Abstract
Pneumonia caused by Rhodococcus equi is a common cause of disease and death in foals. Although agent and environmental factors contribute to the incidence of this disease, the genetic factors influencing the clinical outcomes of R. equi pneumonia are ill-defined. Here, we performed independent single nucleotide polymorphism (SNP)- and copy number variant (CNV)-based genome-wide association studies to identify genomic loci associated with R. equi pneumonia in foals. Foals at a large Quarter Horse breeding farm were categorized into 3 groups: 1) foals with R. equi pneumonia (clinical group [N = 43]); 2) foals with ultrasonographic evidence of pulmonary lesions that never developed clinical signs of pneumonia (subclinical group [N = 156]); and, 3) foals without clinical signs or ultrasonographic evidence of pneumonia (unaffected group [N = 49]). From each group, 24 foals were randomly selected and used for independent SNP- and CNV-based genome-wide association studies (GWAS). The SNP-based GWAS identified a region on chromosome 26 that had moderate evidence of association with R. equi pneumonia when comparing clinical and subclinical foals. A joint analysis including all study foals revealed a 3- to 4-fold increase in odds of disease for a homozygous SNP within the associated region when comparing the clinical group with either of the other 2 groups of foals or their combination. The region contains the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) gene, which is involved in neutrophil function. No associations were identified in the CNV-based GWAS. Collectively, these data identify a region on chromosome 26 associated with R. equi pneumonia in foals, providing evidence that genetic factors may indeed contribute to this important disease of foals.
Highlights
Rhodococcus equi is an important intracellular pathogen affecting horses, most commonly among foals in which it causes chronic, suppurative bronchopneumonia [1], as well as extrapulmonary disorders [2]
Single nucleotide polymorphism (SNP)-based genotyping platforms are available for performing genome-wide association studies (GWAS) in horses [9]
We propose that utilizing average log2 ratios across copy number variants (CNVs) regions is superior because classification of CNVRs by presence or absence does not further characterize a
Summary
Rhodococcus equi is an important intracellular pathogen affecting horses, most commonly among foals in which it causes chronic, suppurative bronchopneumonia [1], as well as extrapulmonary disorders [2]. The cumulative incidence of pneumonia caused by R. equi may be high at breeding farms with affected foals, and this disease may adversely impact future racing performance [3]. Identifying the genetic and biological basis of susceptibility, or perhaps resistance, to R. equi pneumonia in foals is important, because it might lead to the development of diagnostic and therapeutic tools to manage atrisk foals on breeding farms and might shed light on critical host defense mechanisms. Single nucleotide polymorphism (SNP)-based genotyping platforms are available for performing genome-wide association studies (GWAS) in horses [9]. Use of SNP-based genotyping platforms to identify genomic regions associated with particular phenotypes in animals is growing at a rapid pace [9,10,11,12,13,14]. Researchers, veterinarians, and producers increasingly rely on data from these studies to make important production and management decisions [15,16]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
