S1094: Genomic tools to improve equine health, wellbeing and performance

(Multistate Research Project)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[08/03/2023] [03/08/2024] [03/28/2025]

Date of Annual Report: 08/03/2023

Report Information

Annual Meeting Dates: 06/06/2023 - 06/09/2023
Period the Report Covers: 10/01/2022 - 07/14/2023

Participants

Participants: A hybrid business meeting was held on 6/7/23 in conjunction with the Equine Sciences Society annual meeting. All members of the Horse Genome Workshop mailing list (horse-genome-workshop@googlegroups.com) were invited to participate, regardless of membership status in S1094. The following individuals attended and presented station reports:
Bailey, Ernie (ebailey@email.uky.edu) - University of Kentucky;
Brooks, Samantha (samantha.brooks@ufl.edu) - University of Florida;
Coleman, Stephen (Stephen.Coleman@colostate.edu) - Colorado State University;
Loux, Shavahn (slo236@uky.edu) - University of Kentucky;
Kalbfleisch, Ted (ted.kalbfleisch@uky.edu) - University of Kentucky;
McCoy, Annette (mccoya@illinois.edu) - University of Illinois;
Mienaltowski, Mike (mjmienaltowski@ucdavis.edu) - University of California-Davis;
Patterson-Rosa, Laura (Laura.Patterson@sulross.edu) - Sul Ross State University
Petersen, Jessica (jessica.petersen@unl.edu) - University of Nebraska
Staiger, Ann (Elizabeth.Staiger@tamuk.edu) - Texas A&M University – Kingsville

Station reports were also provided by the following individuals who could not attend:
Elaine Norton (elainenorton@arizona.edu) - University of Arizona;
Terje Raudsepp (terje@tamu.edu) - Texas A&M University;
Leslie Lyons (lyonsla@missouri.edu) - University of Missouri

Brief Summary of Minutes

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), welcoming in-person and virtual participants. Angelica Van Goor, National Program Leader for S1094, provided a brief NIFA update. A summary of her overview was provided for distribution to the Horse Genome Workshop community via the mailing list. 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. 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) 31, January 12-17, 2024 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.

Accomplishments

Accomplishments: With the sunsetting of NRSP-8, the National Animal Genome Research Program, in 2023, the equine genetics community identified the need to develop a new umbrella multistate program that would support our collective efforts at developing shared resources and educational tools. A writing committee was identified at the Havemeyer Horse Genome Workshop in summer 2022 (Ernie Bailey, Samantha Brooks, Stephen Coleman, Sian Durward-Akhurst, Ted Kalbfleisch, Annette McCoy, Michael Mienaltowski) and submitted a multistate proposal through the south region later that fall. This proposal was approved in early 2023 and has been designated S1094 “Genomic tools to improve equine health, wellbeing, and performance.” Three co-coordinators were elected: Annette McCoy (University of Illinois), Mike Mienaltowski (University of California-Davis), and Elaine Norton (University of Arizona). S1094 has four objectives:   OBJ 1. Improve detection, curation and annotation of pan-genomic variability for genetic selection, as well as stewardship of genetic diversity, across horse breeds and exotic or feral populations; OBJ 2. Apply and improve genomic resources to increase our understanding of equine performance and disease; OBJ 3. Expand the availability of genetic diagnostic testing and education on its use; OBJ 4. Create platforms for broad sharing of data, technology, and resources to enhance continued development and application of genomics tools in the industry.   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 December 2022 of a new Dominant White allele, termed W13, to the commercial panel 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: <a href="http://www.equinegenomics.uky.edu">www.equinegenomics.uky.edu</a>.   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. All of these resources have been leveraged to produce an updated 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.   Activities: <ol> <li>Equine Genome Workshop, Plant and Animal Genome (PAG) 30, January 14-15, 2023, San Diego, CA.</li> </ol> The meeting was chaired by Dr. Felipe Avila (University of California-Davis) and co-chaired by Dr. Elaine Norton (University of Arizona). More than 70 scientists, trainees, and guests from 35 different universities and organizations from around the world were given the opportunity to hear about research advances from the past year from 15 diverse speakers. This work highlighted the varied applications of genomic and transcriptomic tools and resources developed by the Equine Genome community for investigation of horse physiology and disease over the previous two decades of NRSP-8 support. The workshop’s keynote address was given by Dr. Sue Stover, from the University of California-Davis, a world-renowned expert in the mechanisms of orthopedic injury in racehorses. Her talk highlighted the ways in which genomics tools could be applied to a wide variety of equine health, welfare, and performance issues and illustrated the need for cross-disciplinary collaboration and involvement of partners from the equine industry to move equine research forward. <ol start="2"> <li>Workshop: Genomic tools to improve equine health, well-being, and performance, Equine Sciences Society (ESS), June 6-9, 2023, Grapevine, TX.</li> </ol> The workshop was organized by Dr. Stephen Coleman (Colorado State University), Dr. Annette McCoy (University of Illinois) and Dr. Samantha Brooks (University of Florida). The workshop was intended as a forum for ESS members across specialties to open a dialogue with members of the equine genetics community and hopefully spark ideas and collaborations that could lead to the development of new tools, identification of new lines of investigation, and broader dissemination of existing knowledge and resources. Approximately 50 scientists and trainees attended the workshop, which included a general overview of equine genetics, pre-recorded videos from S1094 members describing the development and applications of genetics tools and resources for equine researchers, and a veterinary perspective on the role of genetics in clinical equine medicine.      Milestones: Several milestones were proposed for the first year of the project: <ol> <li>Engagement of researchers at ~20 stations across the country for multistate participation. Current S1094 members are being asked to actively recruit new participants, with a particular interest in engaging members of the equine industry and extension agents. The ESS workshop was organized in part to engage a different group of stakeholders than is typically reached at PAG and other genetics-focused meetings. To date, S1094 includes 13 researchers at 11 stations across the United States and two researchers at two European institutions.</li> <li>Generation of summary stations’ strengths and collaborative interests ahead of summer workshop meeting. This information was solicited via the call for station reports in Spring 2023.</li> <li>Collaborative, international, summer workshop meeting, focus on drafting and launch of the first stakeholder needs assessment. Work towards this milestone is ongoing, with the goal of launching a stakeholder needs assessment in late 2023.</li> <li>Renew website with lists of educational materials for stakeholders and genomics resources for researchers. A newly redesigned website for the International Horse Genome Workshop includes reports from meetings, identification of participants, and links to community tools. The website can be found at: https://horsegenomeworkshop.com/.</li> </ol>   Impacts: A major focus currently is recruitment to the multistate group, with particular interest in involving extension officers and industry stakeholders. The current members of S1094 have leveraged the resources developed by the equine genomics community for projects that have been awarded grants in the past year totaling more than $3.4 million (complete list in Appendix A). Multistate members provide research and outreach presentations on a regular basis (Appendix B). Two students completed their PhD programs in May 2023 under the direction of the University of Kentucky station (E. Bailey). T. Raudsepp (Texas A&M) continues to operate the only equine clinical cytogenetics service in the United States.   Indicators: The most tangible evidence of industry stakeholder buy-in to community efforts is the widespread adoption of genetic testing among several breed organizations, and the ongoing interest in highly accurate parentage testing. Multistate members working in direct support of these efforts are at the University of California-Davis, University of Kentucky, and Texas A&M University.

Publications

Publications:   <ol> <li>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.</li> </ol>   <ol start="2"> <li>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.</li> </ol>   <ol start="3"> <li>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</li> </ol>   <ol start="4"> <li>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.</li> </ol>   <ol start="5"> <li>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.</li> </ol>   <ol start="6"> <li>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.</li> </ol>  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, <a href="https://doi.org/10.1016/j.jevs.2023.104784">https://doi.org/10.1016/j.jevs.2023.104784</a>. 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, <a href="https://doi.org/10.1016/j.jevs.2023.104673">https://doi.org/10.1016/j.jevs.2023.104673</a>. 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, <a href="https://doi.org/10.1016/j.jevs.2023.104581">https://doi.org/10.1016/j.jevs.2023.104581</a>. 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.   <ol start="12"> <li>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.</li> <li>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.</li> </ol>   <ol start="14"> <li>Shilton CA, Kahler A, Roach JM, Raudsepp T, de Mestre AM. <a href="https://pubmed.ncbi.nlm.nih.gov/36592981/">Lethal variants of equine pregnancy: is it the placenta or foetus leading the conceptus in the wrong direction?</a> Reprod Fertil Dev. 2022 Dec;35(2):51-69. doi: 10.1071/RD22239. PMID:</li> </ol>   <ol start="15"> <li>Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. <a href="https://pubmed.ncbi.nlm.nih.gov/36227030/">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.</a> G3 (Bethesda). 2022 Dec 1;12(12): jkac278. doi: 10.1093/g3journal/jkac278. PMID:</li> </ol>   <ol start="16"> <li>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.</li> </ol>   <ol start="17"> <li>Bailey E. Spotlight: Ancient DNA reveals an early adoption of horse culture by Native Americans. 2023. Trends in Genetics (in press)</li> </ol>   <ol start="18"> <li>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</li> </ol>   <ol start="19"> <li>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.</li> </ol>   <ol start="20"> <li>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.</li> </ol>   <ol start="21"> <li>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 6th Conference of the International Society of Camelid Research and Development (ISOCARD) 2023.</li> </ol>   <ol start="22"> <li>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 6th Conference of the International Society of Camelid Research and Development (ISOCARD) 2023.</li> </ol>   <ol start="23"> <li>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..</li> </ol>   <ol start="24"> <li>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.</li> </ol>   <ol start="25"> <li>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.</li> </ol>   <ol start="26"> <li>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.</li> </ol>   <ol start="27"> <li>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</li> </ol>   <ol start="28"> <li>Taylor WTT, Librado P, Hunska Ta&scaron;unke 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.</li> </ol>   <ol start="29"> <li>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.</li> </ol>   <ol start="30"> <li>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</li> </ol>     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

Impact Statements

Date of Annual Report: 03/08/2024

Report Information

Annual Meeting Dates: 01/13/2024 - 01/14/2024
Period the Report Covers: 06/01/2023 - 03/07/2024

Participants

Antczak, Doug (dfa1@cornell.edu) – Cornell University (also on behalf of Mandi deMestre);
Bailey, Ernie (ebailey@email.uky.edu) - University of Kentucky;
Brooks, Samantha (samantha.brooks@ufl.edu) - University of Florida;
Durward-Akhurst, Sian (durwa004@umn.edu) - University of Minnesota;
Everts, Robin (reverts@etalondx.com) – Etalon Equine Genetics (also on behalf of Christa Lafayette);
Finno, Carrie (cjfinno@gmail.com) - University of California-Davis
Guest, Debbie (djguest@rvc.ac.uk) – Royal Veterinary College (also on behalf Androniki Psifidi and Richard Piercy);
Kalbfleisch, Ted (ted.kalbfleisch@uky.edu) - University of Kentucky;
Lyons, Leslie (lyonsla@missouri.edu) - University of Missouri;
McCoy, Annette (mccoya@illinois.edu) - University of Illinois;
McCue, Molly (mccu0173@umn.edu) - University of Minnesota (also on behalf of Sian Durward-Akhurst);
Mienaltowski, Mike (mjmienaltowski@UCDAVIS.EDU) - University of California-Davis;
Norton, Elaine (elainenorton@arizona.edu) - University of Arizona
Petersen, Jessica (jessica.petersen@unl.edu) - University of Nebraska
Staiger, Ann (Elizabeth.Staiger@tamuk.edu) - Texas A&M University – Kingsville

The following individuals were not available to attend and provided station reports afterwards:
Raudsepp, Terje (terje@tamu.edu) – Texas A&M University (also on behalf of Brian Davis, Rytis Juras, and Gus Cothran)

Brief Summary of Minutes

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.

Accomplishments

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: <a href="http://www.equinegenomics.uky.edu">www.equinegenomics.uky.edu</a>.   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.

Publications

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., &Scaron;ikanjić, 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.

Impact Statements

Impacts: A major focus currently is recruitment to the multistate group, with particular interest in involving extension officers and industry stakeholders. The current members of S1094 have leveraged the resources developed by the equine genomics community for projects that have been awarded grants in the past year totaling more than $3.6 million (complete list in Appendix A). Multistate members provide research and outreach presentations (Appendix B). T. Raudsepp (Texas A&M) continues to operate the only equine clinical cytogenetics service in the United States. Indicators: The most tangible evidence of industry stakeholder buy-in to community efforts is the widespread adoption of genetic testing among several breed organizations, and the ongoing interest in highly accurate parentage testing. Multistate members working in direct support of these efforts are at the University of California-Davis, University of Kentucky, and Texas A&M University.

Date of Annual Report: 03/28/2025

Report Information

Annual Meeting Dates: 01/12/2025 - 01/12/2025
Period the Report Covers: 03/01/2024 - 03/01/2025

Participants

Miller, Don (dm96@cornell.edu) – Cornell University (also on behalf of Doug Antczac and Mandi deMestre); Brooks, Samantha (samantha.brooks@ufl.edu) - University of Florida; Laura Patterson-Rosa (laura.patterson@liu.edu) – Long Island University; Staiger, Ann (Elizabeth.Staiger@tamuk.edu) - Texas A&M University – Kingsville; Durward-Akhurst, Sian (durwa004@umn.edu) - University of Minnesota; Petersen, Jessica (jessica.petersen@unl.edu) - University of Nebraska; Delledonne, Massimo (massimo.delledonne@univr.it) – University of Verona; Kalbfleisch, Ted (ted.kalbfleisch@uky.edu) - University of Kentucky (also on behalf of Ernie Bailey and Jamie MacLeod); Mienaltowski, Mike (mjmienaltowski@UCDAVIS.EDU) - University of California-Davis; Norton, Elaine (elainenorton@arizona.edu) - University of Arizona; Bellone, Rebecca ( rbellone@ucdavis.edu) – UC Davis; Mikko, Sofia (sofia.mikko@slu.se) – Swedish University of Agricultural Sciences (also on behalf of Gabriella Lindgren); Ryder, Oliver (oryder@ucsd.edu) – UCSD/San Diego Zoo; Brian Davis (bwdavis@tamu.edu) – Texas A&M University (also on behalf of Terje Raudsepp, Rytis Juras, and Gus Cothran); Finno, Carrie (cjfinno@gmail.com) - University of California-Davis; McCoy, Annette (mccoya@illinois.edu) - University of Illinois. Station reports were sent in writing from Guest, Debbie (djguest@rvc.ac.uk) – Royal Veterinary College (also on behalf Androniki Psifidi and Richard Piercy); Lyons, Leslie (lyonsla@missouri.edu) - University of Missouri; McCue, Molly (mccu0173@umn.edu) - University of Minnesota.

Brief Summary of Minutes

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 and the update that she sent in advance of the meeting was reviewed. This update will be made available to S1094 members. 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. The results of our equine owner stakeholder survey were presented by Mike Mienaltowski (see more details below). Upcoming events relevant to the participants were announced, with a call for volunteers for 1) development of a stakeholder needs assessment aimed at the scientific community, and 2) development of a workshop for the 2025 Equine Science Society meeting. The group voted for the next S1094 Annual Meeting to be held in conjunction with Plant & Animal Genome (PAG) 33 meeting, January 9-14, 2026 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.

Accomplishments

Accomplishments: 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). Newsletters were produced in 2024 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. In collaboration with Dr. Samantha Brooks (University of Florida), the co-coordinators developed a stakeholder survey aimed at horse owners. Distribution of this survey was facilitated via members (particularly Drs. Molly McCue [University of Minnesota] and Laura Patterson-Rosa [Long Island University]) and extension/industry partners. Preliminary results were presented to the international horse genome community at the 14th Dorothy Russell Havemeyer Equine Genome Mapping Workshop in Caen, Normandy, France in May 2024. Final results were presented at the January 2025 annual meeting and are summarized below:   <ul> <li>412 respondents from 44 states; 60% identified as horse owners and 15% as horse breeders. Nearly 80% of respondents own 10 or fewer horses (62% five or fewer). This was of great interest to us, as many surveys from the horse industry seem to primarily reflect large-scale breeders/trainers.</li> <li>A variety of breeds/disciplines were represented, led by sport horses (33%), stock horses (30%), and Arabians (12%). Racing horses were underrepresented (5%), reflecting the demographics of the respondents.</li> <li>Interestingly, three-quarters of the respondents self-identified as having at least a solid understanding of genetics. They identified their primary sources of genetics knowledge as universities and breed/discipline organizations. To a lesser extent, veterinarians and horse owner community websites/social media were identified as sources of genetics information. Most owners were interested in knowing about genetic diversity levels in their breed of interest, and most were interested in genetic testing for performance genes. Owners of racing horses were particularly interested in performance gene tests.</li> <li>When asked about health concerns of top priority, there were many shared conditions identified across breed/discipline groups. These included arthritis, colic/intestinal disorders, laminitis, metabolic diseases, tendon/ligament injuries, navicular syndrome, and ulcers. Behavior/temperament was also identified as a top priority across groups.</li> </ul>  These results will be shared as an abstract at the 2025 Equine Sciences Symposium. A manuscript is in preparation.  More than a dozen graduate students and two dozen undergraduate students completed their training under the guidance of S1094 members in 2024. Public education and stakeholder outreach efforts by S1094 members are highlighted under Aim 3 accomplishments below.   A major ongoing collaborative effort among S1094 members is the Equid Pangenome International Consortium (EPIC). Led by researchers from the University of Kentucky, University of Minnesota, and Texas A&M University, current contributing members are located at 14 institutions around the world. The aims of this consortium are to develop haplotype phased T2T assemblies from crossbred trios that can be incorporated into an equine pangenome reference. The Thoroughbred T2T assembly was made publicly available this year, and the toolboxes and containerized pipelines being designed by EPIC members are freely available. This effort will completely revolutionize the way that researchers handle genomic data in the horse.    The FAANG data set, which was a major collaborative effort across the S1094 community led by researchers at the University of California-Davis and University of Nebraska was concluded with all data publicly available. The University of Kentucky also hosts an interactive website for these data. The “adopt-a-tissue” initiative helped drive the success of this project, allowing researchers from around the world to contribute financially to the goals of the project even though they were not part of the original project funding proposal.   Additional accomplishments reported by stations specific to the aims of S1094 are detailed below. Though reported by individual stations, activities marked with an asterisk (*) reflect collaborations involving other S1094 stations or stakeholder groups. Publications, research presentations, and grants awarded are detailed in the accompanying appendices.  Aim 1: Improve detection, curation and annotation of pan-genomic variability for genetic selection, as well as stewardship of genetic diversity, across horse breeds and exotic or feral populations. <ul> <li>(Mississippi State) *Launch of a project to identify phenotypical characteristics of U.S. horse breeds to facilitate breeding practices that promote breed preservation. This project is being carried out in collaboration with the Livestock Conservancy, partnering with breed organizations including the Palamino Horse Breeders Heritage Foundation, Palamino Breeders of America Association, and Mountain Pleasure Horse Association.</li> <li>(University of Verona) *We successfully sequenced and assembled the genomes of four horse breeds (Selle Français, Hungarian Sport Horse, Westphalian and Arabian) using deep (30x) ultra-long Nanopore sequencing reads (>1 Mb) from Oxford Nanopore Technologies. These assemblies represent a pivotal advancement in the detection and annotation of pan-genomic variability across horse breeds, significantly enhancing the genetic diversity represented in available reference genomes: the Thoroughbred (EquCab3.0), available since 2018, and the recently assembled Finnish Horse (EquCab_Finn). Compared to EquCab3.0 (genome size: 2.5 Gb; Ncontig: 10,986; N50contig: 1.5 Mb), our assemblies resulted markedly more contiguous and less fragmented (genome sizes: 2.5 Gb, 2.5 Gb, 2.4 Gb, and 2.4 Gb; Ncontig: 172, 148, 178, and 190; N50contig: 53.6 Mb, 58.6 Mb, 56.1 Mb, and 59.9 Mb, for the Selle Français, Hungarian Sport, Westphalian and Arabian horse, respectively), underscoring their utility for accurate curation of genomic variability and stewardship of genetic diversity. These high-quality assemblies are now being integrated into the first equine pangenome graph as part of the Equid Pangenome International Consortium (EPIC).</li> <li>(University of Minnesota) *Mapped >900 equine genomes to the new Thoroughbred T2T reference. The plan will be to use these genomes to improve annotation and investigate population genomics in this population.</li> <li>(University of Minnesota) *I am part of the Equine Pangenome group that is working towards the first equine pangenome.</li> <li>(University of Minnesota) Published on the genetic burden and frequency of disease-causing variants in a population of 534 horses.</li> <li>(UC-Davis) *Provided all FAANG datasets and WGS from multiple breeds to assist with pangenome annotation.</li> <li>(University of Missouri) *We have several horse genomes that we have sequenced at the University of Missouri and then provide to collaborators to help find causal DNA variants. One disease, suspected hematochromatosis, is in a mule, hence the develop of the mule genome will be most beneficial to this project! We have supplied several short read genomes for diversity inclusion.</li> <li>(University of Nebraska) *Participated in the successful PanGenome grant effort. Contributed samples/data from Clydesdales for reference genome assembly. Continued work on genetic diversity of breeds (Thoroughbred, Clydesdale, Shire).</li> <li>(Royal Vet College) We developed and used a polygenic risk score for catastrophic fracture risk in Thoroughbred horses to develop in vitro cell culture models to compare bone forming osteoblasts derived from horses at high and low risk of fracture. This approach identified a functional SNP upstream of the Collagen Type III gene which is associated with catastrophic fracture risk in Thoroughbred horses (Palomino Lago et al 2024). It also identified 112 genes that are differentially expressed in osteoblasts in high and low risk horses (Palomino Lago et al 2025), which suggested that processes regulating the extracellular matrix may be involved.</li> </ul>  Aim 2: Apply and improve genomic resources to increase our understanding of equine performance and disease. <ul> <li>(University of Verona) We are working on an imputation panel tailored for steeplechase horses to enable cost-effective genomic characterization at a population scale. Using 30x Illumina whole-genome sequencing (WGS) data from 35 sport horses representing different breeds, we evaluated six state-of-the-art genotype imputation tools: Beagle, GLIMPSE2, Impute5, loimpute, Minimac3, and Quilt2. Quilt2 achieved the best performance, with >95% accuracy in imputing more than 600,000 genomic variants on three chromosomes in two independent horses. This represents a significant improvement, with >25% and >15% increase in imputation accuracy compared to the panels currently available through Animal-ImputeDB and AGIDB, respectively. These findings directly enhance the utility of imputation for population-scale studies, paving the way for improved insights into equine performance traits and disease mechanisms.</li> <li>(University of Minnesota) Developed 90 equine simulated genomes, which have been made publicly available on the European Nucleotide Archive.</li> <li>(University of Minnesota) *Generated IsoSeq data on 9 equine tissues. These will be used to improve annotation of the equine genome.</li> <li>(University of Minnesota) Investigation of the genetics of exercise associated sudden death and atrial fibrillation in Standardbred and Thoroughbred racehorses.</li> <li>(UC-Davis) *Currently developing large allele frequency database that incorporates all public equine WGS data for SNP variants and small indels.</li> <li>(UC-Davis) Using genomics, we examined the cytoprotective properties of ascorbic acid for stressed tendon and peritenon cells, and we determined the correlations between mare’s milk microbiota and foal age to a healthy equine gastrointestinal microbiota. Moreover, we examined the detrimental effects of anti-inflammatory diclofenac on tendon cells.</li> <li>(University of Nebraska) Continued work to understand the genetics of shivers in draft horses.</li> <li>(University of Nebraska/UC-Davis) Studying chronic progressive lymphedema; we have collected samples, transcriptome and genotype data for this project.</li> <li>(University of Arizona) Identification of gene by environment interaction contributing to equine metabolic syndrome. For this project, we have completed collection of the EMS phenotype data from 690 Arabian horses.  Using the date, we were able to complete a large-epidemiological evaluation of EMS across the Arabian breed and within their subpopulations.  Additionally, we gathered genomic and epigenetic data, which will be analyzed this year to identify potential interactions between genetic predisposition and environmental factors contributing to EMS.</li> <li>(University of Arizona) Insulin dysregulation: placental changes and foal health For this project, we have started phenotype and genotype collection on 45 foals (15 born to foals with EMS, 15 insulin sensitive mare, and 15 insulin sensitive-obese mares).  This includes data for transcriptomics on the foals.</li> <li>(University of Illinois) Ongoing project investigating molecular markers of post-traumatic osteoarthritis in an equine fetlock osteochondral fragment model.</li> <li>(University of Illinois) Ongoing project investigating muscle gene expression response to growth and exercise in foals.</li> <li>(University of Illinois/University of Minnesota) Ongoing projects investigating osteochondrosis dissecans, gait, and performance in Standardbred racehorses.</li> </ul>  Aim 3: Expand the availability of genetic diagnostic testing and education on its use. <ul> <li>(University of Florida) Several lay presentations/podcasts/articles:</li> </ul> Articles: <ul> <li>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).</li> <li>Interviewed in: “How Coat Color and Genetics Influence Equine Behavior” by Sarah Welk Baynum, The Horse, (USA National, March 8, 2024), https://thehorse.com/1125641/how-coat-color-and-genetics-influence-equine-behavior/</li> <li>Interviewed in: “Handling and Training Donkeys” by Haylie Kerstetter, The Horse, (USA National, August 8, 2024), https://thehorse.com/1122463/handling-and-training-donkeys/</li> </ul> Presentations: <ul> <li>Kentucky Equine Research: 27th Equine Health and Nutrition Conference, Ocala FL, February 5-6, 2024 – “Should You Sweat It? Anhidrosis in the Equine Athlete”</li> <li>Equine Affaire, Columbus OH, April 11th 2024 – “DNA & Genetic Testing Isn’t Just for Breeders: Get a Leg Up on Genetics, Tips for Horse Owners”</li> <li>Equine Affaire, Columbus OH, April 12th 2024 – “Galloping into the Future: What’s Next for Equine Genomics, Recent Discoveries and Cutting Edge Applications”</li> <li>2024 Al Khamsa Annual Meeting and Convention, Online, June 15th 2024 – “DNA 101: Genetic Profiling, what is it?”</li> <li>American Trakehner Association, 2024 Annual Meeting, Ocala FL, December 20th 2024</li> </ul> Podcasts <ul> <li>Guest appearance on Scoop & Scale by Dr. Claire Thunes, “Ep. 23: Is How My Horse Sweats Normal?”, Podcast, May 28, 2024.</li> <li>Guest appearance on Tack Box Talk by Kris Hiney, “Sane and Sound: The story of an equine geneticists goal to build a better horse”, Podcast, June 10nd 2024.</li> <li>Guest appearance on Tack Box Talk by Kris Hiney, “Genetics Part 2: The story of fragile foals and muscle disorders”, Podcast, July 22nd 2024.</li> </ul> <ul> <li>(University of Minnesota/UC-Davis/University of Arizona) <ul> <li>ACVIM 1-hour panel: A Panel on Clinical Applications for Complex Genetic Diseases (Drs. Carrie Finno, Sian Durward-Akhurst, Elaine Norton and Lauren Hughes) (~25 attendees, board-certified equine internists and veterinary students, residents and technicians)</li> </ul> </li> <li></li> <li>(University of Minnesota) Presentations for the horse/veterinary community: <ul> <li>Horseracing Safety Integrity Authority and International Federation of Horseracing Authorities – discussed opportunities for genetics to reduce the frequency of exercising associated sudden death in Thoroughbred racehorses.</li> <li>Minnesota Trotting Association – talked about arrhythmias and the genetics or arrhythmias in racing Standardbreds.</li> </ul> </li> <li>(UC-Davis) Provided location of genetic mutation for Equine Juvenile Spinocerebellar Ataxia (EJSCA) to UC Davis Veterinary Genetics Laboratory for 2024 testing.</li> <li>(UC-Davis) Educational presentations on genetics: <ul> <li>American College of Veterinary Internal Medicine Forum, Minneapolis, MN; 45-minute presentation: Ongoing Investigation of Genetic Diseases in Horses (~50 attendees, including board-certified equine internists and veterinary students, residents and technicians)</li> <li>Updated American Association of Equine Practitioner’s Statement on Genetic Defects</li> <li>American Association of Equine Practitioner conference, Orlando, FL; 1.5 hr session: Kester News Hour – included current studies on genetic testing (~3500 attendees, including veterinarians, veterinary students and veterinary technicians)</li> <li>California residents and horse enthusiasts at 2024 UC Davis Horse Day on October 12, 2024.</li> </ul> </li> <li>(University of Nebraska/UC-Davis) Conducted a study focused on validation of a commercial genetic test (test is not valid and should not be offered commercially).</li> <li>(University of Nebraska) Stakeholder outreach sessions: <ul> <li>American Shire Association: approval to conduct a population-level survey of genetic variation, continued interaction with individual breeders</li> <li>Presented to UNL Extension event, “UNL Race Nebraska and Horsemen’s Health Update.” Genetic Diversity in Thoroughbreds: What do we Know?</li> </ul> </li> <li>(Royal Veterinary College) Invited speaker at the International Federation of Horseracing Authorities (IFHA) Global Summit on Equine Safety June 2024.</li> <li>(University of Arizona) Arizona Arabian Association: Did a presentation on EMS and nutrition to 58 members</li> <li>(University of Illinois) Presentation on genetic tools and testing at the American Association of Equine Practitioners, ~100 attendees</li> </ul>    Aim 4: Create platforms for broad sharing of data, technology, and resources to enhance continued development and application of genomics tools in the industry. <ul> <li>(University of Florida) We are continuing to develop tools to enable high-throughput and precise locomotor phenotyping and hope to have several packaged and pipelines published in 2025. A preliminary version of our review dashboard is publicly available on BioRxiv and GitHub: <a href="https://www.biorxiv.org/content/10.1101/2023.10.30.564795v2.full">https://www.biorxiv.org/content/10.1101/2023.10.30.564795v2.full</a></li> <li>(University of Minnesota) *Development of containerized pipelines for analysis of whole-genome sequencing data, RNA sequencing data, and pangenome map creation.</li> </ul>   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 November 2024 of an updated test for gray alleles offered by the University of California-Davis Veterinary Genetics Lab. This now includes a novel gray allele that was recently found to be correlated to increased risk of gray horse melanoma (Rubin et al. Nature Communications 15:7510, 29 Aug 2024) – work that was a collaborative effort between researchers at the University of Uppsala and S1094 members at UC-Davis. 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: <a href="http://www.equinegenomics.uky.edu">www.equinegenomics.uky.edu</a>.   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.   Activities: <ol> <li>14th Dorothy Russell Havemeyer Equine Genome Mapping Workshop, May 12-15, 2024, Caen, Normandy, France</li> </ol> Members of the equine genetics community from around the world gathered to share research findings and strengthen collaborative relationships at this workshop, which has been held every 2-3 years since the 1990s. <ol start="2"> <li>Equine Genome Workshop, Plant and Animal Genome (PAG) 31, January 11-12, 2025, San Diego, CA.</li> </ol> The meeting was chaired by chaired by Dr. Ann Staiger (Texas A&M University – Kingsville) and co-chaired by Dr. Sian Duward-Akhurst (University of Minnesota). More than 50 scientists and trainees from 29 different universities and organizations from around the world were given the opportunity to hear about research advances from the past year from 16 diverse speakers. This work highlighted the varied applications of genomic and transcriptomic tools and resources developed by the Equine Genome community for investigation of horse physiology. The results of the S1094 equine owner stakeholder survey were presented and discussed. <ol start="3"> <li>Workshop Practical Pangenomics: Containerized Workflows for Building Graphs and Variant Discovery in Livestock and Companion Animals Plant and Animal Genome (PAG) 32, January 13, 2024, San Diego, CA. This workshop was a collaborative effort between S1094 members at the University of Minnesota, University of Kentucky, and Texas A&M University highlighting the development of pangenomes for agricultural animal species (using the horse an example) and associated interactive tools. This workshop was open to researchers across species and had a robust attendance.</li> </ol>   Milestones: We continue to work towards several milestones for this project: <ol> <li>Engagement of researchers at ~20 stations across the country for multistate participation. Current S1094 members are being asked to actively recruit new participants, with a particular interest in engaging members of the equine industry and extension agents. We are slowly increasing the number of official participants, with continued robust interactions with researchers who have not yet been able to join. To date, S1094 includes 18 researchers at 14 stations across the United States and three researchers at two European institutions. These members engage in robust collaborative efforts with individuals who are part of the larger equine genetics community but are not yet part of S1094.</li> <li>Generation of summary stations’ strengths and collaborative interests ahead of summer workshop meeting. This information was solicited via the call for station reports in January 2025.</li> <li>Collaborative summer workshop A workshop focused on equine scientists has been accepted for the Equine Sciences Society meeting in June 2025. This goal of this interactive workshop is to provide information about available genetics resources created by the S1094 community, and to facilitate collaborations between equine genetics experts and scientists in related fields.</li> <li>Stakeholder needs assessments. We will be launching two additional stakeholder needs assessments in 2025. The first will be aimed at (non-genetics) researchers, while the second will be aimed at veterinarians. The launches are planned to coincide with the Equine Sciences Society meeting in June (researcher survey) and the American Association of Equine Practitioners meeting in December (veterinarian survey). A summary of results will be shared with the S1094 community and the broader Equine Genome Workshop group, while stakeholder-specific data will be shared with the relevant community.</li> <li>Renew website with lists of educational materials for stakeholders and genomics resources for researchers. A newly redesigned website for the International Horse Genome Workshop includes reports from meetings, identification of participants, and links to community tools. The website can be found at: https://horsegenomeworkshop.com/.</li> </ol>

Publications

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. <a href="https://doi.org/10.1093/jas/skae234.617">https://doi.org/10.1093/jas/skae234.617</a>.  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. <a href="https://doi.org/10.1016/j.jevs.2024.105209">https://doi.org/10.1016/j.jevs.2024.105209</a>.  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.

Impact Statements

A major focus currently is recruitment to the multistate group, with particular interest in involving extension officers and industry stakeholders. The current members of S1094 have leveraged the resources developed by the equine genomics community for projects that have been awarded grants in the past year totaling more than $3.6 million (complete list in Appendix A). Multistate members provide research and outreach presentations (Appendix B). T. Raudsepp (Texas A&M) continues to operate the only equine clinical cytogenetics service in the United States.
The most tangible evidence of industry stakeholder buy-in to community efforts is the widespread adoption of genetic testing among several breed organizations, and the ongoing interest in highly accurate parentage testing. Multistate members working in direct support of these efforts are at the University of California-Davis, University of Kentucky, and Texas A&M University.