Journal of Animal Science and Technology

Korean Society of Animal Sciences and Technology (한국축산학회)
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Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress

  • Received : 2015.09.04
  • Accepted : 2016.03.29
  • Published : 2016.04.30
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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 ($p{\leq}0.05$). 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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References

  1. Ha JH, Alam M, Lee DH, Kim JJ. Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Behavior in Sapsaree Dog (Canis familiaris). Asian-Australas J Anim Sci. 2015;28(7):936-42. doi:10.5713/ajas.14.0941.
  2. Kim KS, Jeong HW, Park CK, Ha JH. Suitability of AFLP markers for the study of genetic relationships among Korean native dogs. Genes Genet Syst. 2001; 76(4):243-50. https://doi.org/10.1266/ggs.76.243
  3. Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, et al. Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. BMC Genomics. 2012;13:473. doi:10.1186/1471-2164-13-473.
  4. Capomaccio S, Vitulo N, Verini-Supplizi A, Barcaccia G, Albiero A, D'Angelo M, et al. RNA sequencing of the exercise transcriptome in equine athletes. PLoS One. 2013;8(12):e83504. doi:10.1371/journal.pone.0083504.
  5. Greiner bio-one (http://www.greinerbioone.com/). Accessed 4 Apr 2016.
  6. PreAnalytiX (http://www.preanalytix.com/products/blood/RNA/paxgene-bloodrna-tube). Accessed 4 Apr 2016.
  7. Clarkson PM, Kearns AK, Rouzier P, Rubin R, Thompson PD. Serum creatine kinase levels and renal function measures in exertional muscle damage. Med Sci Sports Exerc. 2006;38(4):623-7. https://doi.org/10.1249/01.mss.0000210192.49210.fc
  8. Baird MF, Graham SM, Baker JS, Bickerstaff GF. Creatine-kinase- and exerciserelated muscle damage implications for muscle performance and recovery. J Nutr Metab. 2012;2012:960363.
  9. Piccione G, Giannetto C, Fazio F, Casella S, Caola G. A comparison of daily rhythm of creatinine and creatine kinase in the sedentary and athlete horse. J Equine Vet Sci. 2009;29(7):575-80. https://doi.org/10.1016/j.jevs.2009.05.013
  10. Nathwani RA, Pais S, Reynolds TB, Kaplowitz N. Serum alanine aminotransferase in skeletal muscle diseases. Hepatology. 2005;41(2):380-2. doi:10.1002/hep.20548.
  11. Mastorakos G, Pavlatou M, Diamanti-Kandarakis E, Chrousos GP. Exercise and the stress system. Hormones (Athens). 2005;4(2):73-89.
  12. Mindray (http://www.mindray.com/en/products/34.html). Accessed 4 Apr 2016.
  13. SIMENS (http://www.healthcare.siemens.com). Accessed 4 Apr 2016.
  14. Illumina (http://www.illumina.com/products/truseq_rna_library_prep_kit_v2.html). Accessed 4 Apr 2016.
  15. KAPA biosystems (http://www.kapabiosystems.com/product-applications/ products/next-generation-sequencing-2/library-quantification/). Accessed 4 Apr 2016.
  16. Cox MP, Peterson DA, Biggs PJ. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 2010;11:485. doi:10.1186/1471-2105-11-485.
  17. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. doi:10.1186/gb-2009-10-3-r25.
  18. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005;438:803-19. doi:10.1038/nature04338.
  19. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106. doi:10.1186/gb-2010-11-10-r106.
  20. Antoine Lucas. AMAP: Another Multidimensional Analysis Package. R package version 0.8-12. 2014. (http://CRAN.R-project.org/package=amap). Accessed 4 Apr 2016.
  21. Brinkhof B, Spee B, Rothuizen J, Penning LC. Development and evaluation of canine reference genes for accurate quantification of gene expression. Anal Biochem. 2006;356(1):36-43. doi:10.1016/j.ab.2006.06.001.
  22. Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32(Database issue):D258-61. doi:10.1093/nar/gkh036.
  23. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30. https://doi.org/10.1093/nar/28.1.27
  24. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. doi:10.1038/nprot.2008.211.
  25. Han KI, Alam M, Lee YM, Lee DH, Ha JH, Kim JJ. A study on morphology and behavior of the Sapsaree: A Korean native dog (Canis familiaris). J Anim Sci Technol. 2010;52:481-90. https://doi.org/10.5187/JAST.2010.52.6.481
  26. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9. doi:10.1038/nmeth.1923.