Identification and validation of genetic variants predictive of gait in standardbred horses

Annette M. McCoy, Samantha K. Beeson, Carl Johan Rubin, Leif Andersson, Paul Caputo, Sigrid Lykkjen, Alison Moore, Richard J. Piercy, James R. Mickelson, Molly E. McCue

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Several horse breeds have been specifically selected for the ability to exhibit alternative patterns of locomotion, or gaits. A premature stop codon in the gene DMRT3 is permissive for “gaitedness” across breeds. However, this mutation is nearly fixed in both American Standardbred trotters and pacers, which perform a diagonal and lateral gait, respectively, during harness racing. This suggests that modifying alleles must influence the preferred gait at racing speeds in these populations. A genome-wide association analysis for the ability to pace was performed in 542 Standardbred horses (n = 176 pacers, n = 366 trotters) with genotype data imputed to ~74,000 single nucleotide polymorphisms (SNPs). Nineteen SNPs on nine chromosomes (ECA1, 2, 6, 9, 17, 19, 23, 25, 31) reached genome-wide significance (p < 1.44 x 10−6). Variant discovery in regions of interest was carried out via whole-genome sequencing. A set of 303 variants from 22 chromosomes with putative modifying effects on gait was genotyped in 659 Standardbreds (n = 231 pacers, n = 428 trotters) using a highthroughput assay. Random forest classification analysis resulted in an out-of-box error rate of 0.61%. A conditional inference tree algorithm containing seven SNPs predicted status as a pacer or trotter with 99.1% accuracy and subsequently performed with 99.4% accuracy in an independently sampled population of 166 Standardbreds (n = 83 pacers, n = 83 trotters). This highly accurate algorithm could be used by owners/trainers to identify Standardbred horses with the potential to race as pacers or as trotters, according to the genotype identified, prior to initiating training and would enable fine-tuning of breeding programs with designed matings. Additional work is needed to determine both the algorithm’s utility in other gaited breeds and whether any of the predictive SNPs play a physiologically functional role in the tendency to pace or tag true functional alleles.

Original languageEnglish (US)
Article numbere1008146
JournalPLoS genetics
Volume15
Issue number5
DOIs
StatePublished - May 2019

Bibliographical note

Funding Information:
This work was supported by Morris Animal Foundation (D07EQ-500 to MEM), United States Equestrian Federation, Inc. (to MEM), Minnesota Agricultural Experiment Station (AES0063049 to JRM), United States Department of Agriculture (NIFA AFRI 2008-35205-18766 to JRM), and the University of Minnesota Equine Center/Minnesota Racing Commission (to MEM). Partial funding for personnel was provided by the National Institutes of Health (NCRR T32 OD010993 to AMM; NIAMS 1K08AR055713-01A2 to MEM) and the University of Minnesota (Doctoral Dissertation Fellowship to AMM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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