• The need as indicated by stakeholders.

Genetic diversity is a hallmark of horse breeding in the United States. Over 350 breeds are recognized worldwide and perhaps 40 of those originate in the United States, including Quarter Horses, Morgans, Saddlebreds, and the Appaloosa. At the same time, American breeders are highly regarded for improving breeds of international origin, including Thoroughbreds, Standardbreds and Arabian horses. Breeds are genetically distinct, by definition. Yet they are not clonal populations of identical animals.  The goal for breeders is to select their stock for beneficial traits, while selecting against traits that detract from performance, in particular the deleterious traits caused by disease genes. In the horse, some traits and diseases are shared across breeds, while others are breed specific. Investigation of hereditary diseases, identification of genes for performance and assessment of the overall population diversity can be done best using genomic tools under development for use in human medicine and for comparative genomic studies in a wide range of species, including the horse.  

The equine industry in the United States has a great economic impact on the country as a whole; estimated at $122 billion in 2017 (1). Direct and indirect involvement in the equine industry results in the maintenance of 1.7 million jobs in the U.S., many within the agribusiness realm given the farm and ranch settings in which the species are bred, maintained, trained, and expected to perform. Diverse equine populations and activities are found throughout the country, with the largest populations in Texas, California, Florida, Oklahoma, and Kentucky. Stakeholders in the industry include breed registries, breeding facilities, owners, trainers, recreational riders, and coordinators of recreational and competitive events (2). Management of horses requires industry partners in veterinary care, nutrition, hoof care, and training as well as many others, including those supporting the businesses built around equine activities. 

The equine industry shares many of the challenges common to other agribusinesses, as well as some problems that are unique to working with these species. For example, market depression and unwanted or abandoned horses resulting from over-breeding, combined with the strain of the recent economic downturn, resulted in abandoned horses and feral herds. Many breeds, especially those with critically small breeding populations, now must balance selection for performance with the dangers of excessive inbreeding, including reduced animal health due to the increased prevalence of negative traits. Additionally, extensive interstate travel of horses for competitive or recreational events increases the risk of regional disease outbreaks that negatively impact herd health, as well as the economy. The equine industry must also address issues of economic sustainability and the efficiency of their operations, while facing competition for space from urban development and other agricultural activities.

Populated by many small and distinct business operations, the equine industry has less integration of stakeholders relative to other agricultural species, perhaps due to the scattered geography of farms across the country, or the diversity of breed standards and selection strategies (3). As a result, the equine stakeholder population is less prepared to respond to critical or emergent issues in population health with resources like research funding and coordinated sampling efforts. Thus, there is great value for a multistate project in which a collaborative network of researchers can address common problems faced across multiple species, breeds, and operations. 

    Through a survey by the AAEP, veterinarians indicated colic, lameness and laminitis as critical concerns in health management of horses (4). The economic costs of these conditions are difficult to measure, but not insignificant. Early USDA studies on lameness alone estimated costs to the industry of $39 billion, with $10.6 billion spent combating lameness within just the racing sector (5). A similar survey of horse owners found concerns in infectious disease and musculoskeletal problems, as well as gastrointestinal health. Notably, horse owners specifically discussed genetic disease and testing as outside of the veterinary realm, and on par with issues like pain recognition and horse abuse/neglect (4). Yet, despite early success in development of genetic tests, even well-characterized single gene diseases are still a problem for the horse industry. For example, among the 2.1 million American Quarter Horses living in the US approximately 11% are affected with a muscle disease caused by the dominant PSSM1 allele, and another 11% carry the recessive lethal GBED allele (6). The frequency of some disease-causing alleles are actually on the rise, as is the case for HYPP in the American Quarter Horse (6,7).

Impacting diverse traits of fitness and performance, genetic tools for equids likely hold the most potential for quickly improving animal welfare and economic sustainability across sectors of the industry. Effective utilization of these tools, and the insights into health and performance they provide, requires education of the industry on their appropriate use when making breeding decisions, and a better understanding of the relevant biology that underlies genetic testing. Ultimately, there is a critical need to reach those in the industry in producer-assistive ways, both for the currently available genomic technologies as well as the potential for the development of future tools to address genetic improvement in equids. 

• The importance of the work, and what the consequences are if it is not done.

Horses are an important part of the US economy. Though most equine operations are considered small farms relative to today’s corporate agricultural standards, these farms provide agribusiness, agritourism, and recreational dollars to communities across the country. While other commodities are measured in bushels or pounds, the contribution of the equine industry is primarily in recreational dollars (50% of horse use), aiding in farming and ranching (25% of horse use), and in bolstering local,city, and state economies (1). These small farms face increased pressure following the 2007-2008 financial crisis, and need the cost-reducing benefits of genetic selection and genome assisted precision management. Lack of genomic tools will, over time, drive up the costs of horse ownership. 

            Genomics tools are increasingly becoming integrated into breeding practices for many agricultural species and will be critical for reaching future goals of economic and environmental sustainability (8). This is particularly true for horses, as these animals are typically managed at the individual level, not as herds. The knowledge at the individual animal level provided by genomic tools improves efficiency and animal welfare through assisted selection in breeding, and precision management. Indeed, veterinary medical care increasingly uses genomic information, through derived technologies like stem-cell therapies and may soon benefit from approaches developed in human medical care like RNA-based vaccines and precision medicine.  If advanced medical technology is to be applied to equines, genomic information specific to these species needs to be available.  The equine reference genome and subsequent whole genome sequence is the foundation for development of a pangenome reference, functional genomics and identification of epigenetic marks that determine how, when and where genes are expressed.

    At the population level, rare equids and small breeds are at risk for critical losses of genetic diversity. These living resources will prove increasingly important in a changing climate, as many of these small populations provide a pool of potentially beneficial alleles developed over thousands of years of natural selection in unique geographical regions (8). Responsible stewardship of these rare breeds will require outreach and education to enable utilization of genomic tools for quantification of population diversity and optimal mate selection.  

Application of genomic tools has the opportunity to positively impact horses at the individual, herd and ecosystem level, reducing economic and welfare costs. Continued efforts toward genetic improvements in equids and their management, at all levels, will support the future of the industry’s economic contribution, as well as its continuing sustainability. Discontinuation of the collaborative activities begun under the Horse Genome Workshop at the USDA-National Animal Genome Research Program 8 (NRSP-8) will put the horse at a disadvantage compared to more mainstream “food and fiber” agricultural livestock species, reducing the healthy economic diversity of US agribusiness. 

• The technical feasibility of the research.

Our collaborative group has a long history of coordinated research efforts, beginning in 1995 with the formation of the “Horse Genome Workshop” under the support of NRSP-8 and the Dorothy Russell Havemeyer Foundation (see https://horsegenomeworkshop.com/).  Now comprising over 100 scientists from 25 countries worldwide, the collaboration provides an existing leadership structure including rotating coordinators, meeting chairs and chair-elects, and a track record of strong attendance at national and international workshop conferences (typically numbering ~60 attendees at the PAG-based annual meeting).  Research productivity from this group averages 75 publications annually and leverages the tools, resources and connections into $2.2 million dollars in research grants among only the US stations (2016-2019 reporting years). 

The NRSP-8 supported development of genomics tools and a research community to support research in diverse agricultural animal species between 1992 and 2023.  That program is ending in 2023.  The  next steps will be to continue utilizing these community resources and to increase efforts to address  problems specific to the horse industry. The 16 member stations bring a long history of collaboration under the Equine Genome Project to respond to critical needs in horse health and performance.  They provide diverse technical expertise in studies of heritable disease, gene expression surveys to better understand acute conditions and bioinformatic analysis of genome-scale datasets (example references summarized in Table 1). Continuation of this productive research network will lead to ongoing success in the application of genomic strategies to benefit the horse industry.  

Table 1. Examples of practical applications of information from the equine genome sequence to important equine diseases. 

• The advantages for doing the work as a multistate effort.

The 14 participating stations of the Equine Genome Project are tasked with meeting the needs of the owners, veterinarians and allied industry professionals caring for over 7.2 million horses in the US.  A challenge of this scale cannot be met without cooperation across institutions. Furthermore, with the complexity and expense of genome-scale technologies these tools cannot be provided by any single station (for notable examples, see the summary in Table 2). Genetic studies of complex traits, which includes most of the highly detrimental equine diseases, requires genotype and phenotype information from large numbers of horses. A multistate approach will vastly facilitate collection and incorporation of the large numbers of samples required for investigating these complex traits. Across the US, the distribution of breeds, activities and the environmental pressures are diverse, requiring the unique knowledge brought by the local participating station to understand the relevant production issues. Furthermore, the concentration of horse populations in some states (Texas, California and Florida for example) provide research opportunities not locally available to scientists in smaller states. Fortunately, the utility of genomic tools allows application of these approaches regardless of breed or problem under study. Finally, it is well documented that research productivity and quality improves within diverse collaborative teams. Broad collaboration enables sharing of resources, facilitating faster, more efficient and more effective solutions to the problems affecting the horse industry. Furthermore, multistate collaboration ensures that genomics experts across institutions confer on any recommendations made for topics in applications of these technologies, including genetic testing. This is essential for the future success, as incomplete information from multiple sources can confuse owners and other stakeholders leading to mistrust of the scientific community. A multistate effort allows for a united front of the equine genetics community that will help promote stakeholder trust in the resources available to them for equine genomics.

Table 2. Joint publications from the collaborative International Horse Genome Workshop, an expansion of the 16 stations comprising this Multistate Research Project. 

• What the likely impacts will be from successfully completing the work

Genetic technology has proven itself transformative in agricultural research, animal breeding, and veterinary practice. This project will serve to build bridges between these disciplines that will advance the common cause of all, equine health and wellbeing.

Impacts for producers: Genome assisted selection tools for breeding programs, and precision management, as well as assessment of genetic diversity and population health. Source of on-demand species-specific information on applications, improving dissemination of the benefits of equine genomic research.   

Impacts for veterinary professionals and diagnostic laboratories: Additional affordable and non-invasive genetic diagnostic tests to facilitate disease diagnosis and prognostication (31). Targeted research toward development of improved treatment options, through understanding of the genetic bases and pathways contributing to progression of the disease (32). Improved dissemination of equine genomic research, getting these tools and knowledge of their use into the hands of veterinary practitioners and their clients. 

Impacts for researchers: An expanded support network for data sharing, coordinated extension efforts and resource recruitment (technical expertise, diverse samples, grant funding, etc.). Application of tools used in diverse scientific fields like reproductive physiology, infectious diseases, and precision medicine. Fosters a supportive community that promotes retention in the field.

Impacts for students: Meeting need for STEM training in future workforce, improved mentoring support as well as a chance to network with students, researchers and resources from across the project collaborative. Provides access to cutting-edge tools for diverse students to study horses, educating the next generation of producers and  industry professionals.

Our group is historically inclusive, and we intend to invite participation from diverse scientists and stakeholders, including, but not limited to the following: