C., Culwell, J., North, E., Irons, A., Williams, T. (2025). PSIV-26 Tracing changes in coat color phenotype over time within the Mountain Pleasure Horse Association., Journal of Animal Science, Volume 103, Issue Supplement_3, October 2025, Pages 346–347, https://doi.org/10.1093/jas/skaf300.402

Vandiver, M., Nicodemus, M.C., Culwell, J., North, E., Williams, T. (2025). Tracing coat color phenotype over time within the Mountain Pleasure Horse Association. Proceedings of the 2025 Spring Mississippi State University Honors College Undergraduate Research Symposium. Pg. 125-126. https://www.urcd.msstate.edu/sites/www.urcd.msstate.edu/files/2025-05/Spring%202025%20Symposium%20Booklet.pdf.