title: Detection of single nucleotide polymorphisms (SNP) in equine coat color genes using SNaPshotTMmultiplex kit or pluronic F-108 tri-block copolymer and capillary electrophoresis.
abstract: Molecular methods for the detection of mammalian coat color phenotypes have expanded greatly within the past decade. Many phenotypes are associated with a single nucleotide polymorphism mutation in the genetic sequence. Traditionally, these mutations are detected through sequencing, hybridization assays or mini-sequencing. However, these techniques can be expensive and tedious. Previously, CE-SSCP using the F-108 polymer was able to distinguish SNPs for the melanocortin-1 receptor (mc1r) coat color gene in horses (Equus caballus) that differed by one nucleotide substitution. The objective of this study was to expand the detection of coat color SNPs in horses. The genes for the solute carrier family member 2 (slc45a2/matp), type III receptor protein-tyrosine kinase (kit) and mc1r genes using CE-SSCP and F-108 polymer were compared to mini-sequencing with the SNaPshotTMkit. The F-108 polymer reproducibly resolved homozygous and heterozygous individuals for the mc1r and kit markers, but was unable to resolve heterozygous individuals for slc45a2 at 38ºC. The need for temperatures <15ºC, the SNP position being close to the 5'-end, and conformational structures/free energy with similar values resulted in the inability to resolve the secondary structures. Despite this limitation, the CE-SSCP method could be used to provide a rapid phenotypic description for equine forensic investigations.
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.|International Forensic Research Institute, Florida International University, Miami, FL, USA.|Department of Biological Sciences, Florida International University, Miami, FL, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Martin
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.|International Forensic Research Institute, Florida International University, Miami, FL, USA.|Department of Biological Sciences, Florida International University, Miami, FL, USA.
authors.forename: Natalie
authors.initials: N
authors.lastname: Damaso
authors.affiliation: International Forensic Research Institute, Florida International University, Miami, FL, USA. millsd@fiu.edu.|Department of Biological Sciences, Florida International University, Miami, FL, USA. millsd@fiu.edu.
authors.forename: DeEtta
authors.initials: D
authors.lastname: Mills
mesh_terms: D000818:Animals; D019075:Electrophoresis, Capillary / Q000379:methods*; D006200:Hair Color / Q000235:genetics*; D006736:Horses / Q000235:genetics*; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
keywords: Capillary electrophoresis; Equine coat color genes; F-108 polymer; SNP; SSCP