The Harry M. Zweig Memorial Fund for Equine Research

Fine Mapping of Candidate Genes Contributing to Equine Left Recurrent Laryngeal Neuropathy (RLN) in Thoroughbred Horses

Principal Investigator: Dorothy Ainsworth with  Samantha Brooks
Contact Information: Email:; Phone: 607-253-3232
Project Costs: $60,960
Project Period: 1/1/2014-12/31/2015

Ainsworth “Roaring” or recurrent laryngeal neuropathy (RLN) is a common respiratory tract disorder characterized by degeneration, most commonly, of the left recurrent laryngeal nerve.  As a result of nerve dysfunction, the laryngeal muscles weaken and are unable to maintain the larynx in an opened position during breathing.  The ensuing airway obstruction results in diminished athletic performance.  RLN occurs in ~11% of Thoroughbreds (TBs) and between 35-50% of Draft horse breeds.  The disease exhibits a heritable tendency but fails to follow simple Mendelian genetics:  RLN is considered to be a complex (multigenic) disorder.  The search for candidate genes contributing to RLN is the focus of our investigations. 

We have completed a Genome-Wide Association Study (GWAS) of 550 TBs (282 RLN-affected, 268 controls) and found a significant association of RLN with the height genes, LCORL/NCAPG, located on equine chromosome 3 (ECA3).  Using withers height, we also confirmed a strong association of this locus with body size and demonstrated a significant phenotypic and genetic correlation between height and RLN status.  We also identified secondary associations for RLN on ECA18 and chromosome X which did not correlate with height but contained candidate genes influencing muscle physiology (myostatin, integral membrane protein 2A). 

This past year, in an effort to separate the RLN locus from the height locus, we custom-designed a high density SNP panel, re-genotyped and re-analyzed the TB DNA samples.  We successfully improved the resolution of ECA3—the RLN locus is now located further to the right of the height locus—but still remains associated with it. Our inability to fine map this area further is attributed to the long linkage disequilibrium (LD) of TBs.  Specifically, because of low genetic diversity in this breed, long blocks of genes (or SNPs) become tightly associated and are inherited together.  In order to “break up” this 400 kb region on ECA3 (and to identify the RLN genes distinct from the height genes) a new strategy is needed.

In our 2014 study, we propose to investigate the ECA3 locus by utilizing an across-breed genotype mapping strategy.  We will phenotype and genotype Belgian Draft horses which develop RLN (50% prevalence) but which have a significantly shorter average LD length.  The shorter LD, which reflects a greater number of recombination events at a given chromosome region, markedly enhances our ability to break up the 400 kb region on ECA3 and to separate the RLN and height loci.  Identifying the RLN genes brings us closer to reaching our goals of (1) determining the pathophysiological mechanisms of RLN and (2) developing a simple blood test (SNP test) that can identify early those horses predisposed to the development of RLN.