Recurrent laryngeal neuropathy (RLN) is a distal axonopathy that results in the partial or total collapse of the left arytenoid cartilage of the larynx. The ensuing airway obstruction diminishes racing performance and requires surgical correction which is not uniformly successful. RLN, which occurs in ~11% of Thoroughbreds (TBs), exhibits a heritable tendency but does not follow simple Mendelian genetics. RLN is a complex (multigenic) disorder regulated by environmental factors. In our 2010-2012 Zweig award, we conducted a Genome-Wide Association Study (GWAS) of nearly 500 TBs consisting of RLN-affected and control cases with the goal of identifying genes causal for RLN. Using a newly developed Equine SNP70 chip, we identified 3 single nucleotide polymorphisms (SNPs) associated with RLN that mapped to the same location of equine chromosome (ECA) 3. Interestingly, the most informative RLN SNP mapped next to a known equine size gene (LCORL/NCAPG). Yet, our data do not allow us to discern (1) whether these size genes, which contribute to skeletal growth, exert a pleiotropic effect on axonal development such that the length of the recurrent laryngeal nerve exceeds its metabolic support system or (2) whether this RLN gene(s) is simply inherited together with the size genes because of the long linkage disequilibrium (LD; few genetic recombination events) that is characteristic of the TB genome. Our 2nd important finding from the 2010-2012 Zweig data suggests that 3 additional loci on chromosomes 1 (for males), 14 and 23 (for females) are associated with RLN. All of these chromosomal regions require further investigation to identify the genes causal for RLN. In this 2013-2015 Zweig grant, we propose to investigate the ECA3 locus by utilizing an across-breed genotype mapping strategy: We will similarly analyze the ECA3 locus using DNA samples from well phenotyped Standardbreds, which also develop RLN, but have a shorter average LD interval than TBs and thus a greater number of recombination events in this region. The RLN causal gene(s) on chromosome 3 will fall within the narrowest conserved associated region shared by both breeds. To fine map RLN genes on chromosomes 1, 14 and 23 (aim 2), we would use a custom-designed MassArray Assay specifically designed to identify a greater number of informative and segregating SNPs in these 3 regions than exists on the Equine SNP70 chip. Identifying the causal genes within these four loci will bring us nearer to our long-term goals of (1) determining the functional mechanism of RLN; (2) developing a simple blood test (SNP test) that can identify, at an early age, those horses predisposed to the development of RLN; and (3) open novel avenues for early interventional molecular therapy.