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PloS one2014; 9(3); e91418; doi: 10.1371/journal.pone.0091418

Investigation of de novo unique differentially expressed genes related to evolution in exercise response during domestication in Thoroughbred race horses.

Abstract: Previous studies of horse RNA-seq were performed by mapping sequence reads to the reference genome during transcriptome analysis. However in this study, we focused on two main ideas. First, differentially expressed genes (DEGs) were identified by de novo-based analysis (DBA) in RNA-seq data from six Thoroughbreds before and after exercise, here-after referred to as "de novo unique differentially expressed genes" (DUDEG). Second, by integrating both conventional DEGs and genes identified as being selected for during domestication of Thoroughbred and Jeju pony from whole genome re-sequencing (WGS) data, we give a new concept to the definition of DEG. We identified 1,034 and 567 DUDEGs in skeletal muscle and blood, respectively. DUDEGs in skeletal muscle were significantly related to exercise-induced stress biological process gene ontology (BP-GO) terms: 'immune system process'; 'response to stimulus'; and, 'death' and a KEGG pathways: 'JAK-STAT signaling pathway'; 'MAPK signaling pathway'; 'regulation of actin cytoskeleton'; and, 'p53 signaling pathway'. In addition, we found TIMELESS, EIF4A3 and ZNF592 in blood and CHMP4C and FOXO3 in skeletal muscle, to be in common between DUDEGs and selected genes identified by evolutionary statistics such as FST and Cross Population Extended Haplotype Homozygosity (XP-EHH). Moreover, in Thoroughbreds, three out of five genes (CHMP4C, EIF4A3 and FOXO3) related to exercise response showed relatively low nucleotide diversity compared to the Jeju pony. DUDEGs are not only conceptually new DEGs that cannot be attained from reference-based analysis (RBA) but also supports previous RBA results related to exercise in Thoroughbred. In summary, three exercise related genes which were selected for during domestication in the evolutionary history of Thoroughbred were identified as conceptually new DEGs in this study.
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Publication Date: 2014-03-21 PubMed ID: 24658125PubMed Central: PMC3962374DOI: 10.1371/journal.pone.0091418Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses a study aimed at identifying unique genes that are differentially expressed during exercise in Thoroughbred race horses and could possibly be related to their evolution during domestication.

Introduction to the Study

  • The study focuses on two primary aspects. Firstly, it identifies differentially expressed genes (DEGs) using an independent, de novo-based analysis (DBA) in RNA-seq data from six Thoroughbreds before and after exercise. These are called “de novo unique differentially expressed genes” (DUDEG).
  • Secondly, the study combines the traditional DEGs and genes identified as being favored during domestication of Thoroughbred and Jeju pony using whole genome re-sequencing (WGS) data.
  • This approach brings a new perspective to how DEGs are defined.

Key Findings of the Study

  • Researchers identified 1,034 DUDEGs in skeletal muscle and 567 DUDEGs in blood.
  • The DUDEGs in skeletal muscle were significantly linked with certain exercise-induced stress biological process gene ontology (BP-GO) terms like ‘immune system process’, ‘response to stimulus’, and ‘death’ along with KEGG pathways like ‘JAK-STAT signaling pathway’, ‘MAPK signaling pathway’, ‘regulation of actin cytoskeleton’, and ‘p53 signaling pathway’.
  • Several genes, such as TIMELESS, EIF4A3, and ZNF592 in blood, and CHMP4C and FOXO3 in skeletal muscle, were found common between DUDEGs and selected genes identified by evolutionary statistics such as FST and Cross Population Extended Haplotype Homozygosity (XP-EHH).
  • In Thoroughbreds, three out of five exercise-related genes (CHMP4C, EIF4A3, and FOXO3) demonstrated comparatively lower nucleotide diversity than in the Jeju pony.

Study Conclusion

  • DUDEGs are conceptually new DEGs that cannot be obtained from reference-based analysis (RBA), but support previous RBA results related to exercise in Thoroughbred.
  • In summary, the study highlighted three exercise-related genes which were selected for during the domestication in the evolutionary history of Thoroughbred.

Cite This Article

APA
Park W, Kim J, Kim HJ, Choi J, Park JW, Cho HW, Kim BW, Park MH, Shin TS, Cho SK, Park JK, Kim H, Hwang JY, Lee CK, Lee HK, Cho S, Cho BW. (2014). Investigation of de novo unique differentially expressed genes related to evolution in exercise response during domestication in Thoroughbred race horses. PLoS One, 9(3), e91418. https://doi.org/10.1371/journal.pone.0091418

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 9
Issue: 3
Pages: e91418
PII: e91418

Researcher Affiliations

Park, Woncheoul
  • Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Kim, Jaemin
  • Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
Kim, Hyeon Jeong
  • C&K genomics, Seoul National University, Seoul, Republic of Korea.
Choi, JaeYoung
  • Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea.
Park, Jeong-Woong
  • Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea.
Cho, Hyun-Woo
  • Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea.
Kim, Byeong-Woo
  • Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea.
Park, Myung Hum
  • TNT Research, Anyang, Republic of Korea.
Shin, Teak-Soon
  • Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea.
Cho, Seong-Keun
  • Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea.
Park, Jun-Kyu
  • Leaders in Industry-university Cooperation, Pusan National University, Miryang, Republic of Korea.
Kim, Heebal
  • Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea; C&K genomics, Seoul National University, Seoul, Republic of Korea.
Hwang, Jae Yeon
  • Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Lee, Chang-Kyu
  • Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Lee, Hak-Kyo
  • Genomic Informatics Center, Hankyong National University, Anseong, Republic of Korea.
Cho, Seoae
  • C&K genomics, Seoul National University, Seoul, Republic of Korea.
Cho, Byung-Wook
  • Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea.

MeSH Terms

  • Animals
  • Gene Expression Regulation
  • Genome
  • Genotype
  • Horses / genetics
  • Horses / metabolism
  • Physical Conditioning, Animal
  • Transcriptome

Conflict of Interest Statement

MHP has the following financial competing interest: Paid employment in TNT Research Company Limited, Dongan-gu, Anyang-si, Republic of Korea. The rest of the authors have declared that no competing interests exist. This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials. HK has the following financial competing interest: Paid employment in C&K Genomics company INC, C&K genomics Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2. SC has the following financial competing interest: CEO of C&K Genomics company INC, C&K genomics Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2.

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