title: Identification of genomic loci associated with Rhodococcus equi susceptibility in foals.
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.
authors.affiliation: Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, Texas, United States of America.
authors.forename: Cole M
authors.initials: CM
authors.lastname: McQueen
authors.affiliation: Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, Texas, United States of America.
authors.forename: Ryan
authors.initials: R
authors.lastname: Doan
authors.affiliation: Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, Texas, United States of America; Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, United States of America.
authors.forename: Scott V
authors.initials: SV
authors.lastname: Dindot
authors.affiliation: Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, Texas, United States of America.
authors.forename: Jessica R
authors.initials: JR
authors.lastname: Bourquin
authors.affiliation: Department of Electrical and Computer Engineering, Texas A&M University Dwight Look College of Engineering, College Station, Texas, United States of America.
authors.forename: Zlatomir Z
authors.initials: ZZ
authors.lastname: Zlatev
authors.affiliation: Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, Texas, United States of America.
authors.forename: M Keith
authors.initials: MK
authors.lastname: Chaffin
authors.affiliation: 6666 Ranch, 1102 Dash For Cash Road, Guthrie, Texas, United States of America.
authors.forename: Glenn P
authors.initials: GP
authors.lastname: Blodgett
authors.affiliation: Department of Veterinary Physiology & Pharmacology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, Texas, United States of America.
authors.forename: Ivan
authors.initials: I
authors.lastname: Ivanov
authors.affiliation: Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, Texas, United States of America.
authors.forename: Noah D
authors.initials: ND
authors.lastname: Cohen
mesh_terms: D000818:Animals; D004198:Disease Susceptibility; D055106:Genome-Wide Association Study / Q000379:methods*; D006734:Horse Diseases / Q000235:genetics* / Q000382:microbiology; D006736:Horses; D018410:Pneumonia, Bacterial / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D016929:Rhodococcus equi / Q000472:pathogenicity*