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 in attendance. Activities completed in the past year were reviewed, including in-progress publication of the results of our owner stakeholder survey, initiation of scientist stakeholder survey, workshop conducted at the Equine Sciences Society, and newsletter publication (see more details below). Upcoming events relevant to the participants were announced, with a call for volunteers for 1) administration of a stakeholder needs assessment aimed at the scientific community, 2) development of a stakeholder needs assessment aimed at veterinary medicine, 3) planning for workshop at Equine Sciences Society in 2027, and 4) writing team for S1094 renewal. The group voted for the next S1094 Annual Meeting to be held in conjunction with Plant & Animal Genome (PAG) 34 meeting, January 8-13, 2027 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; recently moved to Mississippi State University).

 Communication: Newsletters were produced in 2025 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.

 Stakeholder surveys: The first S1094 stakeholder survey was aimed at horse owners and was completed in late 2024, with final results presented at the January 2025 annual meeting and summarized in last year’s annual report. A manuscript has been submitted and is in final revisions at the Journal of Equine Veterinary Science. In 2025, development of the second stakeholder survey, aimed at non-genetics scientists, was initiated. Preliminary targeted interviews have been completed, and dissemination of this survey is anticipated in mid-2026. The third stakeholder survey, targeting veterinarians, is planned for release in late 2026 and is in the earliest stage of development.

 Equine Sciences Society (ESS) Workshop: This year’s Equine Science Society Symposium in Fort Collins opened with an exciting and interactive workshop hosted by the S1094 multistate project. Titled “Leveraging Genetics and Genomics Tools in Equine Science,” the workshop, proposed by Dr. Annette McCoy, and delivered by Drs. Elaine Norton, Rebecca Bellone, and Michael Mienaltowski, welcomed 15 participants eager to explore how genetics can help improve breeding and horse health. The workshop began with a refresher of basic genetics concepts using live polling questions administered by Dr. Mienaltowski. Then things got competitive with a genetics card game designed by Dr. Norton. Participants worked in teams to match sires and dams with appropriate genotypes to produce offspring with desired coat color and discipline-specific traits. The card game illustrated both how genetics could be used by breeders to achieve desirable outcomes, and to show educators how to train students to think about the complexities and implications of breeding decisions, all while having fun! After the card game, Dr. Bellone provided attendees with real-world success stories where genetics/genomics approaches were used to solve important industry concerns. These included Leopard Complex Spotting, Congenital Stationary Night Blindness in Appaloosas and Tennessee Walkers, and Squamous Cell Carcinoma (SCC) risk. Attendees then got to practice using the Online Mendelian Inheritance in Animals (OMIA) tool to look up traits and diseases of interest, as well as potential causative variants reported across species. As an illustrative example, Dr. Bellone walked them through the record for SCC, then set attendees loose to explore this great resource. The workshop concluded with a conversation on complex traits and diseases, and how the interaction of genes and the environment make these a challenge to investigate. The take-home message was that collaboration between all equine scientists – not just geneticists – owners, and veterinarians will be needed as we seek to learn more about these traits.

 Student training: More than a dozen graduate, undergraduate, and DVM students completed their training under the guidance of S1094 members in 2025. Public education and stakeholder outreach efforts by S1094 members are highlighted under Aim-specific accomplishments below.

 Other community efforts:

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 continues to host 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.

• (Minnesota*) I am part of the Equine Pangenome group that is working towards the first equine pangenome.
• (Minnesota*) Working on developing a standardized pipeline for causative variant discovery in the horse that is applicable to other domestic animal species.
• (TAMU) Generated several hundred short-read and tens of long-read horse WGS
• (TAMU*) Included six long-read genomes of indigenous horses to horse pangenome
• (TAMU*) Contributed to horse Y chromosome T2T assembly and annotation
• (Florida*) Develop methods for phenotyping in locomotor and sensory phenotypes.
• (Florida*) Supported S1094 efforts to publish survey of animal industry needs for genomic tools.
• (Mississippi State) As horse breed associations within the United States are looking to expand their registration numbers, responsible stewardship of breeding practices to preserve phenotypical characteristics unique to a breed are necessary to ensure future breeding stock reflects that of the foundation lines of the breed. Pedigree tracing assists in exploring generational establishment of breeding stock including historical documentation of coat color phenotype, and this can be of value to breeds where registration guidelines are linked to specific phenotypical characteristics. Working with the Palomino Horse Breeders Heritage Foundation Museum, pedigree tracing was utilized to explore the foundation bloodlines of the breed and potential influence of other alleles besides the crème allele that is present within the current population of the stock-type (e.g. Quarter Horse) and pleasure-type (e.g. Saddlebred) horses of the Palomino Horse Breeders of America Association (PHBA). Further collaborations were established for the pedigree tracing of the pleasure-type group that included working with the Golden American Saddlebred Horse Association and the American Saddlebred Horse & Breeders Association. Similar work as the PHBA study was carried out with the Mountain Pleasure Horse Association in collaboration with the Livestock Conservancy with additional analysis of not only coat color phenotype, but supplementary exploration of gait phenotype. As a breed that is currently on the critical breed list within the Livestock Conservancy due to a small population size, breeding practices are being expanded, but these practices should ensure that the phenotypical characteristics of the foundation bloodlines are preserved in order to maintain the historical foundation of the breed. By working with the horse associations and related organizations, information exchange was facilitated through the research process that allowed for findings including research datasets to assist in promoting responsible breeding practices within the associations and to now setup working groups that include producers within the industry that will work with researchers to establish breeding and registration practices that promote breed preservation.
• (Nebraska, Kentucky, TAMU, Minnesota*) The pan-genome effort has moved forward with the initial publication soon to be submitted that describes the mapping of 77 haplotypes representing 24 breeds of horse to the T2T reference genome and subsequent creation of pangenome graphs and variant calling files. This resource allows for the most comprehensive analysis of diversity in equids to date.  Work is continuing to add additional T2T genomes and haplotypes and to build better means by which others can utilize these data.
• (Nebraska) My group is also working to characterize the genetic diversity of the Shire horse, which is considered critical with regard to sustainability of the population. We have generated 70K genotype data on horses representing 3 generations.  This work will be used to describe changes in diversity, provide a comparison of genomic vs pedigree data, and help breed managers in decision making.
• (RVC) We have identified novel genes and variants that are associated with fracture risk in Thoroughbred racehoses and have biological functions in bone formation (unpublished).
• (Kentucky*) Held RCN supported workshop for the assembly of T2T genomes at the University of Kentucky. It was led by Kai Li, and Dr. Temitayo Olagunju.

 Aim 2: Apply and improve genomic resources to increase our understanding of equine performance and disease.

• (Minnesota*) Generated simulated whole genome sequence data for use to test various computational tools (currently in review).
• (Minnesota*) Working on analyzing IsoSeq data of 9 equine tissues – will be used to improve annotation of the equine genome.
• (Minnesota) Generated whole genome sequence of >200 Standardbred and Thoroughbred racehorses with and without cardiac disease. Currently wrapping up genome wide association analyses for exercise associated sudden death and atrial fibrillation.
• (TAMU) Genomic studies of stallion reproduction, equine disorders of sex development, and coat color
• (Verona) We further improved the genome assemblies of the five horse breeds (Westfalen, Oldenburger, Hungarian Sport Horse, Arabian and Selle français) by adopting the latest version of the hifiasm assembler, together with targeted read filtering strategies, to generate high-quality Nanopore genome assemblies. These methodological refinements led to substantial gains in assembly contiguity and overall quality compared to our previous releases, while preserving genome completeness. Notably, the updated assemblies exhibit genome sizes of [2.91 Gb, 2.90 Gb, 2.90 Gb, 2.88 Gb, 2.92 Gb], which closely match the genome size reported for the recently published telomere-to-telomere (T2T) equine reference genome, rather than the smaller size estimated in the earlier EquCab3.0 assembly released in 2018. In parallel, the assemblies show a reduced number of contigs (Ncontig: [127, 104, 164, 399, 189]) and increased contiguity (N50contig: [80.56 Mb, 84.19 Mb, 63.38 Mb, 35.02 Mb, 56.62 Mb] for the Westfalen, Oldenburger, Hungarian Sport Horse, Arabian and Selle français horse, respectively). Together, these improvements further strengthen the suitability of the assemblies for accurate detection and annotation of structural and sequence-level variation, enhancing their value for pan-genomic analyses and for an improved representation of equine genetic diversity. The refined assemblies are being incorporated into the equine pangenome graph developed within the Equid Pangenome International Consortium (E.P.I.C.).
• (Nebraska*) Working with Dr. Finno, we authored two papers focused on the validation of a commercially used marker that is proposed to be a risk factor for equine anhidrosis (inability to sweat). The first publication was based upon phenotyping and genotyping of 50 horses and the second included additional phenotyped horses as well as additional genetic analyses of the putative risk factor.  Both publications failed to support the use of the putative marker as a risk factor for anhidrosis, providing horse breeders and owners with more rigorous information about the commercially provided test.
• (Nebraska*) We also collected ~100 phenotype/genotypes on Shire and Clydesdale horses for studies of Chronic Progressive Lymphedema. This study has expanded to include not only collaboration with UC Davis (Drs. Bannasch, Affolter) but also Belgian scientists (Drs. Janssens, Buys, Brys).
• (UC Davis) Currently working on testing several biomolecules to understand how they improve tenogenic function of equine tendon proper and peritenon cells. We are using genomics tools to evaluate pathways involved in tenogenic, inflammatory, fibrotic, and metabolic pathways.
• (RVC) All of our results will be published open access and WGS data, RNA sequencing data and genotyping data will be publicly available.
• (RVC) We have developed an immortalized equine osteoblast cell line (paper under review) that will be deposited in the European Collection of Authenticated Cell Cultures (ECACC) so that it is available to other researchers.
• (Kentucky*) Developing T2T genomes for a Shire, Arabian, Thoroughbred, Zebra, Haflinger, and Persian Onager, and work to incorporate them into a pangenome.
• (Illinois) Ongoing project investigating molecular markers of post-traumatic osteoarthritis in an equine fetlock osteochondral fragment model.
• (Illinois) Ongoing project investigating muscle gene expression response to growth and exercise in foals.
• (Illinois, Minnesota*) Ongoing projects investigating osteochondrosis dissecans, gait, and performance in Standardbred racehorses.

 Aim 3: Expand the availability of genetic diagnostic testing and education on its use.

• (Minnesota) As a journal reviewer I have been providing education on the steps involved before establishing that a variant should be used as a genetic test.
• (Minnesota) I have been educating vet students on how they can look to see if a variant has sufficient evidence to support using it as a genetic test.
• (TAMU) Clinical cytogenetics, horse ancestry testing, and parentage testing services offered to the general public.
• (Florida) Supported on campus workshops for interdisciplinary efforts to improve phenotyping and -omics assays for pain and sensation phenotypes.
• (Florida) Many interactions with stakeholder groups. Al-Itaq and Al Khamsa, international associations registering Arabian horses. Regional 4H educational symposia. Advisory role with the American Quarter Horse Association, American Trakehner Association and the WBFSH - World Breeding Federation for Sport Horses.
• (UC Davis) Many interactions with stakeholder groups. 46th Lake Tahoe Equine Conference, Lake Tahoe, NV; American Quarter Horse Association, Las Vegas, NV; Equine Sciences Society, Ft. Collins, CO; American College of Veterinary Internal Medicine, Louisville, KY; National Pedigreed Livestock Council, Sacramento, CA; Burroughs Wellcome Becoming Faculty: a short course on launching a scientific career, Raleigh, NC; University of Nebraska Animal Science Seminar Series, virtual; Florida Veterinary Medical Association Promoting Excellence Symposium, Ft. Lauderdale, FL.
• (Nebraska*) I am working with both the ISAG committee on Animal Genetic Testing as well as another international Animal Genetic Testing Standardization committee (with another S1094 member, Dr. Finno) on developing means to classify confidence in genetic testing and pathogenicity of proposed variants. As a result of this work, each test will undergo similar evaluation protocols to provide a more accurate and fair assessment of their utility.
• (UC Davis*) Planning for a second survey is underway. Dr. Mienaltowski is currently interviewing equine scientists to generate appropriate survey questions for scientists in the equine industry.
• (RVC) We have validated a polygenic risk score for fracture in a new cohort of cases and controls (not yet published). We have received UKRI funding to explore its commercialization.

 Aim 4: Create platforms for broad sharing of data, technology, and resources to enhance continued development and application of genomics tools in the industry.

• (UC Davis*) Supported community use for all public equine data generated in our laboratory through the NCBI SRA database, including mRNA-sequencing (spinal cord, liver, small intestine) and whole-genome sequences.
• (UC Davis*) Supported community use of Iso-seq data across eight equine tissues through the NCBI SRA database.
• (UC Davis*) Created an allele-specific expression resource for the equine transcriptome (Harrison, et al. BMC Genomics 2025).
• (Nebraska*) The pangenome effort is working to provide tools for use as explained at several conferences and webinars this year (i.e., AGBG-Ag, PAG).
• (UC Davis*) Survey details will ultimately help prioritize resource development.
• (Kentucky) A result of the USDA/NIFA supported SBIR, my company is developing a data management system for high throughput data.

  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: 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.

 Activities:

1. Workshop Leveraging Genetics and Genomics Tools in Equine Science Equine Sciences Society, June 4, 2025. This meeting was proposed by Dr. Annette McCoy, and delivered by Drs. Elaine Norton, Rebecca Bellone, and Michael Mienaltowski. It welcomed 15 participants (trainees and faculty members attending ESS) eager to explore how genetics can help improve breeding and horse health. The format combined didactic teaching and hands-on activities to maximize participants' engagement with the material. The take-home message was that collaboration between all equine scientists – not just geneticists – owners, and veterinarians will be needed as we seek to learn more about traits that impact horse health and performance.

 2. Equine Genome Workshop, Plant and Animal Genome (PAG) 33, January 10-11, 2026, San Diego, CA. The meeting was chaired by chaired by Dr. Sian Duward-Akhurst (University of Minnesota) and co-chaired by Dr. Laura Patterson Rosa (Long Island University). More than 60 scientists and trainees from 28 different universities and organizations from around the world were given the opportunity to hear about research advances from the past year from 13 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.

 3. Workshop Practical Pangenomics: Containerized Workflows for Building Graphs and Variant Discovery in Livestock and Companion Animals Plant and Animal Genome (PAG) 33, January 12, 2026, 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 (approximately 55 people) with a lot of interactive discussion.

 Milestones: We continue to work towards several milestones for this project:

1. 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 22 researchers at 14 stations across the United States and four researchers at 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.
2. Generation of summary stations’ strengths and collaborative interests. This information was solicited via the call for station reports in January 2026.
3. Stakeholder needs assessments. We will be launching two additional stakeholder needs assessments in 2026. The first will be aimed at (non-genetics) researchers, while the second will be aimed at veterinarians. The launches are planned for June (researcher survey) and December (veterinarian survey, timed with the American Association of Equine Practitioners annual meeting). 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.
4. 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/.

Proposal: Unraveling the Genetic and Transcriptomic Basis of Exercise-Associated Sudden Death in Thoroughbreds
Role: Principal
Status: Recommended for funding
Sponsoring Organization: HONG KONG JOCKEY CLUB EQUINE WELFARE
Date Submitted: February 6, 2025
Purpose: Research

Amount for Entire Grant Period or Proposed Grant Period: $382,798

 Proposal: Unraveling the genetic basis of exercise-association sudden death to improve equine safety and welfare.

Role: Mentor (Kurandina, Regina Principal)
Status: Funded
Sponsoring Organization: FOUNDATION FOR FOOD & AGRICULTURE RESEARCH VETERINARY STUDENT FELLOWSHIP
Date Submitted: February 26, 2024
Purpose: Training/Fellowship

Amount for Entire Grant Period or Proposed Grant Period: $18,000

 Proposal: Characterization of ion channel genetic variation in animal models of sudden cardiac arrest

Role: Mentor (Kurandina, Regina Principal)
Status: Funded
Sponsoring Organization: AMERICAN ASSOC OF VETERINARY MEDICAL COL
Date Submitted: October 29, 2024
Purpose: Training/Fellowship

Amount for Entire Grant Period or Proposed Grant Period: $8,500

 Award: Improving interpretation of sudden arrhythmic death variants using a spontaneous animal model

Project Investigators: Durward-Akhurst, Sian A. (Principal), Dudley, Samuel (Mentor), Kalbfleisch, Theodore (Secondary mentor), Rendahl, Aaron (Secondary mentor)
Status: Funded
Sponsoring Organization: AMERICAN HEART ASSOCIATION, INC
Date Submitted: December 4, 2024
Purpose: Research

Amount for Entire Grant Period or Proposed Grant Period: $230,952

 Proposal: Developing a computational tool for variant discovery in agricultural animals

Project Investigators: Marlowe, J L. (Principal, 100%), Durward-Akhurst, Sian A. (Primary Mentor, 1%), McCue, M E. (Secondary mentor, 1%)
Status: Recommended for funding
Sponsoring Organization: USDA NIFA
Date Proposal Submitted: October 2024
Amount for Entire Grant Period or Proposed Grant Period: $119,656.00

Role: Primary mentor

 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. $124,956.

  USDA-NIFA # 2024-67015-42330: “Functionally Annotated Equine Pangenome with Infrastructure for an Accessible, Integrative, Community Genomics Resource”.

 USDA-AFRI: Exploring the Genomic Component of Equine Sex Development and Reproduction.

 Grayson-Jockey: Genomics of Thoroughbred stallion subfertility

 DOI-Bureau of Land Management: Genetic Analysis for the Wild Horse and Burro Program (WHBP).

 Swedish-Norwegian Foundation for Equine Research: Eyeless Equines – Machine Learning to Examine the Puzzling Genetics of Microphthalmia in Horses.

 Nicodemus, M, Cavinder, C., “Pedigree Tracing to Determine the Origin of the Dilution Gene within Color-Designated Horse Breed Registries Requiring a Golden Coat Color,” Office of Research and Economic Development, Undergraduate Research Program Grant, Mississippi State University, $1,999 (June 2024 – August 2025).

 UC Davis Center for Equine Health 24-08                                           Finno (PI)                               January 2025-Dec 2025

            Role: PI                                                                                                $38,892

Validating an intronic variant in FDXR as the cause of equine juvenile spinocerebellar ataxia
The goal of this study is to perform functional assays to validate FDXR as the cause for equine juvenile spinocerebellar ataxia in Quarter horse foals.

 UC Davis Center for Equine Health 24-04                                           Finno (PI)                               January 2025-Dec 2025

            Role: PI                                                                                                $39,963

Investigating a candidate gene for equine neuroaxonal dystrophy: Niemann Pick C1-Like (NPC1L1) 

The goal of this study is to systemically evaluate NPC1L1 as a candidate gene for equine neuroaxonal dystrophy           

Grayson Jockey Club Foundation                                                        Finno (PI)                               March 2025-Feb 2027

            Role: Principal Investigator                                                                  $143,702

            Genetics of cervical spine malformations in the horse 

The goal of this study is to identify the underling genetic etiology of occipitoatlantoaxial malformation (OAAM) and the transposition of the ventral laminae of the sixth vertebrae to the seventh vertebrae (TC67) in horses

 American Quarter Horse Association                                                   Finno (PI)                               Oct 2025-Sept 2026

            Role: Principal Investigator                                                                  $74,350

            The role of NPC1L1 in vitamin E absorption in horses with equine neuroaxonal dystrophy

The goal of this study is to perform genetic investigations and ex vivo vitamin E transport studies in jejunal samples from eNAD-affected horses to determine the role of NPC1L1 in horses with equine neuroaxonal dystrophy.

 Guest, D. 2026-2030. Hong Kong Jockey Club. Cellular engineering to determine if genes associated with fracture in Thoroughbreds regulate the bone matrix. £220, 672. Principal Investigator.

Guest, D. 2026-2026. Hong Kong Jockey Club. Genetic prediction of stress/non-fatal fracture risk in racing Thoroughbreds. £11,461. Principal Investigator.

 10/2023-9/2025            Title:” Development of Informatics Infrastructure to Support the use of High Throughput Genetic Data for Herd Management on Small and Mid-size Farms”

            Source: USDA/NIFA (SBIR 2023-70436-40539)

            Total Costs: $599,946

            Role:Co-I (PI Morozov)

 7/2024-6/2027 Title:”Functionally Annotated Equine Pan Genome with Infrastructure for an Accessible, Integrative, Community Genomics Resource”

            Source: USDA/NIFA (Award Number: 2024-67015-42330)

            Total Costs: $765,000

            Role:PI

 7/2024-6/2029          Title:”Animal Breeding-RCN: Farm Animal Genomics Collaborative”

                                     Source: USDA/NIFA (USDA-NIFA 2024-67016-42311)

                                     Total Costs: UK Subcontract $416,958

                                     Role:Co-I (Noelle Cockett, Utah State, PI)

 7/2024-6/2025

Title:” Development of Informatics Infrastructure to Support the use of High Throughput Genetic Data for Herd Management on Small and Mid-size Farms”

            Kentucky’s SBIR/STTR Competitive Matching Funds Program

            Source: Kentucky Cabinet for Economic Development (CED No. 043-2024-001-004)

            Total Costs: $149,760

            Role:PI (PI Kalbfleisch)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Appendix B: Research presentations

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 Others self-reported by stations

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

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

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

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

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