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

(Multistate Research Project)

Status: Active

Project Menu

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

Duration: 10/01/2022 to 09/30/2027

Administrative Advisor(s):

Robert A. Gilbert

NIFA Reps:

Angelica Van Goor

Kathe Bjork

Non-Technical Summary

Statement of Issues and Justification

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.

Area of Application	Example References
Equine muscle disease	Mickelson and Valberg, 2015 (9)
Equine sarcoid tumor susceptibility	Staiger et al., 2016 (10)
Inherited diseases in Arabian horses	Brooks et al., 2010 (11)
Equine Immunodeficiency Disease	Tallmadge et al., 2015 (12)
Recurrent laryngeal paralysis	Boyko et al., 2014 (13)
Horse racing distance	Hill et al., 2019 (14)
Locomotion patterns	Andersson et al., 2012 (15)
Equine recurrent uveitis	Rockwell et al., 2020 (16)
Squamous cell carcinoma	Bellone et al., 2017 (17)
Recurrent exertional rhabdomyolysis	Norton et al., 2016 (18)

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.

Area of Genome Characterization	Example References
Linkage Maps	Penedo et al., 2005; Swinburne et al., 2006 (19,20)
Physical maps	Chowdhary et al., 2003 (21); Shiue et al., 1999 (22)
Bacterial Artificial Chromosome Library	Gustafson et al., 2003 (23)
Reference Genomes	Kalbfleisch et al., 2018; Wade et al., 2009 (24,25)
SNP chip arrays	McCue et al., 2012; Schaefer et al., 2017 (26,27)
Expression arrays	Brosnahan et al., 2012; Mienaltowski et al., 2009 (28,29)
Copy number variant arrays	Dupuis et al., 2013 (30)

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:

Name	Affiliation
Ablondi, Michela	University of Parma
Anderson, Kathy	U. NL
Antczak, Doug	Cornell University
Avila, Felipe	UCDavis
Bacon, Elouise	University of Sydney
Bailey, Ernie	University of Kentucky
Barber, Alexa	University of Nebraska - Lincoln
Barrey, Eric	INRAE
Bellone, Rebecca	UC Davis
Blanchard, Kendall	UMinn
Borlle, Lucia	Cornell University
Brinkerhoff, Bruce	US Trotting Assoc.
Brooks, Samantha	UFL
Bruemmer, Jason	USDA-APHIS National Wildlife Research Center
Bryant, Dick	Pyramid Society
Bugno-Poniewierska, Monika	Krakow
Buys, Nadine	KU Leuven
Byron, Michael	Cornell University
Capomaccio, Stefano	University of Perugia
Cappelletti, Eleonora	University of Pavia
Caro, Jessica	Auburn Univeristy
Cercone, Marta	Cornell University
Church, Stephanie	The Horse
Cieslak, Jakub	Poznan
Culbertson, Cynthia	Pyramid Foundation
Cullen, Jonah	UMinn
Coleman, Stephen	Colorado State University
Davis, Brian	Texas A&M University
de Mestre, Amanda	RVC
Delco, Michelle	Cornell University
Dhorne-Pollet, Sophie	INRAE
Diel de Amorim, Mariana	Cornell University
Dini, Pouya	UC Davis
Dimmler, Kirsten	UMinn
Donnelly, Callum	UC Davis
Durward-Akhurst, Sian	UMinn
Dwyer, Ann	Genesee Valley Equine Clinic
Elemento, Olivier	Weill Cornell
Evans, Jacquelyn	Cornell University
Fegraeus, Kim	Uppsala University
Felippe, Julia	Cornell University
Finno, Carrie	UC Davis
Fuentes, Debbie	Arabian Horse Association
Garcia, Brandon	Cornell University
Ghosh, Sharmila	UC Davis
Giulotto, Elena	Pavia
Gmel, Annik	Agroscope
Graves, Kathryn	University of Kentucky
Greene, Betsy	U. Az
Gysens, Lien	Ghent University
Hackett, Eileen	Cornell University
Hamilton, Natasha	Racing Australia
Harman, Rebecca	Cornell University
Harrington, Kellie	Illumina
Hayward, Jess	Cornell University
Hein, Jessica	American Paint Horse Association
Hiney, Kris	OSU
Holmes, Camille	Cornell University
Holtby, Amy	PlusVital
Horin, Petr	University of Veterinary Sciences, Brno
Hughes, Lauren	UMinn
Kalbfleisch, Ted	UKy
Karagianni, Anna	Roslin Institute
Kemp, Kelly	Diagenode
Kingsley, Nicole	UC Davis
Klecel, Weronika	Warsaw
Knickelbein, Kelly	Cornell University
Kuntz, Frank	Nakota Horse Registry
Lafayette, Christa	Etalon Diagnostics
Lawless, Kahlil	Illumina
Li, Kai	UKy
Lindgren, Gabriella	Swedish University of Agricultural Sciences
Mac Smith, Johnny	Grayson Jockey Club
MacLeod, Jamie	University of Kentucky
Maniego, Jillian	Sport and Specialized Analytical Services
Marlowe, Jillian	UMinn
Martinson, Krishona	U. Minn
McCoy, Annette	University of Illinois
McCue, Molly	UMinn
McGowan, Christine	Nakota Horse Registry
Menarim, Bruno	University of Kentucky
Mikko, Sofia	SLU
Miller, Don	Cornell University
Mitchell, Katharyn	Cornell University
Muhammad, Khadijah	UC Davis
Naboulsi, Rakan	Uppsala University
Norton, Elaine	University of Arizona
Orlando, Ludovic	University of Toulouse
Ortega, Janeth	University Nacional
Palmer, Scott	Cornell University
Palomino-Lago, Esther	Royal Vet College
Peng, Sichong	UC Davis
Petersen, Jessica	University of Nebraska
Piras, Francesca	University of Pavia
Powell, Barclay	UFL
Pranzo, Gene	Havemeyer Foundation
Radovic, Lara	University of Veterinary Medicine Vienna
Raudsepp, Terje	TAMU
Rose, Emily	Neogen
Ryan, Stephanie	UC Davis
Ryder, Edward	Sport and Specialized Analytical Services
Ryder, Ollie	San Diego Zoo
Sage, Sophie	University of Bern
Scollay, Mary	RMTC
Smythe, Madelyn	UFL
Soares Feijo, Lorena	Cornell University
Soden, Sarah	Twist Bioscience
Staiger, Ann	TAMU Kingsville
Stefaniuk-Szmukier, Monika	Warsaw
Swiderski, Cypriana	University of Arizona
Tomlinson, Joy	Cornell University
Tozaki, Teruaki	LRC Japan
Trauner, Alex	Montana State
Valberg, Stephanie	Michigan State
Van de Walle, Gerlinde	Cornell University
Velie, Brandon	University of Sydney
Vinardell, Tatiana	QNRF
Walker, Neely	LSU
Wallner, Barbara	University of Veterinary Medicine Vienna
Wehle, Pat	Wehle Farms
Wickens, Carissa	UF
Yousefi, Navid	UKy
Zabek, Tomasz	NRI Poland

Related, Current and Previous Work

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 the NRSP-8 National Animal Genome Research Program, and the Dorothy Russell Havemeyer Foundation (see https://horsegenomeworkshop.com/). Major community accomplishments over the past two decades include publication of a high-quality reference genome (24,25) and development of informative whole-genome SNP genotyping arrays (26,27). These resources empowered international collaborative efforts, currently involving over 100 scientists from 25 countries worldwide, to begin to investigate diverse problems specific to the horse industry (see examples in Table 1). These accomplishments provide excellent support for the pursuit of the objectives of this multistate project.

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.

Identification of sequence and structural variants (all stations)

The WGS resources collated across the equine genomics community resulted in multiple publications on databases of SNP and small structural genetic variation across the equine population (33–35).These catalogs provide background genetic variation data within and across breeds and can be utilized for disease variant prioritization as demonstrated in human medicine (36). Importantly, similar variant databases have been used to highlight false positive disease associations due to the ‘causative’ variant being present in the variant database at a frequency greater than expected given the disease prevalence (37). Large structural variation has been less thoroughly explored, in part due to the cost of long read sequencing but also due to the lack of agreement between computational tools for structural variant identification. Despite this, there have been several phenotypes linked to structural variants in the horse (38–43). The opportunity with this multistate proposal is to combine these smaller populations into a large and publicly available database, providing a resource of background genetic variation for future genomic studies. Public deposition of data is often an activity supported by individual research grants, but effective use of these practices requires an established “research commons community” to define standards and best practices (39). Such a community for equine genomics will be nurtured through the support of this multi-state project.

Creation of reference genomes (UKY, UNL, TAMU)

It has been shown in humans and other agricultural species that a single reference genome is not sufficient for variant discovery, particularly for complex traits. The original reference genome was based on a single Thoroughbred mare, Twilight (25). A more recent reference genome was created using this same horse (24). Work is underway to create reference genomes based on a Shire horse, an Arabian horse and a mule (donkey x Thoroughbred). These efforts are multi-institutional efforts already, and the advantages provided by a multistate project will enable further efforts at additional institutions to capture the background genetic diversity of additional horse breeds.

Development of pangenome (UMN, UKY, UNL, UCD, TAMU)

The equine reference genome is still based on a single Thoroughbred genome. Other species are already highlighting the benefits of pangenomic approaches and even breed or population specific reference genomes. Several of the horse genome community member stations are working to develop reference genomes in additional species that will be utilized to improve equine genome annotation and variant identification in diverse horse breeds. Isolated stations working on pangenome resources with the collaboration of the community will make progress, but a truly multistate approach across these stations will enable a far more complete pangenome effort that will maximize the benefit to the equine community.

Annotation of genome and epigenetics (all stations under auspices of FAANG, UCD, UNL, UKY, UMN)

Every gene is not expressed in every tissue. Differences in management, nutrition and other experiential factors can modify proteins and even DNA bases resulting in constitutive changes in gene expression. The study of these differences is called functional genomics and, currently, the focus is on chromosome binding proteins that activate, repress or enhance gene expression. Under the auspices of the USDA-NRSP8 program, the horse genome research community participated in a program called Functional Annotation of Animal Genomes (FAANG) (33–37).

The equine-focused portion of the FAANG project has been led by researchers at University of California-Davis, University of Nebraska-Lincoln, University of Kentucky, and the University of Minnesota. However, broader participation has been encouraged in the community by implementation of a unique “adopt-a-tissue” initiative, which allows other researchers to contribute with focused monetary or assay-specific resources (38). Currently, more than 50 researchers, worldwide, are actively participating in this effort (www.faang.org).

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

Understanding physiology and disease pathology is a critical step towards both more effective diagnosis and treatment of disease and improved performance/ production. Ongoing projects that fall under this objective include:

Identification of genome-wide signatures of selection in horse breeds (UMN, UNL, Cornell, UF) (40,41);

Identification of causative and modifying variants underlying clinical muscle disease (UMN, MSU, UC Davis, UNL) (18,42–44);

Identification of genetic components to skeletal conformation/growth and risk factors for the developmental orthopedic disease osteochondrosis (UIUC, UMN, UF) (45,46);

Identification of genetic variation of receptors for virus infection (UKY, LSU) (47);

Identification of early molecular markers of osteoarthritis (UIUC, UKY) (48);

Characterization of changes in bone structure during maturation and high speed exercise (UKY, UIUC) (49);

Molecular interventions for equine tendon repair (UC Davis) (50);

Characterization of maternal recognition of pregnancy in mares (CSU, Cornell, UKY) (51–53);

Investigation of interactions between gastrointestinal physiology and the microbiome (CSU, UC Davis) (54);

Classification of diverse phenotypes and identification of genetic risk factors for equine metabolic syndrome (UMN, UC Davis, UF ) (55,56);

Identification of causative and modifying variants underlying ocular diseases including equine recurrent uveitis (UC Davis, Cornell, UMN) (57–61);

Improvement of equine genome annotation (FAANG, UC Davis, UMN, UF, UKY) (24,33–35,62–64).

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

The equine genetics community is committed to the development of accurate genetic diagnostic testing that promotes equine health. However, there is a need for education in the equine industry as to the appropriate use and interpretation of such tests, particularly for complex genetic traits which also involve environmental risk factors. The decision making process for variant discovery and personalized medicine is well documented in humans with standards and guidelines being agreed upon and published across institutions and colleges. At this time, no such statement is available for agricultural species. As DNA sequences are not patentable, there is little motivation for testing providers to invest in extensive validation studies. There is a critical need for feasible guidelines for genetic testing in horses, and these guidelines must be a multistate effort to ensure consensus across the equine genomics community (see the Horse Genome Workshop 2019 Statement on Translation and Application of Equine Genomics: https://bit.ly/GenomicsStatement ). A consistent voice across equine genomic institutions is essential to promote owner and stakeholder confidence in the scientific community. Currently, there are genetic tests commercially available that do not hold up in replication studies. This is of extreme concern for the horse industry as horses are being managed (and even euthanized) based on potentially incorrect diagnoses from these tests. Without a multistate effort to promote conversation across research stations and with industry stakeholders, broader acceptance of genetic testing, and the resulting improvement in horse welfare, will be delayed.

Economically important conditions targeted for development of novel diagnostic testing methods include:

Clinical muscle disease, including recurrent exertional rhabdomyolysis, polysaccharide storage myopathy, pasture-associated myopathy, and others (UMN, MSU, UC Davis, UNL) (44,65);

Osteochondrosis and other developmental orthopedic diseases (UIUC, UMN) (45,66);

Equine metabolic disorders (UMN, UC Davis, UF) (55,56);

Susceptibility to Equine Arteritis Virus Carrier State (UKY) (47);

Coat color and associated pleiotropic disorders (UC Davis, UMN, UF, UKY) (31,59,67);

Collagen and articular cartilage disorders (UC Davis, UKY) (68–70);

Neurological disorders (UC Davis, UMN, UF, Cornell) (71);

Ocular disorders (UC Davis, Cornell) (72);

Cancer risk (UC Davis, Cornell) (10,58).

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

The focus of the current proposal is on application of genomics tools to problems of economic importance in horses. However, the collaborative community will continue to refine and build on existing platforms and resources. This is exemplified by efforts to make data broadly available to community members, with development of an interactive platform which will allow researchers to integrate data from multiple sources for analysis, or for visualization in any genome browser (UKY, UC Davis, UMN, UNL, UF).

Development of platforms for high-throughput genotyping, enabling sharing of data across projects (73);

Previous interactions have established successful collaborations, for example he horse community is a member of the USDA funded Functional Annotation of Animal Genomes project, and the first our of all participating species groups to deposit their data in public archives (38,74);

Applications of “big data” tools to complex traits affecting health and production/performance (numerous examples cited above);

Workshop Website: https://horsegenomeworkshop.com/

Data websites: https://EquineGenomics.uky.edu

Rapid data transfer via methods like the Globus network

Need for online networks to help recruiting samples for studies by connecting researchers to horse owners and DVMs

Enhancement of outreach and educational efforts with better online visibility to stakeholders.

Since 2003, collaborative research in animal agriculture, including equine species, has been federally supported under the NRSP-8 National Animal Genome Research Program (NAGRP). The NAGRP was renewed in 2018, with the caveat that the program would be slated for sunset in 2023 with a progressively diminishing budget. Individual species groups/regional organizations within the NAGRP were advised to seek alternative approaches to support multi-institutional collaborative efforts, including utilization of the existing USDA Multi-state infrastructure. Establishment of this new multistate project now will allow a short time to transition programming and activities already underway to new funding mechanisms and reporting schemes.

The old NRSP-8 supported genomics tools and infrastructure to support research in diverse agricultural animal species, and in our community included important tools for genetics research in the horse (reference genome, SNP chips) (Tables 1 and 2). The next step for the collected research stations in this application will be to take these newly developed genomic resources and extend collaborative efforts in order to address critical needs in horse health and performance. Currently, NECC1700 is the only other equine “health” related multi-state and that effort is currently set to conclude on Sept 30, 2022. Efforts to improve genome functional annotation are coordinated in part under the FAANG initiative (https://www.faang.org/), but it’s unclear how long that will continue, and funding for these efforts have been difficult to obtain. Finally, there is a planned NRSP focused around bioinformatics that will be the new home for tool building, data handling, pipeline construction, and other computational approaches that can be utilized across diverse livestock species.Our goal in this multistate will be to apply the knowledge generated by efforts like FAANG and this new Bioinformatics NRSP to address the needs of the horse industry.

Objectives

Improve detection of pan-genomic variability for genetic improvement and diversity stewardship of equids, including breeds as well as exotic and feral horses.
Expand the availability of genetic diagnostic testing and education on its use.
Improve tools for the application of genomic resources to improve the understanding of equine disease processes.
Create platforms for broad sharing of data and technology to enhance development and application of genomics tools in the industry.

Methods

Studies in Horse Genome Workshop member laboratories employ a diverse array of genomic techniques. Central to the goals of several project objectives is next-generation sequencing and bioinformatics. Collaborative efforts are necessary for the large-scale genomic studies and computational techniques needed to move the equine genomics forward. These multi-state efforts are essential for providing sufficient power to support genome wide association studies, mining of genome sequences for novel polymorphism and investigation of gene expression and structure. Specific projects might also utilize targeted amplification and sequencing of specific regions as well as genotyping by gel electrophoresis and RFLP. Gene expression-based experiments are often begun with total next-generation sequencing of total mRNA and followed up with qPCR and/or sanger sequencing of cDNA.

Specifically, for each objective we will likely employ the following techniques:

OBJ1) Scientists from each station often contribute data from breeds locally available to them for construction of community “pangenome” annotation and resources. Thus, participation of stations from diverse agricultural ecosystems, and representing stakeholder populations from diverse aspects of the industry is key to success in this objective. Availability of high-throughput genome resequencing technologies like Illumina short-read or PacBio long-read approaches have democratized these activities, allowing contribution from datasets originally generated from different experimental aims. Reference-quality assemblies for individual animals are now made possible through the use of approaches like 10x Chromium library preparation, Dovetail proximity ligation technologies like “Omni-C”. Finally, key observations of the accessibility and utilization of regulatory regions of the genome are observed using approaches like RNA-seq, CHIP-seq, and Iso-seq.

OBJ2) Some stations are expert in development of diagnostic assays using genomics while other stations have populations and families that are segregating for the traits of interest. This objective entails systematically creating collaborations to better connect existing expertise to the resources needed to bring these tools to fruition. Crucially, feedback from industry stakeholders identifying local needs will be brought to the community for investigation, and then results can be broadly disseminated by all stations, both via extension efforts and directly to owners/breeders and veterinarians through in-person or virtual interactions. On the extension side, several stations have existing efforts to improve awareness of genetic diagnostics within the horse industry through lay publications, industry speaking events and online short-courses. As genomics tools are most frequently utilized by the horse owner, without a prescription from a veterinarian, improved education on the interpretation of these tools is key to achieving improvements in horse health and welfare. Notably, patents are no longer an affordable or feasible option for securing rights and future income from most genetic testing methods. In the case a patentable technology arises from these efforts, these properties are handled according to the guidelines and collaborative agreements already in place at the institutions housing the research work.

OBJ3) Genomics remains a young technology. Many of the tools, including the whole genome sequence, were not conceivable in 1995 at the beginning of NRSP8. Today, the whole genome sequence is merely the foundation for investigations of functional genomics and epigenetic factors that influence gene expression. We believe that a key to using genomics effectively is developing better approaches and tools to investigate regulation of gene expression. While many of the approaches developed for other species, especially humans, are relevant, major aspects and applications remain species specific. Besides the generation of these data, analytical strategies for these data will also be shared within the group.

OBJ4) Activities in this objective couple genomic studies at the diverse stations with active common bioinformatic platforms to collate, share and assess information, improving utilization of existing datasets in public repositories (i.e. GenBank, NCBI-SRA, ENSEMBL, UCSC, OMIA). This includes the need to liaise with international repositories of information on horse genetics and genomics to ensure accurate and up to date annotation. Specifically, we will work to aggregate derived datasets, and available phenotype data that may be reused for secondary analyses. We will move toward a distributed data storage model, such that no one institution has to bear the full burden of administering these voluminous datasets. This will be accomplished by creating data hubs where data and metadata (that include phenotypes) may be uploaded for subsequent search and use. Commonly used tools and resources such as the UCSC Genome Browser, the Integrative Genomics Viewer, the R programming platform, and association analysis engines such as PLINK will all be able to use data output from our repositories.

Measurement of Progress and Results

Outputs

Publications will convey the underlying basis for diseases affecting the health and performance of horses.
Genetic diagnostic tests based on discoveries of causative mutations or associated linked mutations.
Improvements to treatment, prevention and selection strategies based upon knowledge gained on mechanisms in physiology and pathology.
Collaborations cultivating existing and new research activities.
Equine-specific best practices and protocols for data handling.
Research network for translation and application of data, tools, and resources.
Support efforts for deep-phenotyping of existing teaching and research herds.
Multi-station grant development to diverse agencies.
Extension and outreach opportunities and educational materials for stakeholders.
Training of the next generation of researchers and industry professionals who will utilize these tools via undergraduate research experiences, graduate education programs and professional or continuing education opportunities.

Outcomes or Projected Impacts

Advancement of scientific tools, data and resources to fuel future research efforts.
Better understanding of the interaction between genetics and environmental conditions.
Greater integration of gene interaction and biological pathways in our understanding of equine physiology and disease pathology.
Increased access to existing and new genetic testing diagnostics to inform breeding decisions, facilitate precision management and predict potential for inherited diseases.
Improve precision medicine through prediction of disease progression, allowing veterinarians to consider targeted treatments based on genetic testing results or improved understanding of disease pathology from genomics-reliant studies.
Expanded availability of educational materials to help producers and veterinarians to understand diagnostic assay results.
Identification of key selection goals across the equine industry.
Modernization of approaches to sustainability within the industry to improve economic impacts, promote agricultural efficiencies, and thus mitigate nonpoint source pollution.

Milestones

(2023):Engagement of researchers at ~20 stations across the country for multistate participation. First annual meeting, January 2023.

(2023):Generation of summary stations’ strengths and collaborative interests ahead of summer workshop meeting.

(2023):Collaborative, international, summer workshop meeting, focus on drafting and launch of the first stakeholder needs assessment.

(2023):Renew website with lists of educational materials for stakeholders and genomics resources for researchers

(2024):Submission of collaborative grant based upon discussion of strengths and collaborative interests

(2024):Annual meeting, review results of first stakeholder needs assessment

(2024):Application of first generation of genome annotation and genome functional data to address research questions .

(2024):Community online informatics resources widely applied for research (draft version at https://equinegenomics.uky.edu/)

(2025): Assessments of critical research needs from the scientific community (online and/or in-person at the annual meeting).

(2025):Annual meeting: revise previous stakeholder needs assessment.

(2025):Summer: distribute needs assessment.

(2025): Expand use of online data repositories to facilitate equine research 2026: Annual meeting: review results of second needs assessment.

(2026):Assessment of critical research needs from the scientific community.

(2027):Annual meeting: reflect on multi-state achievements, draft multi-state renewal.

(2027):Revisit website resources, revise as needed.

(2027):Improved strategies for addressing complex genetic traits.

(2027):Improved understanding of hereditary problems in horses.

Projected Participation

View Appendix E: Participation

Outreach Plan

The coordinators maintain an email list and use it to broadcast information relevant to the multi-state participants. Though simple, this method has proven to have the most consistent and broad reach across the group. To expand on this, we aim to create an online blog or e-newsletter. These publications will provide stable, searchable resources for stakeholders. Our participants also individually maintain diverse social media accounts for engaging stakeholders. Extension agents/specialists will be engaged to participate in the workshop, strengthening existing efforts in outreach to industry leadership (like breed registries) and enabling future efforts to assess community needs (including owners/breeders/trainers, diagnostic laboratories, and veterinarians). These assessments may include online surveys and questionnaires and/or live virtual meetings to allow the widest possible participation. Extension agents/specialists will also be critical in the creation and dissemination of annual activity reports aimed at stakeholders.

Extension faculty have not previously participated in the Horse Genome Workshop, primarily due to a lack of funding to cover their travel to annual meetings (typically supplied by research grants). This new multi-state will for the first time give our extension partners a mechanism to support their participation in the workshop. For example, Dr. Carissa Wickens, Extension Equine Specialist at the University of Florida provided feedback on this proposal and hopes to participate in the future. There is a vibrant and active extension service aimed at providing equine specific information, and our hopeful invitation list includes (but not limited to) the following extension faculty who have collaborated with Horse Genome Project members previously: Carissa Wickens, UF, Krishona L Martinson, U. MN, Neely Walker, LSU, Betsy Greene, U. AZ, Kris Hiney, OSU, Kathy Anderson, U. NL.

The proposed multi-state project will for now continue to utilize the annual International Plant and Animal Genome Conference (PAG) as our designated meeting. A horse workshop session is hosted at PAG, and has served as the NRSP-8 annual meeting since the inception of that program. It is also likely that PAG will continue to serve as the meeting of the new Bioinformatics NRSP group, in which many of our multi-state members hope to participate.

In addition to the PAG conference, summer collaborative meetings were historically held once every two years as a Dorothy Russell Havemeyer Workshop (even number years) and in conjunction with our international colleagues at a conference of the International Society for Animal Genetics in odd-number years. Although the Havemeyer foundation has supported past horse genomics meetings upon request, future support is not certain.

New research coordination efforts include quarterly virtual meetings and the organization of “Research Interest Groups” to catalyze collaboration across participating stations. Efforts are also underway to encourage industry representation at these meetings, and send multi-state scientific representatives out to industry meetings, to better engage stakeholders in the formulation of research goals and the translation of research findings into practice.

A newly redesigned website for the International Horse Genome Workshop includes reports from the meetings, identification of participants and links to community tools. The website can be found at: https://horsegenomeworkshop.com/

Organization/Governance

Project organization is built around the existing infrastructure established by the Horse Genome Workshop since its inception in 1995 (https://horsegenomeworkshop.com/) and utilized until recently to serve the responsibilities of participation in the NRSP8: National Animal Genome Research Program. At the first meeting following approval of this project, member stations will elect one species coordinator and two co-coordinators who will provide long term leadership, administer project communications and compile annual/final reports. Annual meetings will be held with the responsibility for organization delegated to a workshop chair and secretary, elected by the project membership. The secretary will become the chair for the next year and a new secretary will be elected at each meeting. In this fashion, each elected workshop officer will have two years to contribute their leadership to the meeting and there will always be one officer with at least one year of experience. The chair leads the meeting, with the Secretary supporting that role and moving into the Chair position the following year. Thus, the workshop chair serves a total of two years as a meeting organizer and there is continual overlap between new and experienced organizers.