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. 2016 Apr 15:58:17.
doi: 10.1186/s40781-016-0097-1. eCollection 2016.

Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress

Ji-Eun Kim  1 , Junkyung Choe  1 , Jeong Hee Lee  1 , Woong Bom Kim  1 , Whan Cho  1 , Ji Hong Ha  2 , Ki Jin Kwon  2 , Kook Il Han  3 , Sung-Hwan Jo  1
Affiliations

Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress

Ji-Eun Kim et al. J Anim Sci Technol. .

Abstract

Background: The Sapsaree (Canis familiaris) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance.

Results: We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type (p ≤ 0.05). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized.

Conclusions: Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.

Keywords: Bioinformatics; Exercise; NGS; Physical stress; RNA-Seq; Sapsaree; Transcriptome.

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Figures

Fig. 1
Fig. 1
HeatMap showing hierarchical clustering of differentially expressed genes regulated by exercise. The log2Ratio for each significantly differentially expressed gene was used. Each column represents a Sapsaree individual, and each row represents a differentially expressed gene. Expression differences are shown in different colors; red indicates up-regulation after exercise, and green indicates down-regulation after exercise. The 525 genes were grouped into two clusters (C1 and C2). The dogs were divided into two groups. Group I included Cheongbaek, Rookie, Chaeum, Hwangryong, and Pyeonggang. Group II included Tong, Huimang, Pyeongtan, Hwangdol, and Bongsik
Fig. 2
Fig. 2
Representative genes that were differentially expressed between the two groups of dogs. The x-axis represents the seven selected genes, and the y-axis represents the log2 fold change (2FC) value of each gene. The 2FC values for each individual are represented by a colored bar. a shows two genes with negative 2FC values in Group I and positive 2FC values in Group II. b shows five genes with positive 2FC values in Group I and negative 2FC values in Group II. The gene identifiers are shown at the top of each histogram: PTPRC (490255, protein tyrosine phosphatase, receptor type c), LOC102157092 (102157092, complement receptor type 1-like), RPL18 (476422, ribosomal protein L18), S100A8 (490461, S100 calcium binding protein A8), LOC612054 (612054, uncharacterized LOC612054), LOC102151356 (102151356, uncharacterized LOC102151356), and EIF1 (403674, eukaryotic translation initiation factor 1)
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