Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses.
Abstract: The athletic abilities of the horse serve as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. We analyzed differentially expressed genes in triceps brachii muscle tissues collected from Eonjena Taeyang and Jigusang Seryeok Thoroughbred horses and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. High-quality horse transcriptome data were generated, with over 22 million 90-bp pair-end reads. By comparing the annotations, we found that MYH3, MPZ, and PDE8B genes in Eonjena Taeyang and PDE8B and KIF18A genes in Jigusang Seryeok were upregulated before exercise. Notably further, we observed that PPP1R27, NDUFA3, TNC, and ANK1 in Eonjena Taeyang and HIF1A, BDNF, ADRB2, OBSCN, and PER3 in Jigusang Seryeok have shown upregulation at the postexercise period. This investigation suggested that genes responsible for metabolism and oxidative phosphorylations associated with endurance and resistance exercise were highly expressed, whereas genes encoding structural proteins were generally suppressed. The expression profile of racehorses at pre- and postexercise will provide credible reference for further studies on biological effects such as responses to stress and adaption of other Thoroughbred horse, which might be useful for selective breeding for improvement of traits in commercial production.
Publication Date: 2016-06-28 PubMed ID: 27351985DOI: 10.1007/s12010-016-2118-4Google Scholar: Lookup
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- Comparative Study
- Journal Article
Summary
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This research investigates the changes in gene expression in the muscles of Korean Thoroughbred horses before and after exercise. The study could inform selective breeding practices to enhance certain traits in these horses.
Methodology and Data Collection
- The researchers examined the differential expression of genes in the triceps brachii muscle tissues of two types of Thoroughbred horses named Eonjena Taeyang and Jigusang Seryeok.
- RNA-sequence dataset was used to compare gene expression before and after exercise, thus aiming to understand the physiology and molecular mechanisms that the horses used to adapt to physical activity.
- The process generated high-quality horse transcriptome data, with over 22 million 90-bp pair-end reads.
Findings
- The research identified certain genes that were upregulated before exercise in both types of horses, including MYH3, MPZ, and PDE8B genes in Eonjena Taeyang and PDE8B and KIF18A genes in Jigusang Seryeok.
- Post-exercise, the study found that PPP1R27, NDUFA3, TNC, and ANK1 in Eonjena Taeyang and HIF1A, BDNF, ADRB2, OBSCN, and PER3 in Jigusang Seryeok were upregulated.
Implications of Research
- The research indicates that the genes responsible for metabolism and oxidative phosphorylations, which are associated with endurance and resistance exercise, were highly expressed in the horses. In contrast, genes encoding for structural proteins were generally suppressed.
- The study thus shows how gene expression can change in response to exercise, an insight which could be useful for selectively breeding horses with improved traits in commercial production.
- The research could also provide a benchmark for future studies examining the biological effects of stress response and adaption in other Thoroughbred horses.
Cite This Article
APA
Ghosh M, Cho HW, Park JW, Choi JY, Chung YH, Sharma N, Singh AK, Kim NE, Mongre RK, Huynh D, Jiao ZJ, Do KT, Lee HK, Song KD, Cho BW, Jeong D.
(2016).
Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses.
Appl Biochem Biotechnol, 180(3), 588-608.
https://doi.org/10.1007/s12010-016-2118-4 Publication
Researcher Affiliations
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang, 627-702, Republic of Korea.
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang, 627-702, Republic of Korea.
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang, 627-702, Republic of Korea.
- BK21+, Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 609-735, Republic of Korea.
- Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, Jammu and Kashmir, India.
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang, 627-702, Republic of Korea. bwcho@pusan.ac.kr.
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea. jeongdk21@gmail.com.
MeSH Terms
- Animals
- Cluster Analysis
- Gene Expression Profiling
- Gene Expression Regulation
- Gene Ontology
- Genome
- Horses / genetics
- Molecular Sequence Annotation
- Muscles / metabolism
- Physical Conditioning, Animal
- Real-Time Polymerase Chain Reaction
- Reproducibility of Results
- Sequence Analysis, RNA / methods
Citations
This article has been cited 7 times.- Khummuang S, Lee HG, Joo SS, Park JW, Choi JY, Oh JH, Kim KH, Youn HH, Kim M, Cho BW. Comparison for immunophysiological responses of Jeju and Thoroughbred horses after exercise. Asian-Australas J Anim Sci 2020 Mar;33(3):424-435.
- Reis Neto RV, Yoshida GM, Lhorente JP, Yáñez JM. Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss). Mol Genet Genomics 2019 Jun;294(3):563-571.
- Wang J, Ren W, Li Z, Li L, Wang R, Ma S, Zeng Y, Meng J, Yao X. Regulatory Mechanisms of Yili Horses During an 80 km Race Based on Transcriptomics and Metabolomics Analyses. Int J Mol Sci 2025 Mar 8;26(6).
- Li BG, Wu WJ, Wang LH, Wang X, Liu C, Du YK, Li BC, Hu JT, Sun SZ. Identification of a novel pathogenic gene, NDUFA3, in Leigh Syndrome through whole exome sequencing. Neurogenetics 2024 Nov 28;26(1):13.
- Lin Y, Sun L, Lv Y, Liao R, Zhang K, Zhou J, Zhang S, Xu J, He M, Wu C, Zhang D, Shen X, Dai J, Gao J. Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance. BMC Genomics 2024 May 4;25(1):443.
- Salichos L, Thayavally R, Kloen P, Hadjiargyrou M. Human nonunion tissues display differential gene expression in comparison to physiological fracture callus. Bone 2024 Jun;183:117091.
- Reißmann M, Rajavel A, Kokov ZA, Schmitt AO. Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability. Genes (Basel) 2023 Oct 24;14(11).
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