Brief Summary of Minutes of Annual Meeting

The meeting was called to order by Annette McCoy on behalf of herself and the other co-coordinators (Mike Mienaltowski, Elaine Norton). Angelica Van Goor, National Program Leader for S1094, could not attend, but her contact information was provided. The S1094 multistate project objectives were reviewed, as was the procedure for joining S1094 via Appendix E in NIMSS or by directly contacting Cindy Morley (cmorley@uark.edu). Meeting participants were encouraged to recruit their colleagues for multistate membership. We are particularly interested in engaging members of the equine industry and extension officers. Station reports were presented by all participants. Activities completed in the past year were reviewed. Upcoming events relevant to the participants were announced. The group decided that the next S1094 Annual Meeting will be held in conjunction with Plant & Animal Genome (PAG) 32, January 10-15, 2025 in San Diego, CA. A call for contributors to the multistate project newsletter was made, and the floor was opened for other announcements. The meeting was then adjourned.

Three co-coordinators continue to serve the S1094 community: Annette McCoy (University of Illinois), Mike Mienaltowski (University of California-Davis), and Elaine Norton (University of Arizona). Three newsletters were produced in 2023 for dissemination to the Horse Genome Workshop listserv (maintained by the co-coordinators) and the general public via member contacts. Each newsletter highlighted meetings and community efforts, including workshops at the Plant and Animal Genome conference, Equine Sciences Society meeting, and International Society for Animal Genetics (ISAG) conference. Stories highlighting partnerships between scientist members and stakeholders were prominently featured, as well as new publications from the group. In collaboration with Dr. Samantha Brooks (University of Florida), the co-coordinators have developed a stakeholder survey that has gotten IRB approval and will be disseminated in spring 2024. S1094 members from the University of Kentucky are investigating population structure of the Thoroughbred horse population in the United States in response to concerns by breeders about loss of diversity and inbreeding with a goal of better management of closed studbooks; similar work is planned to support Saddlebred breeders.

Short-term Outcomes: The members of S1094 leverage community resources in the development of new genetic tests that can then be offered commercially once validated. A recent example is the addition in January 2024 of a new test for Congenial Myotonia in New Forest Ponies offered by the University of California-Davis Veterinary Genetics Lab. Education bulletins are released by the VGL to share updates with stakeholders. One of the major goals of the Horse Genome Workshop community is to make the tools and resources that have been developed easily accessible to the broader community. A web portal which provides resources for accessing equine FAANG data was recently launched, supported by the University of Kentucky. This portal can be freely accessed at: www.equinegenomics.uky.edu.

Outputs: Data from several collaborative projects are being generated and made publicly available in repositories. These include whole genome sequencing, RNAseq, and ChIPseq, all generated as part of the equine FAANG initiative (led by the University of California-Davis and University of Nebraska). As part of the ongoing community pangenome project (led by the University of Kentucky) new shotgun sequencing from horses and non-caballine individuals have been generated and are publicly available. A new telomere-to-telomere (T2T) Thoroughbred reference has recently been completed. All of these resources are being leveraged to update annotation for the reference genome EquCab3.0. Containerized workflows for use with an array of equine genomics data have been developed (led by the University of Minnesota and University of Kentucky) and are available for use. A list of publications from S1094 contributors is included in this report.

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.