title: Identification of genes with nonsynonymous SNP in Jeju horse by whole-genome resequencing reveals a functional role for immune response.
abstract: Jeju horse (Natural Monument number 347) is a breed of horse that has experienced long-term isolation and domestication in Jeju Island, South Korea. We evaluated genetic features of this breed, including SNP, by whole-genome resequencing using an Illumina HiSeq 2000. A total of 5,986,852 SNP were identified in 4 Jeju horses and were divided into homozygous and heterozygous SNP (2,357,099 and 3,629,753 SNP, respectively). It revealed that 63.8% of these SNP resided in intergenic regions. Immune response genes with nonsynonymous SNP were overrepresented in Jeju horses as evidenced by Gene Ontology clustering. Among these genes, Toll-like receptors (TLR) are highly enriched. Comparing TLR genes between Jeju horses and the Przewalski's horse, and genes showed "possibly damaging" mutations in several regions by analysis with PolyPhen-2. These results provide a framework for further genetic studies in Jeju horse by domestication. Furthermore, research on functions of SNP-associated genes would aid in understanding the molecular genetic variation of horse breeds.
authors.forename: J-H
authors.initials: JH
authors.lastname: Lee
authors.forename: K-D
authors.initials: KD
authors.lastname: Song
authors.forename: J-M
authors.initials: JM
authors.lastname: Kim
authors.forename: H-K
authors.initials: HK
authors.lastname: Leem
authors.forename: K-D
authors.initials: KD
authors.lastname: Park
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D016678:Genome; D006579:Heterozygote; D006720:Homozygote; D006736:Horses / Q000235:genetics* / Q000276:immunology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*