title: Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.
abstract: Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in horses.
authors.affiliation: Department of Animal Science, Cornell University, Ithaca, New York;
authors.forename: E A
authors.initials: EA
authors.lastname: Staiger
authors.affiliation: Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman;
authors.forename: M A
authors.initials: MA
authors.lastname: Al Abri
authors.affiliation: Department of Animal Science, University of Florida, Gainesville, Florida;
authors.forename: K M
authors.initials: KM
authors.lastname: Pflug
authors.affiliation: Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York;
authors.forename: S E
authors.initials: SE
authors.lastname: Kalla
authors.affiliation: Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York;
authors.forename: D M
authors.initials: DM
authors.lastname: Ainsworth
authors.affiliation: Baker Institute for Animal Health, Cornell University, Ithaca, New York;
authors.forename: D
authors.initials: D
authors.lastname: Miller
authors.affiliation: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas; and.
authors.forename: T
authors.initials: T
authors.lastname: Raudsepp
authors.affiliation: Department of Biology, La Sierra University, Riverside, California.
authors.forename: N B
authors.initials: NB
authors.lastname: Sutter
authors.affiliation: Department of Animal Science, University of Florida, Gainesville, Florida; samantha.brooks@ufl.edu.
authors.forename: S A
authors.identifier: 0000-0002-5677-0798
authors.initials: SA
authors.lastname: Brooks
mesh_terms: D000818:Animals; D049628:Body Size / Q000235:genetics; D001947:Breeding / Q000379:methods; D002874:Chromosome Mapping / Q000379:methods; D005260:Female; D055106:Genome-Wide Association Study / Q000379:methods; D005838:Genotype; D006736:Horses / Q000235:genetics*; D008297:Male; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics; D013714:Tennessee; D016138:Walking
keywords: LCORL indel; Tennessee Walking Horse; genome-wide association study; horse size; retrogene