Brief Summary of Minutes of Annual Meeting

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: 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: 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. 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:

1. Equine Genome Workshop, Plant and Animal Genome (PAG) 30, January 14-15, 2023, San Diego, CA.

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.

2. Workshop: Genomic tools to improve equine health, well-being, and performance, Equine Sciences Society (ESS), June 6-9, 2023, Grapevine, TX.

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:

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. 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.
2. 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.
3. 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.
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/.

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:  

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

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

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

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

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

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

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

12. Ward J, Raudsepp T, Levine D, Turner R. Theriogenology Query: Severe Hypospadias/Disorder of Sexual Development in a Miniature Equid Hybrid. JAVMA, accepted May 23, 2023, In press.
13. Kania J, Wilson K, Raudsepp T, Castaneda C, Jevit M, Horteloup P, Saklou N, Jula C, Funk R. Double cervices in a Gypsy Vanner mare. Clinical Theriogenology, published April 6, 2023; DOI: https://doi.org/10.58292/ct.v15.9395.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Appendix A: Grants and Contracts Received

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Appendix B: Research presentations and other outreach activities

Research presentations

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Outreach Activities

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

focus on the Shire.  J Petersen*.

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

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

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