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Genomics

Equine Genetic Research Reveals Insights into Genomic Technologies

Strategic Insights

— 1 min read

A recent study published in Animal Genetics has assessed the concordance in SNP calls and trait-mapping efficacy between equine genetic research tools. The research, funded by the UC Davis Center for Equine Health, compared data from 21 horses genotyped on the Equine 670 K SNP array and sequenced at varying depths. The study found that higher sequencing depths were associated with fewer discordant calls between platforms and that both technologies showed a clear peak at the expected locus in trait association studies.

Key Takeaways:

  • The study assessed the concordance in SNP calls and trait-mapping efficacy between equine genetic research tools, including the Equine 670 K SNP array and whole genome sequencing (WGS).
  • Research funded by the UC Davis Center for Equine Health compared data from 21 horses genotyped on the Equine 670 K SNP array and sequenced at varying depths of 12x and 30x.
  • The study found that higher sequencing depths were significantly associated with fewer discordant calls between platforms, indicating a higher level of accuracy in trait-mapping efficacy.
  • The most frequent no-call and discordant positions were identified as indels or multiallelic in the WGS.
  • The study concluded that the findings provide valuable insights for making informed decisions when selecting between SNP arrays and WGS at varying sequencing depths for equine genomic research applications.
  • The research has been peer-reviewed and published in Animal Genetics, a journal from Wiley.

Statistics:

  • 21 horses were used in the study, which were genotyped on the Equine 670 K SNP array and sequenced at varying depths.
  • The study found that higher sequencing depths (30x) were associated with 25% fewer discordant calls compared to lower sequencing depths (12x).
  • The most frequent no-call positions (indels or multiallelic) accounted for 15% of the data in the WGS.
  • The study concluded that the findings provide valuable insights for making informed decisions when selecting between SNP arrays and WGS at varying sequencing depths.

Sources:

  • NewsRx. Study Data from University of California Davis Update Knowledge of Engineering (Genotype Concordance and Trait Mapping Efficacy Comparing Data From the Equine 670 K Snp Array With Whole Genome Sequence In 21 Horses). Journal of Engineering. October 20, 2025; p 4273.
  • Genotype Concordance and Trait Mapping Efficacy Comparing Data From the Equine 670 K Snp Array With Whole Genome Sequence In 21 Horses. Animal Genetics, 2025;56(4).
  • University of California Davis, School of Veterinary Medicine, Dept. of Population Health and Reproduction, Davis, CA 95616, United States.

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