Identification of genes with nonsynonymous SNP in Jeju horse by whole-genome resequencing reveals a functional role for immune response1

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.

Comparison for immunophysiological responses of Jeju and Thoroughbred horses after exercise

“…Thus, the species has become well-adapted to the specific environmental conditions and selection pressures of Jeju island. Compared to Thoroughbred horses, Jeju horses are short, slow, hardy, and have strong immune systems, likely owing to their highly enriched immune-related nonsynonymous genes [1]. Therefore, the identification of Jeju horse-specific traits via comparative study would aid in the utilization and development of their useful characteristics [2,3].…”

“…Comparative studies have investigated the differences between Thoroughbred and Jeju horses in order to identify genetic differences using microsatellites [7] and single nucleotide polymorphism (SNP) chip arrays [8,9]. In Jeju horses, nonsynonymous SNPs are overrepresented in immune response genes including toll-like receptor genes [1]. Physical activity has numerous effects on a variety of metabolic processes in the body, including thermodynamic and physiological biochemical processes (the activity of enzymes, hormones, chemokines, and cytokines).…”

Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse

“…347) in 1986, and started a pedigree registry 3,7 . In 2000, a JH registration agency was established, and currently, approximately 2,500 JH are being raised at local farms 7,8 .…”