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McCue, M. E.

Publications and source records attributed to McCue, M. E..

3 recordsLinked to original sources

United States stakeholder insights on genetic testing for equine health and breeding

The S1094 United States Department of Agriculture (USDA) Multistate Research Project is a community of scientists working together to utilize equine genetics and genomics to improve the health and well-being of horses while also providing educational and genetic testing resources to those in the equine industry. To assess the knowledge and priorities of stakeholders regarding genetic testing, we conducted an online survey targeting horse owners and enthusiasts in the United States. Data were collected from March to October 2024 with 412 respondents from 44 states completing the survey. Most of the survey participants were horse owners, and the two most common age ranges for respondents were 31-50 (33.6%) and 51-70 (33.3%) years old. The two most common use categories for horses reported by respondents were sport and stock horses. The survey revealed that a majority of respondents were confident in their knowledge of genetics and that they relied primarily on breed and discipline organizations, as well as universities for their genetic information. Secondarily they relied upon social media and their veterinarians. Respondents expressed significant interest in genetic testing for diversity and performance traits. Across all horse use categories, arthritis, colic and intestinal disease, laminitis, metabolic disorders, and tendon and ligament issues had the greatest level of concern - all of which are complex genetic traits and will require collaborative efforts to discern levels of genetic involvement. Results from the survey underscore the need for continued outreach and education of horse owners, as well as further development of genetic testing tools to support informed decision-making among stakeholders in the equine industry. Lay SummaryGenetic testing helps horse owners, breeders, and breed registries and associations verify parentage, evaluate health, and improve performance. The S1094 USDA Multistate Research Project has a mission of improving genomics and genetics tools, as well as providing educational resources for those in the equine industry. To better understand the knowledge and priorities of stakeholders in the equine industry, we conducted an online survey netting responses from 412 individuals in the United States. Respondents were primarily horse owners who self-identified as confident in their knowledge of horse genetics. Furthermore, those responding indicated that their primary resources for information about genetics were breed and discipline association websites and universities. They also expressed interest in genetic testing for diversity and performance traits. Across all horse use categories, arthritis, colic and intestinal disease, laminitis, metabolic disorders, and tendon and ligament issues had the greatest level of concern. Given the complex nature of these conditions, collaborative efforts will be required to discern levels of genetic involvement. Respondents felt that genetic testing and education efforts have significant impacts on the equine industry because they aid owners in making breeding decisions and in the management of horse health and well-being. Teaser TextThis nationwide survey of U.S. horse owners discerned strong stakeholder interest in equine genetic testing, determined sources for knowledge acquisition, and highlighted key priorities for the development of genetic tools and educational materials.

genetics↗

EquCab3, an Updated Reference Genome for the Domestic Horse

EquCab2, a high-quality reference genome for the domestic horse, was released in 2007. Since then, it has served as the foundation for nearly all genomic work done in equids. Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference assemblies of large animal and plant genomes in terms of contiguity and composition. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. The result, EquCab3, is presented here. The count of non-N bases in the incorporated chromosomes is improved from 2.33Gb in EquCab2 to 2.41Gb from EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

genomics↗

Development of a high-density, 2M SNP genotyping array and 670k SNP imputation array for the domestic horse

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.\n\nResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of [~]5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of [~]2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of [~]670 thousand SNPs (MNEc670k), was designed for genotype imputation.\n\nConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

genomics↗