Kim, Ji-Eun
(SEEDERS Inc.)
,
Choe, Junkyung
(SEEDERS Inc.)
,
Lee, Jeong Hee
(SEEDERS Inc.)
,
Kim, Woong Bom
(SEEDERS Inc.)
,
Cho, Whan
(SEEDERS Inc.)
,
Ha, Ji Hong
(The Korean Sapsaree Foundation)
,
Kwon, Ki Jin
(The Korean Sapsaree Foundation)
,
Han, Kook Il
(Department of Animal training and event, Daekyeung University)
,
Jo, Sung-Hwan
(SEEDERS Inc.)
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 ...
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 ($p{\leq}0.05$). 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.
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 ($p{\leq}0.05$). 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.
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문제 정의
RNA sequencing and gene expression analysis can be useful for grouping the Sapsarees by body type and response to exercise. This study provides a basis for future research investigating the biologic characteristics of the Sapsaree and the large-scale genomic differences of canines in general.
Therefore, we performed a large-scale analysis of whole-transcriptome data to investigate the gene expression levels before and after exercise in the Sapsaree. This study will provide the basic approach for identified the biologic characteristics and breeding the working dogs.
제안 방법
And then, the final DEGs were identified by a ≥ twofold change in reads coverage, a binomial test with a false discovery rate (FDR) ≤ 0.01, and a read count ≥ 1,000 either before or after exercise.
Ten Sapsarees housed in controlled environmental conditions were used in the experiment. The basic morphological traits of each Sapsaree including body height (BH), body length (BL), depth of chest (DC), body weight (W), and hair color were measured before the experiment. Then, the dogs were exercised one-on-one by trainers for 1 h in 5 min intervals, with the trainers leading the dogs in quick step 10 times around a course on a 20 m × 20 m square field located at the Korean Sapsaree Foundation facility in Gyeongsan.
Then, the dogs were exercised one-on-one by trainers for 1 h in 5 min intervals, with the trainers leading the dogs in quick step 10 times around a course on a 20 m × 20 m square field located at the Korean Sapsaree Foundation facility in Gyeongsan. The exercise course included hurdling (40 cm, 70 cm, and 80 cm), high jumping (50 cm), A-shape hurdling, bridge-shape hurdling, and seesaw hurdling.
There has been little progress, however, in canine-based RNA-Seq studies, which have been limited to certain diseases. Therefore, we performed a large-scale analysis of whole-transcriptome data to investigate the gene expression levels before and after exercise in the Sapsaree. This study will provide the basic approach for identified the biologic characteristics and breeding the working dogs.
This study provides the Sapsaree whole-transcriptome sequence data and identifies genes that are differentially expressed before and after exercise in the Sapsaree, which could be used as markers of exercise stress. The pattern of changes in global gene expression induced by exercise was different depending on the body type.
To identify correlations between the gene expression pattern and body weight, we carried out t-tests comparing W/BH, W/BL, and W/DC values between two groups of dogs that showed different gene expression patterns. To control for group differences in baseline weight, the weight was divided by the BH, BL, and DC.
대상 데이터
The dogs were handled in accordance with Article 23 ‘Experiments with Animal’ of Korea’s Animal Protection Law, 2015, and the Korean Sapsaree Foundation cooperated and approved all animal care procedures prior to the initiation of the experiment. Ten Sapsarees housed in controlled environmental conditions were used in the experiment. The basic morphological traits of each Sapsaree including body height (BH), body length (BL), depth of chest (DC), body weight (W), and hair color were measured before the experiment.
데이터처리
In addition, W/BH, W/BL, and W/DC were each significantly different (p ≤ 0.05) between the two groups based on independent t-tests (Table 3).
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